Event-Fellowship on Open Bioinformatics Foundation

Undergraduate to Best Poster Awardee: My experience at BITS2026 and BioHackathon

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 26 Jun 2026 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Francesco Maria Antonio Micocci, a Undergraduate Student at University Of Turin, was awarded an OBF Event Fellowship to attend the BITS2026 Conference and BioHackathon2026.

Attending a conference for the first time and as an undergraduate student can be really intimidating. Finding yourself in rooms filled with affirmed researchers and topics you’ve not studied before. That was exactly the situation I found myself in at the recent Biohackathon and BITS2026 in the beautiful city of Padova.

I want to thank the Open Bioinformatics Foundation (OBF) for giving me the opportunity to participate in these events, without their support I wouldn’t have been able to embark on this experience.

The BioHackathon

As soon as I arrived in the city and after a rapid lunch, I found myself catapulted right into the action. After the groups were formed by the organizers, we got access to the GitHub repository. As an undergraduate, looking at the assigned tasks was a mix of excitement and panic. Quickly I came to realize that most of what we had to do I had only little knowledge of. While I felt like I couldn’t be of much help to the rest of the group, I got to learn a lot from the other members that didn’t leave me out even when I was clearly having difficulties.

The Conference

After the Hackathon, on the second day the conference finally started. To be really honest, the various talk sessions were packed with advanced topics that were lightyears ahead of my actual knowledge. But while the technical details went mostly over my head, listening to the speakers gave me an idea of where the field of bioinformatics is heading. Instead of feeling discouraged, it was actually motivating. Seeing how some of the knowledge I already possess is used in real life applications gave me a boost.

The Poster Session: The turning point

While I felt a bit out of place during the oral sessions, now it was time for the poster session. That was my chance to share our work and get feedback from the community. At first, I was quite nervous, but soon people came to read our poster and had a chat about it, then all the nervousness faded away. It was amazing to explain our project and to receive feedback from experienced researchers. This fantastic experience ended then with wonderful news. We won the best poster award! Getting this recognition completed this experience in the best possible way. I couldn’t really believe it! For an undergraduate like me getting an award like this and seeing people actually appreciating my work felt unreal. You can view and download the full award-winning poster on Zenodo.

Not only Science

This experience was not only about science. The social moments have been one of the best sides of this conference. Whether it was discussing projects over a coffee during breaks, having a laugh during dinners, or enjoying a drink with people, I always felt welcomed in the community.

Conclusion: A message to other Undergraduate students

Looking back at this whole experience, I think it taught me that you don’t need to know everything to be part of the bioinformatics and open source world. All you need is curiosity and the willingness to learn.

Once again, I want to express my gratitude to OBF for making all of this possible. If you are an undergraduate student thinking about applying for an OBF travel grant to attend these events: don’t hesitate, do it. You could get an opportunity to learn, meet incredible people that you wouldn’t experience otherwise, and you might also walk away with a win you didn’t expect coming!

Call for the second 2026 round of the OBF Event Fellowship & overview of the first round of 2026.

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 24 Jun 2026 00:00:00 +0000

The call for applications for round 2 of the OBF Event Fellowship for 2026 is now open. The deadline for this round is 1 August 2026. You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events between September 2026 to August 2027. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

The Open Bioinformatics Foundation (OBF) Event Fellowship program is now in its 9th year. Since 2023, we have had three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.

Looking back at the first round of 2026, we received 40 applications, and six applicants were selected to support their participation in various events.

Francesco Maria Antonio Micocci: BITS 2026 & BioHackathon 2026, 26-29 May 2026
Aditya Karna: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026
Lee Jia Wei: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026
Anastasia Bratulin: 34th Conference on Intelligent Systems for Molecular Biology, July 12-16, 2026
Jeremy Fan: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026
Neha Arora: Bioinformatics Open Source Conference (BOSC 2026), July 14-15, 2026

Congratulations to all of our awardees! We are delighted to help support their participation in open-source-related events with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 August 2026.

Call for the first 2026 round of the OBF Event Fellowship & overview of the awards made in 2025

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 05 Mar 2026 00:00:00 +0000

The call for applications for round 1 of the OBF Event Fellowship for 2026 is now open. The deadline for this round is 1 April 2026. You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The Open Bioinformatics Foundation (OBF)’s Event Fellowship program is aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities. Awards are made three times a year; the next deadline is April 1, 2026. (For those who want to apply for BOSC, note that this is earlier than the BOSC/ISMB submission deadline of April 9.)

We invite applications from candidates seeking financial support to attend relevant scientific events between May 2026 to April 2027. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Overview of the overall 2025 rounds of OBF Event Fellowship

The Open Bioinformatics Foundation (OBF) Event Fellowship program is now in its 9th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.

We changed the OBF event fellowship policy to say that the event that the applicant is applying to must be high-quality and not predatory. We also require the applicants and awardees write the application and blog draft themselves, and prohibit the use of AI/LLMs for this. These changes are now integrated in travel_fellowship.md and the OBF Event Fellowship application form.

Looking back at 2025, we received numerous applications, and nine applicants were selected from three rounds across 2025 to support their participation in various events. All OBF Event Fellowship awardees are required to write blog posts after their events; two of the people who were selected for awards in 2025 have not yet attended their events. Seven of them have written blog posts sharing their experiences at events that promote open science and open source bioinformatics, with the support of the OBF Event Fellowship. You can read their posts here:

Ruby Krasnow: 2025 ESIIL Innovation Summit: Collaborative and Open Environmental Data Science in Boulder
Tayyaba Alvi: ISMB 2025: A Week of Learning, Teaching, and Connecting in Liverpool
Muhamad Haries Ramdhani: ISMB/ECCB 2025: Liverpool, LLMs and Lessons in Open Science
Fatemeh Mirzadeh Sarcheshmeh: Elixir BioHackathon Experience
Hetvi Jethwani: BioHackathon Europe 2025: A Week full of Brainstorming, Coding & Collaboration
Rafał Miłodrowski: BioHackathon Europe 2025: BUSCO genes, lakeside hacking, and open workflows
David Kiragu Mwaura: Bridging Learning Gaps Through Open-Source Tools

Please share this post and apply for the fellowship before 1 April 2026.

Bridging Learning Gaps Through Open-Source Tools

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 23 Feb 2026 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. David Kiragu Mwaura,_an Assistant Research Scientist at the Kenya Institute of Primate Research, was awarded an OBF Event Fellowship to attend the 2025 AIBBC conference.

Introduction

My desire to share my masters’ research output in a real world demonstration had finally come to fruition. This was achieved by securing a competitive travel grant from the Open Bioinformatics Foundation Event Fellowship. Leaving the chilly landscapes of Glasgow, Scotland for the warm, tropical weather in my home country, Kenya, I was honored to attend the 2025 African International Biotechnology and Biomedical Conference, where scientists from around the world gather to exchange ideas that directly address Africa’s needs.

Poster Presentation

My simple and urgent plan was to showcase that open-source educational tools are practical, fair, high-impact solutions and not just an alternative means to the huge learning gap created by expensive proprietary software, especially in resource-constrained environments like Africa. My core contribution was to demonstrate how freely available platforms, particularly R Shiny, can revolutionize learning. My poster, “BRIDGING TECHNOLOGY AND GENETIC EDUCATION: AN OPEN SOURCE SHINY APPLICATION FOR TEACHING PATERNITY ANALYSIS”, served as the definitive proof of concept.

Standing proudly beside my poster, I highlighted the complexity of teaching kinship inference and presented our solution, DadApp, the open source R shiny tool. I shared the successful results from the Kenya Institute of Primate Research (KIPRE) pilot study that described the increase of interest and confidence upon using DadApp as an active learning tool. The results were uniquely compelling to the audience which sparked the discussion among lecturers and researchers from many institutions across Africa, who recognized the immense value of such open source tools. They saw an accessible, validated tool that could be replicated and scaled here in Africa where technology is gradually accessible.

However, what stood out was how diverse my audience was: Some asked what Open Source is and why it matters in the Biotechnology and Biomedical fields? Whereas some audience members were advanced to ask what license is the Shiny App released under and if it allows commercial use, modification and/or redistribution? The diverse audience validated the continuous need for sensitizing about the importance of Open Source tools and Open Science in general. One of the most satisfying highlights was having a Professor from one of the leading universities in Kenya appreciating the content of the poster and commenting that such Open Source tools are the future as they can help in enhancing flexibility in curriculum design. He further added that lecturers and those passionate in capacity development can tailor such tools to course goals especially in lessons that are mathematically and coding intensive.

Final Thoughts

The AIBBC conference was a humbling experience because for the first time I got to see something that was once a thoughtful concept became a product that was exciting and appreciated by my peers to advanced scientists and lecturers from different scientific backgrounds. However, my greatest achievement was showing that advanced learning does not have to rely on expensive softwares but can also be achieved with an open source Shiny App like DadApp. Students/participants can utilize such open source tools to explore data, visualize results, and understand scientific principles that once felt out of reach. The sparked conversations, encouragement and collaborative opportunities ignited a strong desire amongst the audience to champion genuine scientific equity, and a recognition that every scientist has a role in bringing that future of Open Science to life.

Looking back, the bridge from Glasgow to Kenya became one of ideas, innovation, and global learning. I hope the experience leaves a lasting impact on both myself and the audience long after the conference.

 ‘When knowledge travels freely, learning knows no borders.’

BioHackathon Europe 2025: BUSCO genes, lakeside hacking, and open workflows

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 04 Feb 2026 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. I was awarded an OBF Event Fellowship to attend BioHackathon Europe 2025, held 3–7 November at the Esplanade Resort & Spa in Bad Saarow, near Berlin, Germany. I am a PhD student at the Jagiellonian University in Kraków, working with insect genomes and large-scale comparative datasets. BUSCO is part of my everyday toolkit, so spending a week contributing to a BUSCO-based phylogenomics workflow with an international team felt like a perfect fit. The fellowship covered my travel costs and made it possible for me to fully participate in the hackathon.

A hackathon by the lake

BioHackathon Europe took over a lakeside hotel that turned into a giant shared office for a week: meeting rooms full of laptops and whiteboards, and a steady flow of coffee and conversations. Mornings started with a short plenary, followed by focused hacking sessions in the project rooms. Evenings were more relaxed, with social activities, ad‑hoc debugging sessions, and lots of informal discussions about tools, data and careers.

Project #03: benchmarking BUSCO genes for phylogenomics

I joined project #03, “Automatic workflow for benchmarking BUSCO genes for phylogenomics”. BUSCO lineage datasets are widely used to assess genome completeness and to extract putatively single-copy orthologs for phylogenetic analyses. However, once you look across many genomes at once, especially in groups with whole‑genome duplications, it quickly becomes clear that many BUSCO loci are not truly single copy. Our project aims to make this complexity visible and manageable. The goal for the week was to turn existing scripts and a prototype workflow into a robust Snakemake pipeline that starts from BUSCO output and ends with phylogenomic trees. The workflow includes steps for multiple‑sequence alignment and trimming, gene‑tree inference, detection of in‑ and out‑paralogs, and construction of concatenated supermatrices and species trees that explicitly account for paralogy.

My role: testing and debugging

Coming from a background of running Snakemake pipelines on HPC systems, I focused on the “does this actually run for a new user?” side of the project. A surprising amount of hackathon time can disappear into environment issues, so as a team we invested early in getting a clean, reproducible setup with conda and Snakemake with clearly pinned software versions. My main contribution was to run the pipeline on a curated set of genomes and report back where things broke or behaved unexpectedly. This included checking intermediate outputs (alignments, gene trees, paralog reports), tracking down missing dependencies, and helping to standardise file naming conventions for genome FASTA files and BUSCO output directories. These details may sound minor, but they are crucial when scaling up to dozens or hundreds of genomes.

Community and mid‑week reporting

A highlight of the week was the mid‑week reporting session, where each project prepared a short poster and gave lightning updates. Walking around the room, it was impressive to see the variety of topics being tackled in parallel: workflows, training materials, AI‑readiness, data standards and more. Presenting our BUSCO project forced us to summarise why this workflow matters, not just how it works. The poster session also helped to connect with people from other projects who use BUSCO or phylogenomics in their own work. Several visitors were interested in applying the workflow to their clades, and their questions helped us clarify which configuration options and outputs will be most useful for future users.

Take‑home messages

The week left me with a few key lessons:

Reproducible workflows are a collective effort. Agreeing on file naming, pinning software versions and writing documentation takes time, but doing it together during a hackathon pays off immediately.
“Single‑copy” genes are often more complicated than they look. The preliminary results we explored during the week highlight just how common paralogy is, even in supposedly universal BUSCO sets.
Hackathons are great for collaboration across time zones. Our work in Bad Saarow connected with contributions from an Australian outpost of the project, with progress passed back and forth through shared repositories and notes.
Open tools lower the entry barrier. By investing in a polished, documented workflow instead of a one‑off analysis, we make it easier for others to reuse and extend our work.
Pipelines live and grow in the open. The BUSCO phylogenomics pipeline we worked on is being developed in the open as the “buscophy” workflow on GitHub. It takes BUSCO output from many genomes, aligns and trims the corresponding genes, builds gene trees, flags in- and out-paralogs, and then builds concatenated supermatrices and summary species trees from the filtered genes. Having all of this encoded in one reproducible pipeline means others can rerun exactly the same analysis, adapt it to their own taxa, or extend it with new methods.

What comes next

The work we began at BioHackathon Europe 2025 will continue as the team refines the workflow, runs it on additional clades and prepares it for broader release. For my own research, I am excited to apply the BUSCO phylogenomics pipeline to insect genomes and to compare patterns of paralogy across groups with very different genome architectures. I expect this will directly improve the robustness of the phylogenies I use in my PhD.

Acknowledgements

I am very grateful to the Open Bioinformatics Foundation for the Event Fellowship that made my participation in BioHackathon Europe 2025 possible, and to the organisers from ELIXIR for creating such a welcoming environment. I would also like to thank the BUSCO phylogenomics project leads and all my teammates for their patience, good humour and willingness to explain things one more time when the logs got confusing. Finally, I appreciate the support of my home institution and colleagues in Kraków, who made it easier for me to step away from local duties for a week of focused hacking. Thank you, OBF!

Elixir BioHackathon Experience

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 04 Dec 2025 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Fatemeh Mirzade, a PhD researcher at the University of Antwerp, was awarded an OBF Event Fellowship to attend the BioHackathon Europe 2025 (https://biohackathon-europe.org/2025).

My BioHackathon Experience: Contributing to Open Science in Proteomics

From the 3rd to 7th of November 2025, I had an incredible opportunity that shaped my early PhD journey: participating in BioHackathon Europe 2025 as part of Project #29 on proteomics quality control. Thanks to the Open Bioinformatics Foundation (OBF) Event Fellowship, I joined a team of bioinformaticians and proteomics researchers working to solve a critical challenge in our field.

🔗 Project #29 repository: https://github.com/MS-Quality-Hub/biohackathon2025 🔗 OBF on GitHub: https://github.com/OBF

Why I Joined

As someone just starting their PhD, I was both nervous and excited to dive into this collaborative coding event. Our project aimed to build automated quality control frameworks for public proteomics repositories like PRIDE, which contains over 31,000 datasets. The problem? Without standardized quality metrics, researchers can’t confidently reuse existing data, essentially flying blind when trying to assess if a dataset is suitable for their analysis.

My Contribution: Making Sense of Quality Metrics

I was assigned to create a formal taxonomy for QC metrics in mass spectrometry. When I first looked at the existing PSI-MS Controlled Vocabulary, I was overwhelmed. There were metrics scattered everywhere, categorized in ways that mixed fundamentally different information together.

Working with the team, I helped develop a seven-dimensional classification system that describes each metric along orthogonal axes:

workflow stage
analytical dimension
information dependency
measurement scope
acquisition strategy
quality interpretation
metric value type

I compiled and classified 94 metrics from scientific literature, covering everything from chromatographic performance to identification confidence. For each one, I documented PSI-MS accession numbers, wrote descriptions, specified units, and noted applicability to different acquisition workflows. The work was tedious but deeply educational. By the end, I understood what “quality” actually means in proteomics.

What Open Source Contribution Feels Like

This was my first real experience contributing to open-source infrastructure that will be used globally. The spreadsheet I created is now feeding directly into updates to the PSI-MS Controlled Vocabulary. The team used my work to add new relationship types to the ontology, enabling tools to automatically understand what each metric means.

What struck me most was the collaborative nature of open science. I watched established researchers patiently explain concepts, saw consensus emerge through respectful debate, and learned that asking “stupid” questions often reveals important assumptions.

Meanwhile, other team members built incredible tools:

an mzQC export function for pMultiQC
an ID-free QC calculator using pyOpenMS
a web-based validator for our classification system

These weren’t just internal prototypes but contributions to the broader proteomics ecosystem.

Beyond Technical Skills

Yes, I learned about mzQC formats, PSI-MS ontologies, and GitHub workflows. But the most valuable learning was about how open science actually functions. I experienced the generosity of researchers who take time to mentor newcomers, learned that technical decisions involve tradeoffs between elegance and practicality, and discovered that it’s okay to feel out of your depth because that’s where real learning happens.

Coming in as a fresh PhD student, I felt intimidated by fast-moving technical discussions and unfamiliar acronyms. But that initial disorientation became exactly what made the experience valuable. I’m leaving not just with new technical knowledge but with lasting connections to a community committed to collaborative infrastructure development.

Why This Matters

We’re building something that will help researchers worldwide make better use of public proteomics data. Imagine filtering datasets by quality before downloading terabytes, training machine learning models on curated high-quality data, or conducting meta-analyses that properly account for technical variation. That’s the future we’re working toward.

This hackathon showed me what open science looks like in practice: people from different backgrounds coming together to tackle shared challenges, contributing their expertise freely, and building infrastructure that lifts the entire field.

I’m grateful to the Open Bioinformatics Foundation for making my participation possible and excited to continue contributing throughout my PhD.

Want to Explore More?

❖ Full story on Medium: https://medium.com/@fatemehmirzadehsarcheshmeh/building-the-future-of-proteomics-quality-control-my-experience-at-biohackathon-europe-2025-8487191e170f

❖ Project repo: https://github.com/MS-Quality-Hub/biohackathon2025

❖ OBF GitHub: https://github.com/OBF

BioHackathon Europe 2025: A Week full of Brainstorming, Coding & Collaboration

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 02 Dec 2025 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Hetvi J, a PhD student at Imperial College London, was awarded an OBF Event Fellowship to attend BioHackathon Europe 2025.

Thanks to the Event Fellowship from the Open Bioinformatics Foundation (OBF), I had the opportunity to attend BioHackathon Europe 2025 located in the beautiful city of Bad Saarow, Germany. I’m currently a 3rd year PhD student in Biostatistics and my work focuses on human mitochondrial genetics. Specifically, I construct statistical models to test whether the presence or absence of somatic mitochondrial variants is associated with gene expression changes indicative of stress and aging. As part of my PhD, I work with single-cell -omics data, and run bioinformatics pipelines over high performance computing systems. My broader interests in the fields of open-source scientific computing and bioinformatics motivated me to participate in this hackathon.

Background on the Hackathon

This event was a 5 day Hackathon with 31 projects, attended by 170+ in person and 200+ online. The hackathon began with presentations of each project & we started working with our chosen teams on day 1. Every day, we had hacking sessions from 9am until 5:30pm & the evenings were followed by social events to facilitate networking between people.

During the hacking sessions, participants would work together with their project teams on assigned tasks & make progress by co-working with team members. On the last day, we had final presentations detailing work done and future plans from the diverse range of projects.

The projects are all in bioinformatics but spanning a variety of topics— everything from sustainable cluster computing to metadata standardization to building new pipelines. A full list of projects can be found here: https://biohackathon-europe.org/projects/

Brief information about my project

I was part of Project 4: Beyond Beacons- Establishing genomic background in European and international biobanks.

We had 5 in person members and 1 online member working collaboratively on this project. The broad goal of this project was to assess the effect of genomic context as defined by haploblocks on the penetrance of mendelian variants.

We segregated sequences from specific haploblocks that contain genes of interest and clustered them using mmseqs2 over 2600 individuals from the 1000 genomes project. Further, we developed a nomenclature system using binary strings to jointly-label the chromosomal, haploblock, cluster, and variant context per individual.

We also made progress on sketching statistical models that would help associate these per-individual hashes with phenotypes. I contributed to building the nomenclature rules, and to model development and the codebase. More information on the project can be found at our Github repository. We will be releasing a Docker pipeline and a pre-print based on our work soon!

Our Github: https://github.com/collaborativebioinformatics/Haploblock_Clusters_ElixirBH25

The hackathon had some amazing social events I took part in.

On Day 2, we had ‘Chain Reaction’ - an event where we made a creative obstacle course with all sorts of materials like wood or rubber ducks or even bubble machines to create a visual spectacle across 12 tables (the pictures will help!). A very unconventional but incredibly fun social activity- it was one of my favourite parts of the hackathon!

On Day 3, we had a mid-week progress update from each team through a Poster session. This was a great opportunity to learn about other projects in more detail and learn about their technical & organizational approaches to the hackathon.

Every day, we had walks at 6pm led by one of the hackathon organizers - which was a nice chance to see the lovely town of Baad Saarow with other participants.

Learning experiences

Even with my limited background in the topic of recombination & haploblocks— I was able to rapidly understand the project context & make meaningful contributions through collaborating with others & learning from them. It was also fun working collaboratively on a codebase.

Moreover, getting a chance to interact with people from the wider bioinformatics community across sub-disciplines was very valuable for me. It was fascinating to hear about the interesting and diverse backgrounds other participants came from— my learnings from these conversations will definitely guide me as I progress in my career.

Thanks again to OBF for enabling my participation in this project.

2025 ESIIL Innovation Summit: Collaborative and Open Environmental Data Science in Boulder

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 03 Nov 2025 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Ruby Krasnow, a PhD student at the University of Maine, was awarded an OBF Event Fellowship to attend the 2025 ESIIL Innovation Summit. My team (Group 4) from the 2025 ESIIL Innovation Summit.

Introduction

Thanks to the support of an OBF Event Fellowship, I attended the 2025 Environmental Data Science Innovation & Impact Lab (ESIIL) Innovation Summit in Boulder, Colorado. An annual event, this year’s ESIIL Summit had the following goals:

Explore big data to understand environmental tipping points and transformations by identifying data synthesis opportunities and utilizing ESIIL cloud-compute capabilities.
Promote best practices in ethical, open science by supporting accessibility and usability of environmental data by all stakeholders.
Champion ethical practices in environmental science, and encourage the responsible use of AI.
Support teams by establishing collaborations around data-inspired themes across different disciplines, sectors, and career stages.

Summit participants at the Sustainability, Energy and Environment Community (SEEC) building, part of the University of Colorado Boulder.

The Summit was designed as an “unconference,” where much of the time was dedicated to forming teams that each tackled a specific research question related to understanding and predicting environmental tipping points and working in those teams to begin a collaborative project that ideally lasts far beyond the end of the in-person gathering. This event was a remarkable opportunity to meet and collaborate with other scientists from a variety of backgrounds.

I learned a great deal about the conference theme as well as the open-source software tools that support the use of big data to answer questions related to the environmental transformations or disturbances. The topics chosen by the groups were extremely diverse, such as:

Examining how hydrology, governance, and management interact within and across the Snake, Green, and Wind River Basins in the western U.S. - Synthesizing forest management and intervention strategies that can mitigate the impacts of linked disturbances (e.g., drought, windstorm, wildfire, and insect/pathogen disturbances).
Creating a dashboard and interactive search tool for tribal decision-makers to access and understand meaningful information about extractive activities in the HeSapa (Black Hills) through >2,400 Environmental Impact Statement/Assessment documents from the U.S. Forest Service, Bureau of Land Management, and other agencies.
Evaluating how the order, duration, frequency, and intensity of disturbances affect the likelihood of regime shifts from forests to nonforests.
Tackling broad questions about how to ensure greater data interoperability within the environmental data science community.

My team chose to focus on environmental tipping points within freshwater food webs, exploring how the stability and resilience of food webs might be affected by—or serve as an early warning signal for—environmental tipping points or “regime shifts.” As an initial case study, we concentrated on Lake Champlain, a relatively data-rich system that one of our team members, Dr. Alyssa Gleichsner, knows well.

Preliminary drafts of a simplified food web of the Lake Champlain ecosystem, with more (left) or less (right) abstraction of individual species into trophic groups. Dates in parentheses in the right figure indicate the year of first appearance for invasive species.

ESIIL staff encouraged us to use reproducible data analysis workflows from the very beginning of our project. Each team received a template GitHub repository to track progress and share code, which we used when presenting our initial results during report-back sessions to all participants. Looking ahead, we plan to submit a proposal to form an ESIIL working group, which would provide additional support to expand this project’s scope and impact. Whether or not we receive funding, we aim to publish an open-access paper describing our results. In keeping with OBF and ESIIL’s open science ethos, we will publish our data and code alongside the paper so other researchers can reproduce, reuse, and extend our analysis to other freshwater systems.

In addition to the time spent in working groups, the Summit featured several keynote presentations, including discussions on causal inference to identify climate impacts on ecological systems, predicting and managing ecological transformations in climate-adapted landscapes, and the use of AI in environmental data science. Perhaps the most meaningful aspect of the event was the emphasis on learning from and co-creating knowledge with the Indigenous peoples whose land we live and work on.

It was impossible not to be moved by the words of the Indigenous leaders present at the Summit, who spoke about the deep connection we have to every part of the natural world and our responsibility to honor and protect the land, water, and life around us. Although I was aware in an academic sense of Traditional Ecological Knowledge (TEK) and efforts to incorporate TEK with traditional western science, the Summit was the first place I’ve experienced it in action, and it was very powerful to see how diverse ways of knowing can be weaved together to support environmental protection and management efforts.

Pictures of the mountains in Boulder and a grazing mule deer taken while walking to the University of Colorado Boulder East Campus, where the Summit was held.

In many ways, the Summit showed me the value of diversity in scientific communities and the importance of community itself in maintaining hope and joy when facing immense challenges. Having learned more about ESIIL and its core values, I see many similarities with OBF, and I hope that OBF’s support of my participation in this ESIIL event will be only one of many examples of collaboration between the two organizations.

Acknowledgements

“Thank you to my Group 4 team members and to the OBF Event Fellowship for supporting my travel to the 2025 ESIIL Innovation Summit!”

Call for the third 2025 round of the OBF Event Fellowship & overview of the second round of 2025

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 06 Oct 2025 21:30:32 +0000

The call for applications for round 3 of the OBF Event Fellowship for 2025 is now open. The deadline for this round is 1 December 2025. You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

We invite applications from candidates seeking financial support to attend relevant scientific events between January 2026 to December 2026. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Overview of the Second 2025 round of the OBF Event Fellowship

The Open Bioinformatics Foundation (OBF) Event Fellowship program is now in its 8th year. Since 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.

In the second round of 2025 (August 2025), we received numerous applications, and five applicants were selected for funding to support their participation in various events. Congratulations to the following recipients:

David Kiragu Mwaura - Africa International Biotechnology and Biomedical Conference
Elminah - Systems biology: from large datasets to biological insight
Fatemeh Mirzadeh Sarcheshmeh - BioHackathon Europe 2025
Hetvi Jethwani - BioHackathon Europe 2025
Rafał Miłodrowski - BioHackathon Europe 2025

Notably, the OBF Events Fellowship sponsored three participants at the BioHackathon Europe 2025.

We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:

Tayyaba Alvi (left) attended the ISMB/ECCB2025 Conference, supported by OBF Event Fellowships. Read about their experience here.

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 December 2025.

ISMB/ECCB 2025: Liverpool, LLMs and Lessons in Open Science

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 04 Sep 2025 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Muhamad Haries Ramdhani, a PhD Student at the University of Aberdeen, was awarded an OBF Event Fellowship to attend ISMB/ECCB 2025.

The Journey to Liverpool

I had heard about ISMB before, but I wasn’t entirely clear on its joint conference format with ECCB. What I did know was that ISMB/ECCB is arguably the biggest conference for computational biology in the world. For months, my attendance felt uncertain, as I initially didn’t know if the 2025 edition would be held in the UK. When the location was confirmed as Liverpool, it was a huge relief. Being a UK-based student meant I was fortunate enough to avoid a lengthy and often stressful visa application process.

As a PhD student, attending my first major international conference was a significant goal. My research focuses on benchmarking and cell-to-cell communication and the ISMB/ECCB program felt perfectly aligned with my work. I was particularly drawn to the DREAM Challenges track, as it offered a chance to see a wide variety of approaches to benchmarking, which is central to my own projects. Furthermore, the conference provided an ideal venue to present my own poster and receive feedback from experts in the field. Beyond the formal sessions, I was very excited about CollaborationFest. The opportunity to contribute directly to open-source projects and network with the developers behind the tools we use every day was a major motivation for me to apply and attend.

Navigating a Massive Conference

Upon arriving, I realised the main conference didn’t formally kick off until Monday. Sunday’s schedule was composed mostly of tutorials and the student council symposium, both of which required extra payment to attend. However, the scientific energy began to build that evening with an incredible opening keynote from Nobel Prize winner Dr. John Jumper. In his talk, “Predicting the universe of biomolecular interactions with artificial intelligence,” Dr. Jumper walked attendees through the evolution of the AlphaFold project. He shared insights into the technical and conceptual milestones behind each generation of AlphaFold, including innovations like rawMSA masked language models, Evoformer modules and the importance of self-distillation. He emphasised that no single breakthrough carried the project, instead, AlphaFold’s success came from a steady accumulation of improvements and a methodology rooted in biological intuition and empirical iteration.

From Monday onwards, the conference was in full swing and the buzzing atmosphere truly hit. I have never been in a building with so many people. With over 2300 attendees, it was incredible to be surrounded by peers who all share a deep interest in computational biology. The sheer scale of the event was an experience in itself, requiring constant movement between auditoriums to attend the specific talks that aligned with my interests. My primary focus areas were the tracks for MLCSB, the NIH Track on GenAI, Cyberinfrastructure, Digital Twins and Quantum Computing and the DREAM Challenges. As my own research is in benchmarking, I spent the most time at the DREAM Challenge sessions. It was really nice to see the different and creative approaches people were taking to benchmark complex biological problems. I also made a point to attend talks in the Sysmod track, mainly because I was in a Systems Biology lab during my undergrad and the field still piques my interest.

The keynotes each provided a masterclass in a different corner of our field:

Amos Bairoch, in his talk “Plus ça change, plus c’est la même chose…”, delivered a powerful history lesson on 45 years of biocuration. He charted the field’s course from manually typing protein sequences in 1980 to leading the first Swiss-Prot release in 1986. Bairoch’s central message was a crucial paradox: despite incredible technological progress, the foundational work of expert curation still faces the same core challenges of being underfunded, undervalued, and wrongly assumed to be replaceable.
James Zou, the 2025 Overton Prize winner, explored the transformative potential of AI agents in his talk, “Computational biology in the age of AI agents.” He presented a compelling vision of AI “scientists” like the Virtual Lab, which can autonomously design research and CellVoyager, which reanalyses complex genomic data. His closing point emphasized that the future is not about replacement but a powerful synergy between AI’s scale and human creativity.
Charlotte Deane offered a dose of critical realism in her keynote, “Building the future of AI-driven structure-based drug discovery,” examining both the hype and the hurdles. While showcasing powerful tools from her own lab, she cautioned that the field is hampered by biased training data and flawed benchmarks. Her talk served as a crucial reminder that new AI models do not always outperform traditional methods on realistic test sets, raising serious questions about their true ability to generalize.

Posters, Serendipity and Collaboration

The poster sessions were immense, with what I estimated to be around 500 posters presented each day in a massive venue. I came prepared with a list of posters I wanted to see and enjoyed many engaging conversations with the authors. The hall was also a hub of serendipitous networking. While wandering the aisles, I met a new friend, a fellow PhD student from Indonesia who is now at Nottingham.

The final day brought an event I had been looking forward to with great anticipation: Collaboration Fest. I have always wanted to join a Collaboration Fest and I was very excited for the opportunity to engage directly with the community in a hands-on setting dedicated to advancing open-source projects. It represented the perfect way to cap off a week of intense learning, shifting the focus from listening to actively participating and networking with developers to contribute to the tools that are so vital to our field. In Collaboration Fest, I worked with Phil Reed from schemas.science which is an initiative to improve the findability on the web of scientific research data, products and resources. I worked on improving the process of generating training guides for domain-agnostic schemas.science using LLM. I also had the chance to present my own poster on benCCChmarker, which is a software to benchmark multiple single-cell RNA-seq cell-to-cell communication algorithms. benCCChmarker provides an easy to use framework to compare different algorithms using simulated cell-to-cell communication single-cell RNA-sequencing data and curated data. I received a very interesting visit from people who work directly in the field, which led to a fantastic discussion about my work.

Lessons Learned and Reflections

Attending ISMB/ECCB 2025 was an invaluable experience that taught me several key lessons:

The Scale of Community is Motivating: There is a unique energy that comes from being in a space with over 2300 people who share your specific scientific interests. The “buzz” in the venue was a powerful reminder that we are all part of a large, collaborative and global effort to advance science.
AI is a Tool, Not a Panacea: The keynotes collectively painted a realistic picture of AI in biology. It is a transformative tool, but its success depends entirely on thoughtful model design, rigorous evaluation and most importantly, robust, well-curated data. Professor Deane’s talk was a particularly important reminder to remain critical and avoid being biased by hype.
Foundational Work is Irreplaceable: Professor Bairoch’s talk was a crucial counterpoint to the focus on cutting-edge AI. It underscored that foundational resources built on expert human curation are the bedrock upon which new technologies stand. This work is vital, yet it continues to be undervalued and underfunded.
Embrace Serendipity: While I had a schedule, some of the most memorable interactions were unplanned, like bumping into an old friend or starting a conversation at a poster. These moments are where new ideas and collaborations often begin.

This conference broadened my perspective on the challenges and opportunities in computational biology and gave me new ideas to apply to my own research. It was an intense, exhausting but ultimately rewarding week.

Acknowledgements

I am thankful to the OBF Event Fellowship for the travel award which allowed me to attend ISMB/ECCB 2025. My thanks also go to the University of Aberdeen for funding my PhD research and to my mentor, Dr. Michael Morgan, for his invaluable guidance and wisdom.

Links and Resources to Open Science

Schemas.science branch that I worked on during Collaboration Fest https://github.com/schemas-science/schemas-science.github.io/tree/ismbeccb2025-cofest
benCCChmarker https://github.com/MorganResearchLab/benccchmarker

ISMB 2025: A Week of Learning, Teaching, and Connecting in Liverpool

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 25 Aug 2025 00:00:00 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Tayyaba Alvi, a PhD student at Fritz Lipmann Institute on Aging, was awarded an OBF Event Fellowship to attend ISMB/ECCB2025.

Thanks to the Event Fellowship from the Open Bioinformatics Foundation (OBF), I had the chance to attend the 33rd Conference on Intelligent Systems for Molecular Biology (ISMB 2025) in Liverpool. It’s the annual meeting of the International Society for Computational Biology (ISCB) and the biggest conference in the field. This year, it brought together over 2,000 researchers from all over the world at ACC Liverpool, a beautiful venue right by the Albert Dock.

Day 1: Teaching and Kicking Things Off

The conference started with workshops and tutorials, along with the ISCB Student Council Symposium. I was excited (and a little nervous!) to help organize and lead a tutorial on Mendelian Randomization (MR), together with two colleagues from my group. We had around 17 participants from different backgrounds and career stages join us for an interactive session on causal inference. We covered key assumptions, common pitfalls like pleiotropy, and hands-on examples in R. It was really rewarding to see people engage, ask questions, and reflect on how these methods might apply to their own work. If you are interested, you can find the tutorial slides and other information on the Tutorial Page.

In the evening, we heard a fantastic keynote from John Jumper, who shared the story behind AlphaFold. He walked us through the ups and downs of building such a groundbreaking method, and how many of their ideas came from trial and error. It was fascinating and also really encouraging to hear how persistence and curiosity shaped their success.

Day 2–4: Talks, Posters, and Conversations

The second day opened with a keynote from Amos Bairoch, who spoke about the ongoing challenges in biocuration. With so much biological data being generated, his talk highlighted just how important curated, high-quality data resources are, and how we need to keep investing in them. After that, the days were packed with talks across different tracks and COSIs. I attended sessions from:

GenComp (Comparative Genomics)
DREAM
BOSC (Bioinformatics Open Source Conference)
And MICROBIOME, which had some especially interesting talks on Tuesday and Thursday

There was a lot to take in—talks ranged from methods development to applications in systems biology, single-cell data, and microbiome analysis. One of the talks that really stood out to me was James Zou’s keynote, where he introduced the idea of a virtual AI lab. He talked about how AI agents and language models are starting to help with experiment planning, literature synthesis, and even idea generation. It felt like a sneak peek into how computational biology might look just a few years from now.

Outside the talks, the poster sessions and coffee breaks were great for meeting people. I had lots of interesting conversations, some about research, others just about navigating PhD life or sharing career advice. Chatting with poster presenters also helped me learn about tools and approaches I hadn’t seen before. Those casual exchanges were honestly one of the best parts of the week.

The conference wrapped up with a conversation with David Baker, who shared his insights on protein design and creative science, followed by a final keynote from Fabian Theis. His talk focused on atlas-scale data integration and the Human Cell Atlas, a huge and ongoing effort to map cell types across tissues and conditions. It was a powerful reminder of how large-scale collaboration can really push the field forward.

Exploring Liverpool

In between conference sessions, I made sure to explore a bit of Liverpool. The dockside area near the venue was lovely to walk around—full of history, great views of the Mersey, and a surprisingly peaceful vibe despite all the conference hustle.

Final Thoughts

ISMB 2025 was a really full and energizing week. Between leading a tutorial, hearing inspiring talks, and connecting with scientists from all over, I came away with lots of new ideas and a deeper appreciation for the community we’re part of. I’m super grateful to OBF for supporting my attendance. It made it possible for me to not only learn from the best in the field but also contribute something back through our tutorial. I’m excited to take these experiences into my own research and hopefully return to ISMB again in the future.

Call for the second 2025 round of the OBF Event Fellowship & overview of the first round of 2025

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 15 Jul 2025 21:30:32 +0000

The call for applications for round 2 of the OBF Event Fellowship for 2025 is now open. The deadline for this round is 1 August 2025. You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

We invite applications from candidates seeking financial support to attend relevant scientific events between September 2025 to August 2026. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Overview of the First 2025 round of the OBF Event Fellowship

In the first round of 2025 (April 2025), we received numerous applications, and four applicants were selected for funding to support their participation in various events. Congratulations to the following recipients:

Ruby Krasnow 2025 ESIIL Innovation Summit September 23-25, 2025
Tayyaba Alvi International conference on Intelligent Systems for Molecular Biology (ISMB) 20-24 July, 2025
Seun Olufemi RSECon25 9-11 September 2025
Muhamad Haries Ramdhani ISMB/ECCB 2025 20th July 2025 - 24th July 2025

We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:

Masturina Binti Md Mansor (left) attended the 2025 International Statistical Genetics Workshop, supported by OBF Event Fellowships. Read about their experience here.

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 August 2025.

The 2025 International Statistical Genetics Workshop - a goldmine of open-source genetic analysis tools and tutorials

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 30 Apr 2025 00:00:00 +0000

Thanks to the Event Fellowship from Open Bioinformatics Foundation (OBF), I was privileged to attend the 2025 International Statistical Genetics Workshop (ISG). ISG is an intensive, week-long workshop held annually in Boulder, Colorado that provides hands-on training in the principles and application of over a dozen open-access bioinformatics tools for analysis of genomic data. This workshop has been running since 1987 and boasts a faculty of world-renowned experts in statistical genetics from around the globe. The curriculum switches annually between family-based and population-based genetic studies. The focus this year was on the theory, performance, and interpretation of genome-wide association studies (GWAS) and their downstream analyses.

The workshop was a combination of lectures and collaborative hands-on practicals

The schedule was intensive and jam-packed with learning. Each day we gathered from 8am-5pm for a combination of lectures and hands-on practicals. We covered various aspects of genome-wide association studies, from the theory and principles behind the analyses, to the logistics of running them, to how to perform downstream analyses to investigate biological mechanisms. We learned how to perform analyses on multiple platforms including the terminal, RStudio, and Jupyter. On Monday we learned about classic and modern statistical approaches for genetic modeling; population genetics; how to generate, QC, and impute data using plink; and how to perform principal components analysis using plink and GCTA. Topics on Tuesday included how to access different data, including recruiting participants for your own studies and accessing biobanks; theory and performance of GWAS association tests using SAIGE; meta-analysis of multiple GWAS using METAL; and calculation of polygenic risk scores using SBayesR. Wednesday was a relatively light day, with a only a few sessions which were focused on calculating SNP heritability and genetic correlations with LD score regression. We also had a poster session on Wednesday, during which I presented my work on using the open-access tool PRS-CSx for improving polygenic risk score prediction for severe mental illness in diverse populations.

The tabletop poster session - I presented a poster on using the open-source algorithm PRS-CSx

On Thursday we continued with post-GWAS analyses, including additional SNP heritability calculations with GREML; pathway analysis with MAGMA; eQTL analysis with PEER and MatrixEQTL; and fine mapping and colocalization with SUSIE and coloc. Finally, on Friday we went through statistical power and how to calculate it with R and online tools; identifying causal and confounding factors with Mendelian Randomization in R; and performing rare variant analyses using Hail.

A huge benefit of this workshop, besides the technical skills it imparted, was the ability to network with such an experienced and diverse group of people in an intimate setting. We had direct face time with world leaders in the statistical genetics field, who headed off any intimidation we might have felt by reminding us in the very first lecture that we were all colleagues and insisting that we call them by their first names. In addition to being extremely knowledgeable, they were friendly, warm, and happy to answer one-on-one questions and give advice. Meeting and working with the other attendees - many of whom were from across the country or the world - was also fantastic, and was an opportunity I would have never had otherwise. I was even able to meet some of my own collaborators from the PsycheMERGE consortium, who I had only previously met over Zoom, in person for the first time!

When the workshop wasn’t in session, I visited as many places in Boulder as I could. The hotel was located steps from the historic Pearl Street Mall which is home to tons of restaurants and shops. My favorite visits were to the Piece, Love & Chocolate shop for some rich sipping chocolate; BarTaco for some scrumptious tacos, Gemini for some refined and delicious tapas; and The Attic for arcade games and satisfying American food. My favorite eatery was Rosetta Hall, an upscale food hall steps from the hotel with diverse, beautiful culinary options and live music. I also had a delightful visit to the Boulder Bookstore, which had 20,000 square feet of space and three floors containing over 100,000 books of every genre imaginable.

Enjoying some delicious cuisine at Rosetta Hall

Perhaps the best part of Boulder was its natural beauty. The hotel was located near the Boulder foothills which contain the famed Flatirons formation. This view was a stunning backdrop that we were able to enjoy during lunch, networking sessions, and on a group hike on Wednesday.

The workshop was a short walk away from the stunning Flatirons and the Open Space park

I also found some time to take an Uber up into the mountains to visit the incredible Lost Gulch Overlook, which boasts views of the forest and snow-capped peaks of the Continental Divide. The combination of the stunning view, the peaceful silence, and the crisp, cold air was otherworldly.

Breaktaking views from the Lost Gulch Overlook

The week was over before I knew it. I left with new connections, the knowledge and confidence to conduct my own GWAS analyses, and the ability to pass on my knowledge to my colleagues. The best part: all of the materials, including the code, from recent ISG workshops are freely available online on ISG’s website! Additionally, the workshop will be virtual next year to help accommodate a wider range of attendees. I highly encourage you to go!

All of the ISG 2025 attendees

THANK YOU OBF!!!

Call for the first 2025 round of the OBF Event Fellowship & overview of the last round of 2024

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 03 Mar 2025 21:30:32 +0000

The call for applications for round 1 of the OBF Event Fellowship for 2025 is now open. The deadline for this round is 1 April 2025. You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The Open Bioinformatics Foundation (OBF)’s Event Fellowship program is aimed at increasing diverse participation at events promoting open science in the bioinformatics and biological research communities. Awards are made three times a year; the next deadline is April 1, 2025. (For those who want to apply for BOSC, note that this is earlier than the BOSC/ISMB submission deadline of April 17.)

We invite applications from candidates seeking financial support to attend relevant scientific events between May 2025 to April 2026. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Overview of the third 2024 round of the OBF Event Fellowship

In the third round of 2024 (December 2024), we received numerous applications, and four applicants were selected for funding to support their participation in various events. Congratulations to the following recipients:

Jacqueline Wahura: the Royal Entomological Society Conference 2024.
Kyra Feuer: 2025 International Statistical Genetics Workshop.
Zoé Pochon: ISBA11 (International Symposium on Biomolecular Archaeology) and SPAAM7 (Standards, Precautions, and Advances in Ancient Metagenomics) in Turin, Italy

We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:

Masturina Binti Md Mansor (left) attended the 1st Asia & Pacific Bioinformatics Joint Congress 2024, supported by OBF Event Fellowships. Read about their experience here.

Erin Krichilsky received the award to attend the 27th International Congress of Entomology (ICE2024 Kyoto) and shared their story here.

Jacqueline Wahura attended the Royal Entomological Society Conference 2024, virtually. They reported their experience here.

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 April 2025.

Jacqueline Wahura: experience at the Royal Entomological Society Conference 2024

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 07 Jan 2025 15:12:20 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Jacqueline Wahura Waweru, a PhD researcher at the University of Cape Town and International Center of Insect Physiology and Ecology, was awarded an OBF Event Fellowship to attend the annual Royal Entomological Society Conference (Ento24).

I was privileged to virtually attend the annual Royal Entomological Society conference Ento24 ( Ento24: In-person - Royal Entomological Society), which took place on 10th to 12th September at the University of Liverpool, UK. The theme of the conference was insect science. Diverse speakers spanning various sub-themes, including pest and natural enemies, host microbiome interactions, genetics and genomics, vector surveillance and control, among others were present. This being the first broad range insect conference that I have ever attended, the diversity in the range of sub-themes covered at the conference made me fully appreciate the diversity in research and interests in the various insect species being presented. Each speaker was eligible to give a 15-minute presentation on their work.

The conference started with a keynote talk on Conservation Biology by Prof Michael Samways from Stellenbosch University, who is the author of the recently published “Conservation of Dragonflies”. This talk was very insightful in highlighting the challenges in protecting species from extinction. In addition, he highlighted some of the drivers of insect species extinction and the challenge that has on the ecosystem. With the threat that climate change presents, and the effect of human activities on the ecosystem, insect species must be protected to protect biodiversity and the gains that come with having insects in the environment, such as offering pollination services to plants used for human food.

During the pests and natural enemies session, I was excited to hear a diverse range of strategies being employed to control pests and natural enemies including the use of insect endosymbionts. It was exciting to hear of symbiosis research in insects like aphids, given that symbiosis is a theme on which my current research focuses, albeit in a different insect model, the mosquito. In addition, there were talks on controlling the Fall armyworm insect, which is a major pest in maize, through intercropping and push pull technology.

It was during the host microbiome interaction session that I was privileged to do my presentation titled “An influential insider: Microsporidia MB influences the gut microbiota composition in Anopheles arabiensis mosquitoes” ( RES_annual_conference_JWahura). Microsporidia MB is an insect endosymbiont in Anopheles arabiensis mosquitoes that was shown to impair the transmission of Plasmodium falciparum. In my talk, I highlighted my key findings that Microsporidia MB influenced the gut microbiota in infected mosquitoes to favor microbes with the Plasmodium transmission blocking phenotype. I outlined the steps followed in my methods and provided a GitHub link to the audience detailing the steps I followed in analyzing the gut microbiota data. It was interesting to see how my research, which is still in its infancy, stirred interest in the audience, and I received feedback on considerations I ought to take in my analysis pipeline as well as research gaps to consider filling.

Other interesting talks during the host microbiome interaction session included those of the effect of different environmental variables on the gut microbiota of mosquitoes, the effect of endosymbionts in aphids on the host microbiome and the protective effect of microbiomes in insects such as ants on fruits such as apples.

The second day of the conference started with a keynote talk on tsetse fly ecology and control by Prof Steve Torr from Liverpool School of Tropical Medicine. During this talk, we were brought to speed on the history of the tsetse fly and the burden of the disease associated with it. In addition, he highlighted all the control strategies that have been developed to reduce the burden associated with the disease and the outlook of gaps to be addressed in the future.

The genetics and genomics session was highly exciting to me as it aligns with my interests in bioinformatics. Various interesting talks on topics such as reproductive manipulation of insects for massive field releases, understanding the genetic drivers of polyphagy in plant pests and talks on genome assemblies formed the basis of this session. The range of talks during this session provided insight into the breadth of genomics research and the scale of adoption of open science practices in insect science. Additionally, there was a strong highlight on the application of insect endosymbionts such as Wolbachia in managing key vectors, including Anopheles gambiae and Aedes aegypti, during the vector surveillance session.

The last keynote talk on the last day was on “Co-evolution in social parasites and their hosts” by Prof Suzanne Foltzik from Johannes Gutenberg, University of Mainz. She did an excellent talk spanning genomics, microbiomes and proteomics and showcased the progress they have made in understanding the co-evolution of parasites and their host ants and bees.

This conference was one of a kind to me in helping me gain a broad perspective on insects and the dynamic range of ongoing research on various insect models. I was also able to gain new insights on alternative niches I could explore in my work by attending this conference. Although I was attending the conference virtually, I managed to get the emails of some attendees with whom I was interested in having follow up discussions on potential avenues of collaboration. It was also exciting to see how different scientists and students are embracing open science globally and also how they are contributing to developing open-source tools.

I am sincerely thankful to the Open Bioinformatics Foundation (OBF) for supporting my attendance at the Royal Entomological Society’s Ento24 conference and for allowing me to contribute to open science by sharing my approaches to malaria transmission blocking using insect endosymbionts.

Erin (Rin) Krichilsky: Leveraging Open Data to Address the Bee Biodiversity Crisis

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 21 Nov 2024 15:54:50 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Erin (Rin) Krichilsky, a PhD researcher at Columbia University and the American Museum of Natural History, was awarded an OBF Event Fellowship to attend the 27th International Congress of Entomology (ICE2024 Kyoto).

This year, I had the privilege to co-host the symposium “Bee diversity in East and Southeast Asia: Systematics and Status of the Fauna” at the International Congress of Entomology (ICE) in Kyoto, Japan. The symposium hosted eight researchers from Korea, Malaysia, Taiwan, China, Singapore, Thailand, and Nepal working in universities and government institutions. Each researcher gave a 15-minute presentation about bee studies in their region. Open data was a central theme, as many novel findings are discovered through DiscoverLife and the community science platform iNaturalist, and project results are posted to the Global Biodiversity Information Facility (GBIF) and the International Union for the Conservation of Nature (IUCN).

Figure 1. Images of bees from insect collections in Taiwan

It is estimated that bee species records are lacking for 79-90% of the global land area outside North America and Western Europe. However, those numbers are based on what is published online and do not reflect the reality of efforts beyond those two regions. The goal of our symposium was to create a network of researchers working on bees in Asia, as there are many projects with overlapping objectives, as well as unite ideas on how to use open data to mitigate biodiversity loss and improve faunistic understanding.

ICE only takes place once every four years, with a changing location. This year, it was estimated that there were over 4,000 attendees from 83 countries. Additionally, this was the fourth time in the near one hundred year history that the conference was held in Asia. We wanted to seize the opportunity of location to connect bee researchers in the region and show a global audience the many research projects happening there.

In addition to the symposium, we hosted a gathering where the presenters and those not participating in the event but conducting research on bees in Asia could meet. This event gathered nearly 20 individuals from ten different countries.

I am an Entomologist and PhD student studying the evolution and diversity of bees and apoid wasps. Before starting my degree, I lived in Taiwan, working with and learning from colleagues on a national checklist of the bee species there, Dr. Sheng Shan Lu and Wen-Chi Yeh of the Taiwan Forestry Research Institute and Dr. I-Hsin Sung of Chiayi University. We received funding from GBIF called the data mobilization grant to digitize bees in all national collections, which resulted in open source species and distribution data. Open data is essential for establishing a baseline biodiversity list, as it reveals novel information on species’ biology, range, and/ or morphology, as well as undescribed taxa. Dr. Sung presented our research, his talk “A Bilingual Open-Source Checklist and Digitization of Taiwan’s Bee Fauna" and others in the symposium showcased how platforms like GBIF, IUCN, DiscoverLife, and iNaturalist are critical for bee studies in the region. Additionally, since many bee groups have a taxonomy that has not been revised in up to a century, being able to see label data, images, and maps of fauna from neighbouring countries helps progress local efforts.

Figure 2. Digitization images of bee specimens from Taiwan and their label data. Notice the range in collection dates from 1910 to 2019!

Publicly available field and natural history collection data brings awareness and efforts to bee studies globally. The ICE symposium provided the opportunity for bee researchers to network and discuss projects, collaborations, and best practices for open-source tools. I am endlessly grateful to the Open Bioinformatics Foundation (OBF) for supporting my attendance at ICE, allowing me to enact our goals to contribute to open science by sharing our approaches and ideas to mitigate gaps in bee biodiversity knowledge. ICE has by far been my favorite conference I have ever attended! In addition to the success of the symposium, I was selected to receive a Presentation Award for Young Scientists (PAYS), all thanks to OBF. I highly encourage applications to the OBF Event Fellowship, as without their generosity, I would not have been able to meet such an important and inspiring group of researchers.

Figure 3. Symposium speakers, organizers, and attendees at ICE 2024.

Masturina Binti Md Mansor: My experience at the first APBJC2024 in Naha city, Okinawa, Japan

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 19 Nov 2024 16:11:11 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Masturina Binti Md Mansor, a PhD student at the Universiti Putra Malaysia, was awarded an OBF Event Fellowship to attend Asia & Pacific Bioinformatics Joint Congress 2024.

I flew in to Okinawa, Japan, from Kuala Lumpur, Malaysia on 21st October 2024 for the first ever Asia Pacific Bioinformatics Joint Conference 2024 (APBJC). It was my first international conference as a PhD candidate, a memorable milestone that I will cherish as I push forth in my research journey. This APBJC was successfully brought together by the big houses of bioinformatics in the region, namely the Japanese Society for Bioinformatics (JSBi), the Asia-Pacific Bioinformatics Network (APBioNET), the International Society for Computational Biology (ISCB), the Genome Informatics Workshop (GIW), and the Asia-Pacific Bioinformatics Conference (APBC). Digital advertisements flashed through the streets of Kokusai Dori in Naha in anticipation of the 4-day event (22nd October - 25th October) as the city welcomed around 700 participants from all around the world, bringing together researchers, scientists, academicians, industry players and other science/tech enthusiasts alike. The conference took place at the Naha Cultural Arts Theatre (NAHart), off the main street of Kokusai Dori.

Digital adverts along Kokusai Dori welcoming APBJC2024

With the generous funding from the Open Bioinformatics Foundation (OBF), I was able to gain exposure to the different trends in bioinformatics, and network with other bioinformaticians in the field. Not only were researchers and academicians present, but industry players like Amazon, Megazone and Alafia also provided luncheon seminars on integrating their services in bioinformatics and healthcare. One thing I have noticed about being in the bioinformatics/computational biology field, is the exponential pace trends and new ideas are generated. This conference was a great opportunity for me to not only learn from other bioinformaticians, but also for me to gain feedback on my research as well.

Me with my poster on the ‘Structure and Function of Aquaporin from Antarctic Pseudomonas’

Engaging with another poster presenter on her research

The focus this year oriented around the integration of AI in bioinformatics and healthcare research. It was interesting to see how most oral and poster presenters integrated AI into their research. From protein structure prediction to omics data analytics, and to those who were complimenting computational work with experimental methods, AI was a big theme everywhere. It also gave me ideas on how to better leverage open source tools and other best practices for reproducible science, which I am eager to share with my colleagues back home in Malaysia. Being able to converse and exchange knowledge with other participants in APBJC on how AI would help us advance bioinformatics research was especially enlightening to me. It felt like the future was already here!

Seminars and workshops

Together with the members of APBioNet

Whilst my journey to Okinawa was primarily to attend APBJC, I could not help but notice the charm and allure of the island. Even the airport was set at a picturesque background, with the turquoise waters of the sea visible from the airport terminal as I landed. It is a land rich in natural beauty, food, culture and welcoming people. The city was a unique mix of modern and old design, giving it that Okinawan identity.

A backdrop of the sea at the airport terminal

Exploring the streets of Naha, Okinawa

Enjoying an authentic Omakase dining

Overall, the first APBJC was a huge success, of which I am grateful to have had the opportunity to be part of. It was truly a hallmark moment for the bioinformatics community in Asia and Pacific, coupled with Okinawa’s warm hospitality and welcome. I am hopeful this pivotal event will pave the way for more to come over the years as we endeavour together to advance and make science and technology accessible. Till we meet again next time!

A group picture with some of the organisers, volunteers and participants before the networking session

Discovering Okinawa at APBJC 2024: Tanakamol Mahawan's First Conference Back in Asia

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 07 Nov 2024 13:09:25 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Tanakamol Mahawan, a PhD student at the Institute of Systems, Molecular and Integrative Biology , University of Liverpool, was awarded an OBF Event Fellowship to attend Asia & Pacific Bioinformatics Joint Congress 2024.

This year’s Asia & Paciﬁc Bioinformatics Joint Conference (APBJC 2024) in Okinawa was a special milestone for me; it was the first conference I attended since moving back to Thailand from the UK. Now a new lecturer at a Thai university, I felt a unique excitement and gratitude stepping into this event, thrilled by the chance to reconnect with the vibrant bioinformatics community in Asia Pacific and meet others passionate about advancing open science.

Falling in Love with Okinawa

From the moment I landed at Naha Airport, I was charmed by Okinawa. The warm weather was a welcome reminder of home, and as I walked toward my hotel, I found myself surrounded by the sights and sounds of the Okinawa Traditional Eisa Festival, a lively celebration filled with rhythmic drumming and dance. The island’s beauty was undeniable—pristine beaches, lush landscapes, and a culture that exudes warmth. Walking through the streets, I saw the incredible fusion of Okinawan tradition and modernity, from the traditional shisa lion statues guarding doorways to bustling markets selling both local delicacies and modern treats. Okinawa instantly felt like the perfect setting for an international gathering focused on innovation and collaboration.

Pic 1 : Okinawa Traditional Eisa Festival 2024

The Science of Batch Effect Correction

At the conference, I had the opportunity to present my research, “A Comprehensive Approach to Batch Effect Correction in Machine Learning: A Case Study Using Pancreatic Cancer RNA-Seq Data.” This was a moment I had been working toward, sharing insights from my PhD on tackling one of the core challenges in omics data analysis. I highlighted the importance of open science principles—transparency, reproducibility, and community collaboration—all of which are essential in bioinformatics.

It was encouraging to see a strong interest in my poster, with attendees eager to discuss the nuances of batch effect correction. We discussed why quality checks are crucial before using any batch-corrected data in downstream analyses—a topic that resonated with many who had experienced the complexities of multi-source data integration firsthand. As part of my commitment to open science, I shared the link to my GitHub repository, where others can access the code and workflow I developed for batch correction. This, I believe, contributes to a collective effort in making bioinformatics research reproducible and accessible to all.

P ic 2 : Poster presentation

Pic 3 : Workshop on Drug Response Prediction and Graph Neural Network(GNN)

Building Quality Connections

One of the most enriching parts of the conference was meeting new friends and potential collaborators. A memorable group of PhD students from Osaka, Hokkaido and Oxford brought fresh perspectives and infectious enthusiasm, making our post-conference discussions both lively and enlightening. We shared experiences and stories over local food, discussing everything from research challenges to future aspirations.

Pic4 -5 : A group of friends from Osaka , Hokkaido and Oxford

Another exciting connection was Dr. Nok, a researcher from Singapore and a senior in machine learning research. We bonded over our shared interests and began brainstorming ideas for a potential collaborative project. Meeting these brilliant minds underscored how bioinformatics is more than just science—it connects researchers across borders, allowing us to work together towards common goals.

Pic 6 : Dr. Chayaporn Suphavilai (Nok), My future collaboration in Machine Learning projects

Embracing Open Science and Representing Thailand

My participation in APBJC 2024 was more than just a chance to present my work; it was an opportunity to promote open-source bioinformatics and open science, fields where transparency and accessibility are essential. My research, part of which has been published in BMC Medical Informatics and Decision Science, is available on GitHub, where I’ve shared tutorials and workflows aimed at making complex analyses more accessible. This commitment to open science is something I hold close, as it embodies the collaborative spirit that drives meaningful progress in bioinformatics.

Attending APBJC 2024 also held a personal significance for me. As a Thai researcher in the relatively underrepresented field of bioinformatics in my region, I am passionate about bringing a unique perspective from Thailand to the global stage. This conference allowed me to represent Thailand, contributing to diversity in the open science community while fostering interdisciplinary connections.

In the end, APBJC 2024 was much more than a scientific gathering—it was an inspiring experience highlighting bioinformatics’s collaborative essence. I left Okinawa with a renewed sense of purpose, new friendships, and the excitement of upcoming projects. I look forward to continuing this journey and, hopefully, inspiring the next generation of scientists from Thailand and beyond. Thank you APBJC 2024, for arranging the wonderful event and OBF Event Fellowship for giving me this great opportunity.

Exploring Open Science in Computational Virology: Li Chuin Chong's Journey at ECCB2024

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 04 Nov 2024 11:26:48 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Li Chuin Chong, a PhD student at the TWINCORE Centre for Experimental and Clinical Infection Research GmbH & Medizinische Hochschule Hannover, Germany, was awarded an OBF Event Fellowship to attend 23rd European Conference on Computational Biology (ECCB2024).

I sincerely offer my gratitude to Open Bioinformatics Foundation (OBF) for the partial support, which allowed me to participate in the 23rd European Conference on Computational Biology (ECCB2024) in Turku, Finland. This was a milestone in my academic journey, as it marked my first international bioinformatics conference as a PhD candidate and my first-ever visit to Finland. This enabled me to share our findings from my PhD project, besides offering a platform to meet and interact with computational scientists from worldwide.

This 5-days conference with the theme of ‘Data and Algorithms for Health and Science’ was well attended by over 750 participants from 50 countries, featuring around 90 talks and 400 poster presentations. ECCB2024 offered five keynote talks and even a lively scientific debate. One talk that particularly stood out to me was by Peer Bork, who delivered an engaging presentation on planetary metagenomics. He discussed SPIRE (Searchable, Planetary-scale Microbiome Resource), a groundbreaking database that compiles microbiome data on a global scale. This resource allows for extensive mining of microbiome information, enabling researchers to identify novel baseline findings through meta-analysis. Bork’s team demonstrated how SPIRE is advancing data-driven discoveries, offering a transformative tool for microbiome studies, with wide-ranging applications in ecology, health, and global biodiversity.

Apart from the interesting talk, ECC2024 gave me an invaluable opportunity to present my research work, entitled “Towards quantifying zoonotic spillover risks of RNA viruses: A comprehensive approach using next-generation sequencing data”. My presentation focused on the identification of novel flaviviruses and coronaviruses, analyzing their hosts and assessing the potential for spillover events. I introduced our open-source software tool, virushunter-virusgatherer (available on GitHub: https://github.com/lauberlab/VirusHunterGatherer), which facilitates novel virus identification, showcasing how it integrates with other bioinformatics tools to provide a robust framework for RNA virology. This opportunity sparked meaningful discussions on the importance of open science and the role of interoperable frameworks in predicting zoonotic events, aligning with the core principles of the OBF. On the last day of the conference, I was excited to receive a free book from Oxford University Press titled ‘An editor’s guide to writing and publishing science’, which will undoubtedly be a valuable resource in my academic journey.

Lastly, I am very grateful to my supervisor, Prof. Dr. Chris Lauber for supporting my attendance at this conference. Again, I thank the OBF for awarding me a travel fellowship to partially cover my travel expenses, and extend my appreciation to the CoViPa consortium, which supports this project. Their support has been instrumental in making my participation at ECCB2024 possible.

Memories from ECCB2024 – Sharing insights from my research and discussing the open science perspective, while connecting with new colleagues from around the world.

Jacob González Isa: Bioinformatics, Spain and I

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 24 Oct 2024 10:20:01 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Jacob González Isa, a PhD student at the University of Cambridge (started October 2024) and formerly an MSc student at the Technical University of Madrid, was awarded an OBF Event Fellowship to attend the first Congress of the Spanish Society of Bioinformatics and Computational Biology (SEBiBC).

From October 16 to 18, 2024, Valencia hosted the first Congress of the Spanish Society of Bioinformatics and Computational Biology (SEBiBC), which I attended thanks to the Event Fellowship awarded by the Open Bioinformatics Foundation (OBF).

This was set to be a turning point for me—and not only because SEBiBC debuted and brought together over 300 attendees—an impressive feat for a society less than three years old. It was something else. Something personal. It was like a bittersweet farewell. This congress took place right in the middle of a professional transition: I finished my bachelor’s and master’s degrees in Spain and am now moving abroad to pursue a PhD.

Family picture at the end of the 1st Congress of the SEBiBC.

Let me tell you about three aspects of my experience at this conference and why it was so important to me:

1. First time as a symposium organiser

It was the first time I organised a Networking session at the Student Symposium as a member of RSG (the Regional Student Group in Spain of the ISCB). We created a sort of card game in which the participants, during lunch, had to assemble a bioinformatic pipeline combining their cards. It was so gratifying to see how this “nerdy” twist on networking helped foster connections and spark discussions among the attendees!

Jacob explaining the rules of the “Pipeline Assembly” networking activity.

2. The commitment to Open Science

Open and FAIR bioinformatics was omnipresent during the congress. Christine Orengo, from the University College of London (UCL), told us about their latest work, The Encyclopedia of Domains (TED) into CATH (https://www.cathdb.info/) and its relevance beyond structural Bioinformatics. Jaime Huerta-Cepas, leader of important work in open software and databases like ETE and EggNOG, shared their FESNov catalogue (https://novelfams.cgmlab.org/), with Álvaro Rodríguez as first author, which compiles more than 400,000 novel gene families unique to uncultivated microorganisms. Christine and Jaime had a common view on the cruciality of the open bioinformatics tools and databases they have used, such as Foldseek, MMseqs2, ETE, GMGC, ColabFold and Merizzo. Without these accessible resources and the community’s efforts, their groundbreaking work simply would not have been possible.

Jaime Huerta-Cepas emphasises the importance of the open-source tools and community behind his work. Image taken from @SEBiBC_es

In this congress, I understood the excellence of Spanish bioinformatics and its commitment to open science and reproducibility. The list of accomplishments and initiatives is impressive. From digital twins projects led by the Barcelona Supercomputing Center, home to one of the world’s most powerful supercomputers, MareNostrum 5, to cutting-edge tools like SQANTI3 for long-read transcriptomics developed by the Ana Conesa lab, Treeprofiler by Ziqi Deng, ETE4 by Jordi Burguet and CAASTools by Fabio Carteri, and many more that I don’t have space to mention. More than 100 posters filled the room with innovative tools. Everything is open and accessible.

On a 1000-fold smaller scale, I was excited to present my M.Sc thesis work with a poster, where I developed a pipeline called MetEOr to mine enzymes of biotechnological interest. The feedback I received was incredibly helpful and will guide me in refining the documentation and improving how I share my work moving forward.

During the poster session, I presented my tool MetEOr (https://github.com/jacgonisa/MetEOr) and the results derived from it with the plastic-degrading enzyme family.

3. Where I come from and where I go

To be fair, six years ago, I could have never imagined being in an event like this and starting to feel like a scientist. I am a first-generation university graduate who grew up and studied in a very humble background in one of the poorest regions in Spain, Andalusia. My home city has one of the highest youth unemployment rates in Europe.

In 2023, I found an incredible opportunity in Madrid and joined the Jaime Huerta-Cepas group, where I’ve learned more than I ever have in my entire life. While there, I also discovered RSG, SEBiBC, and Spain’s longstanding commitment to open bioinformatics. It was there that I truly found my place in the bioinformatics community.

However, life has exciting, unexpected turns, and another fantastic opportunity came my way that I couldn’t pass up… So, I packed my bags and started a PhD in October at the University of Cambridge.

I have never hidden that I am scared of going abroad for long periods, but experiences like the one I had this week in Valencia inspire me to kick off a career in bioinformatics internationally with confidence and enthusiasm.

I can’t envisage my professional journey without Spain. This congress in Valencia was so important to me because I believe it’s essential to represent the Spanish (and Andalusian) community while I’m in the UK. Even as I embark on my PhD abroad, I wish to have strong roots in Spain, with tangible connections with people that I can call friends. I want to bring the best Bioinformatics from Spain to the UK and vice versa.

In Valencia, I learnt that bioinformatics is an especially interconnected, transversal discipline, perhaps due to the huge set of crosscutting skills we develop and the fact that international mobility is commonplace. It was inspiring to see foreign researchers thriving in Spain and Spanish scientists like Luz García Alonso (another keynote speaker and a bioinformatician at the Sanger Institute) doing great science abroad.

The Open Bioinformatics Foundation has helped me lay the first stone in the bridge I want to build between Spain and England, and I couldn’t be more grateful.

¡Gracias y hasta pronto!

After three tiring and overwhelming days, I deserved a delicious dish of paella! Fun fact: paella originated in Valencia, so it is actually more a regional, Valencian dish than a Spanish one.

Call for the third 2024 round of the OBF Event Fellowship & overview of the second round.

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 11 Oct 2024 15:45:44 +0000

The call for applications for round 3 of the OBF Event Fellowship for 2024 is now open. The deadline for this round is 1 December 2024. You can submit your application through this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events between January and December 2025. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Screenshot of our application form information section

Overview of the second 2024 round of OBF Event Fellowship

In the second round of 2024 (August 2024), we received numerous applications, and four applicants were selected for funding to support their participation in various events. Congratulations to the following recipients:

Jacob González Isa: The 1st Congress by The Spanish Society of Bioinformatics and Computational Biology.
Tanakamol Mahawan: Asia & Pacific Bioinformatics Joint Conference 2024.
Masturina Binti Md Mansor: Asia & Pacific Bioinformatics Joint Conference 2024.
Keerthana P.: Transatlantic Behavioral Neuroscience Summer School 2024, Mikolajki, Poland.

We require each awardee to write a blog post about their conference experience, to share what they learned with the wider community. Here are some examples from our recent awardees:

Urszula Włodkowska summarised their experience attending the University of Waterloo’s Nengo Summer School with the help from OBF Event Fellowships. You can read about their journey here: Building Brains in Canada .

Zehra Köksal received the award to present their work at the International Society of Forensic Genetics (ISFG) in Spain and shared their story here.

Felipe Castañeda attended an online EMBL-EBI Cancer Genomics and Transcriptomics 2024 course, with registration fee covered by OBF event fellowship. They reported their experience here.

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 December 2024.

With a little help from your friends! -Learning bioinformatics online.

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 05 Oct 2024 05:12:05 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Felipe de Jesús Castañeda Córdova, an MD/MS student from LIIGH-UNAM (Laboratorio Internacional para la Investigacion sobre el Genoma Humano) Mexico was awarded an OBF Event Fellowship to attend the EMBL-EBI Cancer Genomics and Transcriptomics 2024.

My name is Felipe de Jesús Castañeda Córdova. I am an MD/MS student from Mexico, primarily focusing on the wet lab aspect of lab work at the Cancer Genetics and Bioinformatics Lab. I had limited experience with bioinformatics (I performed some transcriptomic analyses for my master’s project, and I got the bug!), so I decided to apply to the online EMBL-EBI Cancer Genomics and Transcriptomics 2024 course. I was fortunate to be accepted into the program and receive an OBF Event Fellowship, which helped me cover the registration fee.

The EMBL-EBI Cancer Genomics and Transcriptomics 2024 course was a week-long intensive course aimed at an international audience. It focused on the theoretical and practical aspects of the most popular bioinformatics analysis tools for cancer research. Despite the time difference between Europe and home, I really enjoyed the entire course. Most of the theoretical classes were inspiring, and the practical portions helped ground our knowledge and resolve most of the questions and doubts that came up as we worked on our scripts. I liked the RNA-seq part of the course, probably because of my previous experience with the subject. Student experience and participation enhanced this section by helping to address many of the questions that typically arise when interpreting GSEA results. During the practical sessions, we had the chance to engage with other students and learn more about their projects and research.

I have already started using the skills and insights gained from this course to impact my research. I am reanalyzing my transcriptomic data, considering the new parameters we discussed during the course, and I am excited to apply the new programs and techniques we were introduced to.

The knowledge I gained from this experience goes beyond technical skills. It has broadened my perspective and deepened my understanding of the bioinformatics community as a whole. It has made me more aware that regardless of our geographical location, we all encounter similar challenges and obstacles. It has also emphasized the importance of collaboration and continuous learning, which are essential for progress in this rapidly evolving field.

I am deeply grateful to the Open Bioinformatics Foundation for providing me with this fellowship and the opportunity to attend the EMBL-EBI Cancer Genomics and Transcriptomics 2024 course. The experience has been immensely rewarding, both professionally and personally. I encourage anyone interested in bioinformatics to consider participating in such events and to take advantage of the opportunities offered by organizations like the OBF.

Zehra Köksal: My unforgettable experience presenting accessible software to 1000 forensic experts

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 26 Sep 2024 06:37:11 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Zehra Köksal, a Research assistant at the University Of Copenhagen and Karolinska Institute was awarded an OBF Event Fellowship to attend the 30th Congress of the International Society for Forensic Genetics.

In September 2024, the Open Bioinformatics Foundation enabled me to attend the biennial conference for Forensic Geneticists from the biggest forensic genetics society worldwide – the International Society of Forensic Genetics (ISFG) - that took place in Santiago de Compostela in beautiful Spain.

River in Ribadeo, Ría de Ribadeo o del Eo, separating Galicia and Asturias.

To appreciate the beauty of Spain prior to the conference, I embarked on a journey along the northern coast of Spain from Cantabria over Asturias and finally to Galicia, where the pilgrimage town Santiago de Compostela is located. My first lesson from this journey was that the north of Spain is not called “Green Spain” for no reason.

Cathedral in Santiago de Compostela.

Around 1,000 forensic experts attended the ISFG2024 in Santiago de Compostela. One of these experts was me! Attending the ISFG2024 has been extremely valuable for me personally and professionally.

#1 Connecting with peers and experts

I was able to meet previous colleagues and collaborators spread across the globe. I reconnected with old study mates, celebrated our successes, discussed our career paths, and motivated and inspired each other. I could exchange PhD experiences with peers, meet my mentor and role models, and receive invaluable advice from them.

#2 Looking beyond everyday research

Our daily work revolves around research and academia. Thus, it was very important to look beyond this by talking to government-funded institutions and commissions to widen my horizon and get different stimulations to gain creativity.

#3 Updating on current research in the field

The scientific program was extremely stimulating, with great key notes and presentations. I particularly enjoyed the presentations on forensic microbiology and phenotyping, among many other interesting topics covered by experts.

#4 My talk

Starting my presentation on our software PhyloImpute.

This leads me to presenting my work in a 10-minute talk in front of 1000 experts. In my talk “PHYLOIMPUTE – Impute missing data on non-recombining DNA using SNP phylogeny” I presented a new software I was working on over the last months for imputing missing SNP data. The main goals of my talk were to convey the need for my tool and its algorithm in a simple and entertaining way with interesting storytelling and visual aids. Further, I wanted to make my tool accessible to people with different degrees of experience and interest in programming. Thus, I provided both a command-line tool (available via https://github.com/ZehraKoksal/PhyloImpute) and a graphical user interface (available via https://zehrakoksal.com/Y_software.html). With accessibility being a major goal, I had also made a video tutorial that I uploaded on my new webpage. Since one rarely gets an audience that big, I used this opportunity well and received great interest after my talk. Although nerve-wracking beforehand, presenting my work in front of so many experts was also a very calming and extremely rewarding experience that I will not forget so easily.

Concluding my presentation on our software PhyloImpute.

Finally, I want to express my deepest gratitude to the Open Bioinformatics Foundation for supporting me on this journey. Particularly as a recent PhD graduate – a time of great changes – attending conferences like these is so important professionally and personally. Feeling supported when celebrating small successes is a big motivator. So, with this, I am encouraging everyone reading this to apply for the fellowship offered by the Open Bioinformatics Foundation!

My Amazing BOSC 2024 Experience

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 02 Aug 2024 18:00:06 +0000

By Beatrice Mihalache

Examining open source projects has been most useful to me while I am sharpening my coding skills, so I was excited to learn about the Bioinformatics Open Source Conference – BOSC. I am a rising senior at UCLA, studying biophysics and data science. I strongly believe in open source, so I submitted the work I’d done with my PI and my grad student collaborator for a poster presentation at BOSC. My research lab at UCLA allocates conference participation funds only for graduate students, therefore I also included a request for fee waiver with my conference submission. I was excited when a few weeks later I received notification that not only I was accepted as a poster presenter, but that I also got free registration to both BOSC and to the entire ISMB (Intelligent Systems for Molecular Biology) conference!

Attending BOSC and ISMB was such an incredible experience. On Saturday and Sunday I attended different sub-conferences at ISMB including multiple talks on deep-learning applications to biological problems such as enzyme design and protein function prediction. I was stoked and humbled by how much I learned. The coffee and lunch breaks were a super welcome opportunity to network and talk to other poster presenters about their research.

Palais de Congress, the conference venue, at night. The colorful window architecture is cool.

On Monday, BOSC kicked off with Melanie Courtot’s keynote about the necessity for better quality data. I learned more about Findable, Accessible, Interoperable, Reusable (FAIR) code, as this was never explicitly mentioned in any of my computer science classes at school.

Tuesday’s talks were also very cool, the most memorable to me being Andrew Su’s keynote, specifically the part where he had us imagine what AI would be like in the future. In a world that is changing at an accelerated pace, this is a difficult exercise, but a valuable one that also gives insight into the skills that will be most valued in future researchers such as creativity and linking interdisciplinary applications together well.

Me in front of my poster at BOSC, enjoying this most awesome experience

One of my favorite conference experiences was going to dinner with some of the conference attendees. Monday night we ate at LOV McGill, an impressively delicious vegan restaurant. It was so valuable to personally connect with people. I sat between Andrew Su, a professor and researcher at Scripps who would be giving the next day’s keynote, and Bhavesh Patel, the founder of the FAIR data innovations hub. It was nice to learn about people’s personal experiences, about how they got to where they are, and also random snippets and stories.

I am most grateful to BOSC’s sponsors Seqera, NIH ODSS, the Chan Zuckerberg Initiative, and GigaScience for helping me attend BOSC. This experience has been invaluable. I am inspired and energized by it. I look forward to applying the things I’ve learned to new projects. I will make sure that all my future projects’ code is FAIR.

The conference was hosted in Montreal, and I had never been there before, so I took this trip as an opportunity to do some sightseeing and exploring, by staying a few extra days after the conference. I was impressed by how well Montreal blends the old architecture with the modern. I climbed the stairs of Mont Royal, ate poutine with some friends I made at the conference, and visited the Museum of Fine Arts and the Archeology and History Museum.

Urszula Włodkowska: Building Brains in Canada

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 18 Jul 2024 12:11:01 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Urszula Włodkowska, a PhD Researcher at the Nencki Institute of Experimental Biology PAS was awarded an OBF Event Fellowship to attend the University of Waterloo’s Nengo Summer School.

In June of 2024, I had a great opportunity to attend the University of Waterloo’s Nengo Summer School (also known as Brain Camp). This was only possible thanks to the fellowship I received from the Open Bioinformatics Foundation.

Urszula Presenting her project to the group.

This summer school was an important event for many reasons. First, I was excited to learn about the Nengo simulation package (https://www.nengo.ai/), which is a powerful platform for designing cognitive and neural systems. Nengo has recently become open source, and for me, using open tools means having not only a better understanding of how they work but also being able to contribute to and influence their growth. This creates a community of users that give back and support each other. The fact that Nengo is newly open source also provided a unique opportunity to talk to the creators about the challenges of transitioning into that mode.

The Nengo Summer School also provided an introduction to the Neural Engineering Framework. The NEF has been developed by the Computational Neuroscience Research Group led by Chris Eliasmith at the Waterloo Centre for Theoretical Neuroscience as a tool for understanding neurobiological principles through constructing simulations of neural systems. Learning about it provided a satisfyingly complete view of the subject - connecting tools with theory and reasoning behind how the tools have been constructed.

The two weeks I spent in Waterloo were intense. The first week focused on the introduction to the framework and practical tutorials translating theory into code. On top of that, with other participants and TAs we discussed projects that everyone brought with them to work on during the school, looking for common interests and ways to collaborate. During the second week, we worked on our projects and attended tutorials on advanced applications of Nengo. The school ended with project presentations - first, for other participants, and then in an open event at the University of Waterloo.

Tutorial at the Waterloo Centre for Theoretical Neuroscience

My project focused on simulating how a mouse learns to optimally explore the environment while gradually learning the rules governing the behavioral setup. I learned a lot, especially thanks to the help of one of the TAs - Nicole Dumont. I intend to continue working on this project, so the summer school leaves a lasting impression on my research.

But my personal gain was not the only reason I wanted to attend this school. As a part of the Nencki Open Lab initiative (https://nenckiopenlab.org/) that connects young neuroscience researchers from underprivileged regions, I always see the events I attend as an opportunity to share the knowledge and connections I’ve made with others. The Nencki Open Lab events touch on two aspects - teaching people how to use open tools and how to approach research as a part of a bigger picture, connecting theory and practice. The Nengo Summer School helped me grow in both of these areas and I hope to bring the concepts and the people I’ve met there to our own summer schools.

Group photo of this year’s attendees and teachers

Call for the second round of OBF Event Fellowship 2024 & overview of the last round of 2023.

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 18 Jun 2024 13:05:37 +0000

The call for applications for the OBF Event Fellowship 2024, round 2, is now open. The deadline for this round is 1 August 2024. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from September 2024 to March 2025. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Screenshot of our application form information section

Overview of the first round of OBF Event Fellowship 2024

The Open Bioinformatics Foundation (OBF) Event Fellowship program is now in its 8th year. Starting in 2023, we have three application rounds per year with the following deadlines: 1 April, 1 August, and 1 December.

In the first round of 2024 (April 2024), we received numerous applications, and seven applicants were selected for funding to support their participation in various events. Congratulations to the following recipients:

Urszula Włodkowska: Nengo Summer School
Tolulope Uzoka: Bioinformatics for Immunologists/EMBL-EBI Training
Sushma Naithani: BOSC 2024
Li Chuin Chong: 23rd European Conference on Computational Biology (ECCB2024)
Zehra Köksal: 30th Congress of the International Society for Forensic Genetics
Erin (Rin) Krichilsky: International Congress of Entomology (ICE)
Felipe Castañeda: Cancer Genomics and Transcriptomics 2024

This fellowship will provide financial support to enable them to attend the aforementioned events.

We recently published a blog post from our latest awardee summarising their experience attending an event with help from OBF Event Fellowships:

Thea Fennell: Open Data, Open Doors

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 August 2024.

Open Data, Open Doors

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 27 Mar 2024 05:34:04 +0000

A PhD student’s perspective on attending the 17th Annual International Biocuration Conference in Faridabad, India

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Thea Fennell, a PhD Researcher at the MRC Laboratory of Molecular Biology, was awarded an OBF Event Fellowship to attend the 17th Annual International Biocuration Conference.

“The best use for your data will be thought of by someone else” — Rufus Pollock encapsulates this concept in all its power and humility. It is at the core of open science and biocuration. Almost by definition, FAIR data is non-proprietary, yet the work done to generate, curate, and share it is invaluable. Recent proceedings at the 17th Annual International Biocuration Conference (AIBC), hosted at the Indian Biological Data Centre (IBDC) in Faridabad, were a testament to this duality.

The Indian Biological Data Centre, Faridabad, just an hour’s drive from New Delhi.

Opening the conference, Professor Saurabh Raghuvanshi emphasised the altruistic nature of the field and its principles: integrity, accessibility, and usability. He went on to highlight the milestones reached thanks to this public-minded approach to biodata within India: development of the ZyCoV-D vaccine, widespread HPV vaccine distribution, and establishment of the world’s only Crop Phenome Database. These positive achievements prove what open bioinformatics can do – when there is sufficient political will.

This necessary symbiosis between institutional support and open science principles can also be observed at the international level. In the first conference session, covering the International Sequence Database Collaboration (INSDC), Dr Guy Cochrane highlighted how international data sharing has facilitated breakthroughs worldwide: from global virome discoveries to COVID vaccines to – of course – AlphaFold. This initial session also revealed how data standards depend upon institutional policy at multiple levels.

Professor Masanori Arita touched not only on how academic publishing companies have begun to mandate data submission to the INSDC – connecting primary researchers to data sharing by default – but also on growing links to industry data, such as through liaison with the Japanese and Korean Patent Offices. Meanwhile, the constituent members of the INSDC – the DNA Data Bank of Japan (DDBNJ), the European Bioinformatics Institute (EBI), and the National Centre for Biotechnology Information (NCBI) – are themselves governmental institutions with a corresponding role to play in shaping data policy.

The 17th AIBC was ceremonially inaugurated by Minister of State, Dr Jitendra Singh.

International collaboration remained a key theme throughout the proceedings in the context of various global concerns, from food security to epidemiological modelling. These collaborations are evidently not without their challenges, as evident from the conference’s session on global biodata. Decentralised collaboration may be an asset in linking efforts more directly to the coalface of primary research. However, it can also lead to conflict regarding scientific or political priorities. These competing interests are writ large in the competing policies on FAIR data – from the Convention on Biology Diversity (CBD) to the World Health Organisation (WHO) to country-specific guidelines.

Data accessibility appeared to be an area of particular contention. Professor Arita initiated the discussion, delineating how FAIR principles can conflict with guidelines on indigenous data governance – the CARE principles – reflecting an ambiguity in negotiating accessibility for sensitive data over which specific individuals or groups may reasonably claim authority. This thread was taken up again by Dr Ilene Mizrachi, whose US-based work at NCBI is subject to fewer legal restrictions regarding data ownership, and then again by Dr Harpreet Singh, whose work with the Indian Council of Medical Research necessitates policy compromise in the form of “responsible data sharing”.

Despite these difficult and necessary conversations, the overall feeling of the conference was one of optimism. Perhaps, as the speakers took to the stage in the newly built IBDC, they thought of the public good – vaccines, plant breeding, drug development – already enabled by biocuration and the wider world of open bioinformatics. Perhaps, too, they were bolstered by the profession’s reputation for handling complexity, facing challenges not only with intellectual rigour but with informed compassion; what Dr Sarah Davies terms “care-ful work”. Indeed, Dr Davies’ talk – on her ethnographic study of biocurators – provided vital context for the conference (and profession).

Outlining the discipline, Dr Davies described biocuration as “being precise and exact […] to support the people in our community”, which aligned well with the technical scholarship and ethical concern showcased throughout the conference. However, she also observed economic precarity among curators, exacerbated by epistemic exclusion and “fauxtomation”. In the words of one of her study’s subjects, many database users see biocurators as “some kind of gnome, that fills the database at night”, diminishing or erasing their scientific contribution and labour without necessarily intending to do so.

Delegates, speakers, and organisers came together from all around the world.

Whilst Dr Davies’ talk was the only one to take biocuration itself as the object of study, her findings were consistent with many of the themes that emerged at this year’s AIBC. Economic sustainability, in particular, was a recurring focus – with environmental and social dimensions acknowledged but shelved in the face of even more pressing matters. It transpires that biocuration is precarious not only in terms of individual curators “living on those short-term contracts”, as demonstrated by Dr Davies but also at the institutional level. Dr Lynn Schriml, Professor Arita, Dr Frederic Bastian, and Dr Cochrane focused on the latter scale of economic insecurity and how best to ameliorate it. Dr Schriml, specifically, stressed the importance of database longevity – along with reliability and availability/access – as a pillar of effective biodata sharing and re-use.

Altogether, this proved an enlightening exchange for me as an early-career scientist, illuminating the peaks and pitfalls of the funding landscape. It shed light, too, on the transient availability of institutional funding and support. This can, in turn, cause the casualisation of curational labour, contributing to institutions undervaluing biocurators’ expertise and employment. No wonder, then, that so many of the pioneering collaborations covered in this conference began either as solidifications of informal researcher networks – e.g. the Global Biodata Coalition – or under the aegis of more specialised funding bodies – e.g. Bgee, as a Swiss initiative “of national importance”.

I was honoured to present my work on synthetic cell types to a global audience.

As a young researcher – with all the idealism and enthusiasm that implies – I am inclined to hope that biocuration will receive the recognition due to it in time. Certainly, I see no reason why a career dedicated to enabling ethical, open bioinformatics should be any less deserving of professional recognition – let alone a living wage – than any industry researcher or governmental policymaker. That said, shifting the culture of science (not to mention society!) will hardly happen overnight. I am also aware that the issues of ethical conundra and economic precarity are widespread in academia. However, biocuration as a discipline is especially unsung, offering fewer research grants and individual awards than other biological fields. Nor is it a coincidence that most curators were and are women – invisible women, doing invisible work.

Fittingly enough, for a female-dominated field, International Women’s Day fell during the conference itself. Whilst AIBC’s speaker lists have yet to achieve gender parity, the hosts at IBDC nevertheless took the opportunity to give women their flowers, literally. I can truthfully say I was touched by the gesture (and the beautiful bouquet of roses and baby’s breath). As discussed though, professional accreditation is far more crucial to effect change. It is a first step towards ensuring economic security for databases and their curators and cultivating mutual respect between curators and the communities they serve.

Thank you to the IBDC, the ISB, and the OBF for making this award possible!

I am immeasurably grateful to this year’s organisers for awarding “Best Flash Talk” for my presentation on the application of biocuration standards for innovation in direct cell reprogramming. My thanks must also go to the Open Bioinformatics Foundation – without being awarded an OBF fellowship, I could never have afforded to present my doctoral work at AIBC. So, in the best tradition of open bioinformatics – epitomised in every speaker and delegate I had the pleasure to meet – I shall do my best to pay it forward. After all, to paraphrase Dr Pollock, the best use for my success is to open doors for someone else. And isn’t that what open science is all about?

Call for the first round of OBF Event Fellowship 2024 & overview of the last round of 2023

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 23 Feb 2024 17:37:07 +0000

The call for applications for the OBF Event Fellowship 2024, round 1, is now open. The deadline for this round is 1 April 2024. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from May 2024 to December 2024. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Screenshot of our application form information section

Overview of the last round of OBF Event Fellowship 2023

In 2023 round 3 (December 2023), we received numerous applications, of which one applicant was awarded a fellowship for the event they were participating in. Congratulations to Thea Fennell. This fellowship will support their participation in the 17th Annual International Biocuration Conference to present their work on “Developing an open-source atlas charting functional module distribution across cell types in a range of mammalian species”.

We recently published blog posts from two of our latest awardees summarising their experiences attending events with help from OBF Event Fellowships:

Raquel Garcia: My Journey at the nf-core Hackathon and Nextflow Summit 2023: Coding and Community
Yvonne Walburga: Journeys across oceans

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 April 2024.

My Journey at the nf-core Hackathon and Nextflow Summit 2023: Coding and Community

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 17 Dec 2023 16:00:38 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Raquel Manzano Garcia, a PhD researcher at the University of Cambridge, was awarded an OBF Event Fellowship to attend the Nextflow Summit 2023 .

This October, I had the incredible opportunity to attend the Nextflow Summit 2023 in Barcelona, thanks to the support of a generous travel grant from the Open Bioinformatics Foundation (OBF) and my supervisor Prof. Carlos Caldas. The eent wasn’t just a conference; it was a confluence of ideas, coding, and camaraderie, set against the vibrant backdrop of one of Spain’s most iconic cities.

One of the most memorable aspects for me was the transition from digital interactions to real, meaningful connections. Meeting individuals I had previously only connected with online, such as my nf-core mentor, Maxime Garcia, was an incredible experience. The chance to collaborate in person, beyond the confines of a shared screen, was both enriching and inspiring. It brought a fresh and exciting dimension to our ongoing work.

The hackathon wasn’t just about coding; it was about building connections. I found myself surrounded by beautiful minds. The experience of learning new tricks and tips in such a collaborative setting has prompted me to reflect on my career trajectory, reaffirming my desire to thrive in similar environments. I am immensely thankful for the individuals I encountered – their patience, kindness, and enjoyable approach to addressing every question, discussion or concern were truly remarkable. Among them were professionals from my own area, with whom I’ve not only reconnected since the event but also started making plans for potential collaborations.

Additionally, I got the opportunity to meet Geraldine Van der Auwera, someone whose work I’ve followed and admired for quite some time. Her work has always amazed me, and meeting her in person was another highlight. This experience was enriched when I was invited to do an interview for the Nextflow podcast channel, an unexpected but thrilling event as it was a first for both of us.

I also had the chance to present my work at the Nextflow Summit in a talk. The interaction with the audience during my presentation reinforced the sense of collaboration and community, making it clear that my coding efforts were part of a larger, shared journey. It’s these moments of exchange and learning that represent the spirit of the Nextflow Summit.

Left: hackathon buzz; right: me presenting my talk at the Nextflow summit

Raquel’s presentation at the Nextflow Summit.

But it wasn’t all work! The summit ensured our schedules were packed with fascinating talks and social events. Making paella, going for runs, and attending a fancy party at the Barcelona port with Seqera’s new sponsored team were just a few highlights. These experiences were fun and engaging, truly enjoyable events. Plus Barcelona, with its incredible beauty, was the perfect host. A walk – and a run – along the beach was a nostalgic reminder of my coastal hometown (Cadiz, Spain), bringing a piece of my heart into this global gathering.

Top: Morning run along the beach; bottom left Shoko dinner party; bottom right: Social event in La Patente - cooking traditional paella.

In conclusion, the nf-core Hackathon and Nextflow Summit 2023 were more than just gatherings; they were vibrant showcases of innovation, collaboration, and diverse cultures. With the support of the OBF travel grant and my supervisor, I’ve come back not only re-energized about my work but also enriched with valuable new professional connections.

Participants at the nf-core hackathon

Yvonne Walburga: Journeys across oceans

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 13 Dec 2023 13:59:53 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Dr Yvonne Joko Walburga, a Post-doc at the University of Cambridge, was awarded an OBF Event Fellowship to attend the African Organisation for Research and Training in Cancer (AORTIC) Cancer Conference.

I initially applied for the OBF Travel Fellowship to attend the African Organisation for Research and Training in Cancer (AORTIC) Genomics Conference, and was accepted, but the timing was too tight. Happily, the board agreed to defer my funding to the next AORTIC Conference in November 2023 instead. So, I could make it for the AORTIC conference in Dakar, Senegal from November 2nd – 6th 2023 with support from the OBF Travel Fellowship and the African Cancer Registry Network.

And what a conference it was!

This was the third in-person AORTIC conference I have had the opportunity to present at. At this AORTIC conference, I was invited to give two oral presentations on work we had done during my PhD with the African Cancer Registry Network ( https://www.afcrn.org), at the University of Oxford, under the supervision of Prof. Max Parkin and Dr Paul McGale.

It was an opportunity to give back and report on the work carried out by the registrars, who meticulously collect data on cancer incidence across sub-Saharan Africa. The AFCRN works with cancer registrars across the continent to harmonise the data collection, building capacity for robust data collection and analysis, and on how to use the CanReg5 software. CanReg5 is a freely accessible open-source tool that is used to input, store, quality check and analyse cancer registration data. ( http://www.iacr.com.fr/index.php?option=com_content&view=article&id=9:canreg5&catid=68&Itemid=445). This generated data is used by national cancer control programs and by the International Agency for Research on Cancer (IARC) for the GLOBOCAN data reports https://gco.iarc.fr/today/home.

The first day of the conference (November 2nd, 2023) gave me the opportunity to join the satellite meeting of the Network for Oncology Research in Africa (NORA) consortium and to listen to and contribute to ideas on how we could collaborate and build partnerships for cancer surveillance and genomics research in sub-Saharan Africa.

Following the NORA session, the organisers of the NORA consortium carved out time at the end of the session to visit the Island of Gorée. In typing Gorée, my English word editor quickly underlines it; curious as to what suggestions it would give me, I let my mouse hover.. it suggested “Gore” which means “Blood, Stab, Violence”. The Gorée Island is unspeakably beautiful; however, within its beauty, along its shores and especially at the “Door of No Return” – “Porte du Voyage sans Retour”, we must grapple with our shared history – that of slavery and its consequences – and also of a history stripped with Gore – blood, stabs and violence. As a post-doctoral researcher in cancer epidemiology who is now exploring population-level cancer genomics – I constantly think about the consequences of our shared ancestry with African- Americans, the immigrants from the Caribbean to the United Kingdom, and the Africans living on our beautiful African continent. However, there is such under-representation of this vast continent with very diverse populations, and in the era of personalised medicine and personalised risk reduction, we would widen health inequities if we do not improve access to progress in genomics to under-represented populations.

Figure 1: The “Door of No Return”/ “Porte du Voyage Sans Retour”, Gorée, Senegal

My first oral abstract presentation on November 4th, 2023, was on “Cancer Survival in sub-Saharan Africa”. In this work, we described the population-level cancer survival outcomes of more than 10,000 sub-Saharan African patients with 18 different cancer types. This work was done with data from the African Cancer Registry Network, and in collaboration with the International Agency for Research on Cancer (IARC) and Vital Strategies. We highlighted the disparities in access to care and diagnostics for patients with cancers in sub-Saharan Africa and the resultant disastrous health outcomes. This work would not have been possible without working alongside the cancer registrars to improve the quality and representation of population-level cancer survival data, via the use of the open source CanReg5 software developed by IARC.

Figure 2: Oral presentation at the African Organisation for Research and Training in Cancer Meeting, Dakar 2023

My second oral presentation was part of the African Cancer Registry’s Network session on “Cancer Surveillance in sub-Saharan Africa” on November 5th, 2023. In this session, I gave a talk on the “Incidence trends, stage and survival from breast cancer in sub-Saharan Africa”, the subject of my doctoral thesis. Studying trends in cancer incidence requires the availability of good quality data spanning several years. This was possible for 12 sub-Saharan African countries, largely thanks to the work of the AFCRN, on improving data coverage for cancer surveillance in Sub-Saharan Africa.

Figure 3: Presenters at the session on “Cancer Surveillance in sub-Saharan Africa”, hosted by the African Cancer Registry Network (AFCRN) at the African Organisation for Research on Cancer Conference (AORTIC), Dakar, Senegal.

From left to right: Myself (Dr.Yvonne Joko Walburga), Dr. Mazvita Sengayi (Head of Department, National Cancer Registry South Africa), Prof. Cesaltina Lorenzoni (Pathologist, Head of the National Cancer Control Program at the Mozambican Ministry of Health and President-Elect – African Organisation for Research and Training in Cancer), Ms Biying Liu (Administrator of the AFCRN), Ms Lydia Businge (Rwanda Cancer Registry), Prof Max Parkin (Coordinator of the African Cancer Registry Network) and Dr. Muluken Gizaw (Assistant Professor, Addis Ababa University)

I also had the opportunity to present an abstract titled “Systematic Review of Breast Cancer Risk Factors in sub-Saharan Africa” during the poster sessions. This enabled me to meet with, and discuss with researchers across the continent on how we could build collaborations to ensure more robust studies are conducted on the burden of risk factors pertinent to our context and to explore unique gene-environmental interactions.

This AORTIC conference was my first post PhD, and during which I strongly felt that, the onus is on us to drive the change we want to see in terms of research, mentoring and collaboration. We are of the generation who can return to the land they could never return to. We must answer the questions that are pertinent to our continent, and we must leverage the power of our networks, our teams, and leap-frogs in technology to generate the data necessary to answer our health challenges. However, I know it is not an easy task; in a continent with a history of exploitation, how do we ensure that sharing our data brings the greatest good for all involved? Yet, as a continent, in spite of its history, we are known for our generosity, for being our brother’s keeper, and for the concept of “Ubuntu”. Thus, I strongly believe that together, we would find ways of tapping into what unites us, to carry out and share the benefits of our research on the African continent with those who need it most, and to help close the gaps of equity in access to quality healthcare.

Finally, reflecting on this journey I made to Senegal, and on all the journeys we make across all types of boundaries and oceans, we must remember, we are never really alone, we are carried by the love and support of our families, by the encouragement of our mentors and advisers, and by the courage of those who went before us.

Call for the third round of OBF Event Fellowship 2023 & overview of the second 2023 round.

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 19 Oct 2023 00:27:40 +0000

The call for applications for the OBF Event Fellowship 2023, round 3, is now open. The deadline for this round is 1 December 2023. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from January 2024 to August 2024. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Screenshot of our application form information section

Overview of round two of OBF Event Fellowship 2023

The Open Bioinformatics Foundation (OBF) Event Fellowship program is now in its 7th year. Starting in 2023, we open three calls for applications with the following deadlines: 1 April, 1 August, and 1 December.

In 2023 round 2 (August 2023), we received numerous applications, of which one applicant was awarded this fellowship for the event they were participating in. Congratulations to Raquel Manzano Garcia. This fellowship will support her participation in the Nextflow summit, where she will be presenting her work on “Development of an Integrated DNA and RNA Variant Calling Pipeline”.

We recently published blog posts from three of our recent awardees summarising their experiences attending conferences with help from OBF Event Fellowships:

Nehemiah Ongeso: Embracing Science and Culture: My Memorable Conference Experience at SMBE23 in Ferrara, Italy
Daniela Senra: My Experience at the Human Cell Atlas General Meeting 2023
Michell Salcan My Wonderful Experience at LANET 2023 in Cusco, Peru

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 December 2023.

Michell Salcan: My Wonderful Experience at LANET 2023 in Cusco, Peru

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 16 Sep 2023 08:28:55 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Michell Salcan, an undergraduate at the Universidad Regional Amazonica Ikiami, was awarded an OBF Event Fellowship to atten d The 3rd Latin American Conference on Complex Networks in Cusco, Peru.

The week of August 21 to 25 has been one of the most beautiful and satisfying experiences of my personal life and the beginning of my professional life because I had the opportunity to attend and present my undergraduate thesis at the LANET 2023 event.

Photo of Qoricancha Temple, one of the most representative archeological places of the Inca Empire.

During the event, there were introductory talks, talks on research lines of network science or complex networks applied to different fields of science, and cultural and tourist activities organised by Andean University of Cusco. Throughout the days, networks were reviewed to understand social, dynamic, technological, biological, neuroscience, and epidemiological aspects like opinion states, modelling crime, Kuramoto Oscillators, synchronisation of neuron models, and metapopulation models to explain the spread of diseases.

The main talk that captivated me was entitled “Identification of areas for the release of Wolbachia for dengue control using a metapopulation model,” which is mainly based on the biological control of the vectors that transmit the dengue virus. This talk particularly resonated with me because my work, “Bipartite network modelling and analysis to understand the dynamics of dengue incidence in Ecuador during the 2014-2021 period”, is based on identifying the main areas for the chemical control of these vectors.

Speakers discussed the limitations of their research, with the lack of open data being the main problem in many of them. Since access to certain types of data is not free, or in some other cases, the data ceased to be accessible a few years ago, it is no longer possible to update the research. Many speakers, including me, promoted open source and open data approaches. As I have mentioned many times, open source allows collaborations between scientists, promoting the accessibility, modification, distribution, and expansion of software in various lines of study.

Photo of Shirley giving her talk about the dengue epidemiological network.

On the day of my talk, I was nervous at first since it was my first time at this type of event, and I felt scared. Then friends that I had made during that week told me, “You will do super well, you are wonderful and talented,” and “Just enjoy the adrenaline.” After that, I understood that I was not the only one and that probably many experts like them always felt nervous before giving a presentation, and that beyond the nerves, perhaps it was simply the emotion.

In my presentation, I was able to relax more and was able to explain my research. At the end, there were congratulatory comments which made me feel proud. But there were also constructive comments that motivated me more to continue in my line of research and to perfect my disease diffusion model. Also, it allowed me to engage in conversation with an invited speaker whose research was also based on the spread of dengue, and she offered to review my work, which made me very happy.

I understood then that this event allows you to get to know other places and cultures, make friends, and establish collaborations. For that, I sincerely thank the Open Bioinformatics Foundation for their support. Without it, my participation in LANET would not have been possible.

Photo of Shirley with other LANET participants from Mexico, Guatemala, Colombia, and Peru.

Embracing Science and Culture: My Memorable Conference Experience at SMBE23 in Ferrara, Italy

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 07 Aug 2023 19:23:59 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Nehemiah Ongeso, an MSc graduate at the University of Nairobi, was awarded an OBF Event Fellowship to attend the SMBE23 conference.

Attending a prestigious conference can be a turning point in any scientist’s career; for me, it was no exception. The Society of Molecular Biology and Evolution (SMBE) conference, hosted in Ferrara, Italy, was an unparalleled experience that combined cutting-edge scientific research with a unique cultural immersion. As a recipient of a travel grant from the Open Bioinformatics Foundation, I participated in the extraordinary SMBE23 conference, which broadened my horizons and inspired me to pursue even greater heights in my postgraduate research.

The Unconventional Conference

The SMBE23 conference was unlike any other I had attended before. Breaking away from the traditional hotel-based format, the conference was diffused across Ferrara. The diffused nature of the conference allowed attendees, including myself, to interact with the local community, experience their culture, language, religion, history, cuisine, and even engage with local authorities. The city of Ferrara became an integral part of the conference experience, fostering a unique atmosphere that encouraged both intellectual exchange and personal growth.

Presenting my Postgraduate Work

One of the highlights of my journey was the opportunity to present my postgraduate work titled " Co-expression network analysis of genes mediating Meloidogyne incognita parasitism in tomato-plant nematode interactions." Sharing my research findings with a diverse audience of scientists and graduate fellows was exciting and nerve-wracking. To my delight, my work garnered attention from numerous researchers interested in advancing their studies in systems biology. The constructive feedback and stimulating discussions further motivated me to explore new avenues and refine my research objectives.

Symposium on Regulatory Evolution and the Emergence of Diversity

During the conference, I actively participated in a symposium titled “Regulatory Evolution and the Emergence of Diversity.” The symposium proved to be an eye-opening experience as I learned valuable skills in effectively communicating scientific breakthroughs, including new concepts, methodologies, models, and potential areas for collaboration. Engaging with like-minded individuals from diverse backgrounds sparked my enthusiasm for interdisciplinary research, and I left the symposium with a fresh perspective on my work.

Open Science and Networking for Global Advancement

On the last conference day, I participated in the SMBE-IDEA symposium, which provided a platform where the SMBE society and affiliate research groups committed to advancing science in the global south while eliminating the detrimental effects of “helicopter science.” I actively contributed to and championed for SMBE to adopt open science practices. By advocating for accessible data, reproducibility, and collaboration, I aimed to advance science in the global south while ensuring equitable opportunities for researchers from all regions. The conveners of the symposium passed a resolution to sensitize donors and collaborators to always listen to the needs of researchers from the global south.

Through the symposium session, I was privileged to connect with researchers who shared similar passions for promoting diversity, inclusivity, and equity in the scientific community. The interactions opened doors to future collaborations and partnerships, potentially broadening the impact of my research and fostering international connections.

Humanizing Science

An intriguing observation during the conference was witnessing senior scientists actively participating in poster presentations. It was heartening to see that their dedication to science extended beyond their academic achievements, and they remained humble and open to sharing their knowledge and insights with their peers. Additionally, some senior scientists were accompanied by their non-scientist spouses, which humanized the experience and emphasized the importance of maintaining a balanced and fulfilling personal life alongside a successful scientific career.

Acknowledgement

I sincerely thank the Open Bioinformatics Foundation for their generous travel grant, which made this life-changing experience possible. Additionally, my heartfelt thanks go to the organizers of SMBE23 for orchestrating an exceptional conference that transcended the boundaries of traditional academic events. As I return to my research station, I carry with me the valuable lessons learned and the lasting memories of a conference that will forever hold a special place in my heart. The memories and knowledge gained will undoubtedly shape my future endeavours as a scientist and global citizen.

Daniela Senra: My Experience at the Human Cell Atlas General Meeting 2023

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 02 Aug 2023 04:36:21 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Daniela Senra, a PhD researcher at Centro Regional de Estudios Genómicos, Universidad Nacional de La Plata, was awarded an OBF Event Fellowship to attend the Human Cell Atlas General Meeting 2023.

In July, I had the incredible opportunity to attend and present a lightning talk at the Human Cell Atlas General Meeting 2023, that took place in the city of Toronto, Canada, from July 10th to July 12th, 2023.

Photo of Daniela giving her talk and sharing about the open-source tool ORIGINS2.

Discovering New Insights at the Meeting

The three-day event was packed with activities, including keynote speeches, breakout sessions, lightning talks, and poster sessions covering various topics.

On the first day, I was particularly captivated by talks that resonated with my research interests. Notably, the presentation on ‘What makes a stem cell a stem cell and how does it go bad’ held great relevance to my PhD thesis, focusing on stem cells and cancer stem cells. Additionally, a breakout session on ‘Increasing accessibility/building great scientific communities’ struck a chord with me as someone from Argentina—a developing country—where access to public data and open-source pipelines is crucial for contributing to the scientific community. Later, I had the privilege of sharing my own research in a talk titled ‘Stem cell determination from scRNA-seq data using a protein network-based approach.’ My work, an open-source R package developed in collaboration with my advisors Luis Diambra and Nara Guisoni, originally aimed to quantify pluripotency from scRNA-seq data but evolved into a computational technique to quantify any biological process using protein-protein interaction networks. The application that motivated this work was the identification of stem cells, serving as a starting point for performing trajectory inference. For those interested in our work, the publications can be accessed using the links: https://www.sciencedirect.com/science/article/pii/S2215016123001796 and https://www.sciencedirect.com/science/article/pii/S2215016122001583.

The second day’s focus on machine learning was especially appealing to me, given my frequent use of unsupervised learning techniques in my research. I also found the section on spatial methods intriguing, considering their potential relevance to my future work. The third and final day concentrated on biological function, directly related to my presentation, making it an interesting topic.

Open source as a central topic

In my lightning talk, I was able to promote my open source project, as many participants also highlighted. Throughout the conference, the importance of open source became a transversal theme. Undoubtedly, open source plays a pivotal role in science, accessibility and transparency allows scientists to freely access, modify and distribute software tools and solutions. This democratization of knowledge not only enhances the quality of research but also enables scientists from developing countries to actively participate in shaping the future of science and technology.

Empowering Personal and Professional Development

Having attended virtual HCA events during the pandemic, the opportunity to participate in person at the General Meeting was unique for me. It was my first time participating in an international event, and I was very excited. Yet, two months before the event, I was unsure if I could afford to attend, as the travel costs seemed impossible. Securing funding for such activities can be a daunting challenge for scientists in developing countries. However, my hopes were restored when I received an email from the Open Bioinformatics Foundation informing me that I had been awarded the OBF Event Fellowship. This news enabled my participation, which was especially meaningful as I am on the brink of completing my PhD and exploring new opportunities for my future endeavors.

The experience was undeniably one of the highlights of my ongoing PhD journey. I had the privilege of connecting with fellow researchers who shared similar interests—an opportunity that is limited in Argentina, given the still-developing nature of this area of research. The networking opportunities were invaluable, allowing me to build strong connections with professionals worldwide. Moreover, I believe that being part of this event contributed to promoting diversity, as Latin America is often underrepresented in international scientific gatherings. To my surprise, some participants approached me to express that I was the first person from Argentina they had met working with scRNA-seq data. This realization filled me with pride and a sense of responsibility, as I hope to see more Latin American scientists, especially women, gain more opportunities and equitable representation in the global scientific community.

A Heartfelt Thanks to the OBF

None of this would have been possible without the support of the Open Bioinformatics Foundation. I am immensely grateful to the OBF for their generous support, which made my participation in this exceptional event a reality.

In conclusion, the Human Cell Atlas General Meeting 2023 was an unforgettable experience that broadened my professional and personal horizons. I left the event with new knowledge, invaluable connections, and a renewed determination to contribute to the scientific community.

Spotlight on diversity: Jenea Adams

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 10 Jul 2023 21:25:30 +0000

Diversity, inclusion and accessibility (also known as Diversity, Equity and Inclusion, DEI) are a major part of BOSC’s mission and core values, and we pursue these goals in multiple ways. BOSC 2022, for example, included a panel on Building and Sustaining Inclusive Open Science Communities, with panelists who not only were experts on the topic but also themselves belong to various groups that are typically underrepresented in our community. And with generous support from our sponsors, each year we provide free registration to 10-20 BOSC participants as part of the OBF Event Fellowship program), which aims to increase diverse participation at events related to open source bioinformatics and open science.

Jenea Adams, a Presidential Ph.D. Fellow in Genomics and Computational Biology at the University of Pennsylvania, epitomizes our commitment to fostering diversity and inclusion in the open source bioinformatics community. Jenea served as one of the panelists on the Building and Sustaining Inclusive Open Science Communities panel, and her registration fee and travel expenses were covered by an OBF Event award.

Jenea commented, “BOSC not only showcased the remarkable strides made in computational biology but also emphasized the power of collaboration and inclusivity. Through my participation in the panel on Building and Sustaining Inclusive Open Science Communities, I witnessed the true potential of harnessing diverse perspectives to drive innovation and create a sustainable foundation for open science.”

In addition to her PhD studies, Jenea is the Founder and Executive Director of The Black Women in Computational Biology Network, which aims to amplify the voices and foster community among Black women in computational biology. Jenea observed, “Having support to attend BOSC 2022 made it possible for me to connect with new and familiar faces in person while providing a platform to share the work and progress of The Black Women in Computational Biology Network.”

Jenea summed up her thoughts about BOSC – thoughts we strongly agree with – as follows: “This conference reinforced the notion that by being intentional about accessible science and sharing knowledge, resources, and ideas openly, we can collectively advance the field of computational biology and pave the way for transformative discoveries.”

We thank Jenea for contributing her knowledge and community-building spirit to BOSC, and wish her the best in all her endeavors!

Above: Panel on Building and Sustaining Inclusive Open Science Communities: Jason Williams (moderator); panelists Jenea Adams, Monica Munoz-Torres, Rachel Torchet, and Gary Williams; BOSC Chair Nomi Harris

Call for the second round of OBF Event Fellowship 2023 and the first 2023 round overview.

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 05 Jul 2023 05:05:05 +0000

The call for applications for the OBF Event Fellowship 2023, round 2, is now open. The deadline for this round is 1 August 2023. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling out the form – make a copy of this template.

The OBF Event Fellowship program aims to increase diverse participation at events that promote open-source bioinformatics and/or open science. We invite applications from candidates seeking financial support to attend relevant scientific events from September 2023 to April 2024. These events include conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Screenshot of our application form information section

Overview of the round 1 of OBF Event Fellowship 2023

The Open Bioinformatics Foundation (OBF) Event Fellowship program is now in its 7th year. We open three application calls yearly with the following deadlines: 1 April, 1 August, and 1 December.

In 2023 round 1 (April 2023), we received 23 applications, of which three applicants were awarded this fellowship for various events they were participating in. Congratulations to Yvonne Ateh Joko Walburga Epse Fru, Shirley Salcan and Daniela Senra.

Nehemiah Ongeso Mosioma, who had been previously awarded a fellowship for attending the Vienna BioCenter PhD Program Symposium “Pushing Boundaries”, but due to visa delays, could not attend the event. The OBF Fellowship Award chairs redirected this award towards attending the Society of Molecular Biology and Evolution (SMBE) 2023.

We recently published blog post from two of our latest awardees summarising their experiences attending conferences with help from OBF Event Fellowships:

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 August 2023.

Winfred Gatua: Hybrid Carpentries workshop supported by OBF Event Fellowship

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 29 Mar 2023 15:15:59 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Winfred Gatua, Doctor of Philosophy, Bristol Medical School , was awarded an OBF Event Fellowship to organize a Hybrid Carpentries workshop at Laikipia University, Kenya.

Hosting and facilitating a hybrid carpentries workshop in my home country is an excellent highlight for me. I am very grateful to have received the OBF Event Fellowship 2022.

Among my goals is mentorship and training of younger researchers in Kenya, especially those in remote Kenyan universities with no access to many resources; instead, being stuck in the traditional way of doing research, including contracting experts to do the data analysis for them; a costly ordeal. However, I wanted to change the narrative and open these scientists to the world view of data, how to make their research work reproducible, and shed insights into what is open science and collaborations.

Despite spending my time as a volunteer instructor in institutions abroad, I have always wanted to host and run a carpentries-based workshop in some institutions in Kenya. However, the cost associated with running any workshop is immense; therefore, when I saw the call for an OBF event fellowship, this was a perfect opportunity for me to try it.

Upon receiving an award email, I was excited and eager to carry on with the workshop to ensure that students know in advance bioinformatics, open science, and reproducible research before they leave their bachelor’s studies.

With the assumption that since the pandemic, institutions have adapted to online teaching, I designed the training to be exclusively online while applying for funding. Upon assessing the resources available, I decided to adopt a hybrid workshop with a resident helper at the University helping the students. In contrast, other instructors/helpers of the workshop joined online and taught modules online.

While all participants were novices when we began the workshop, by the close, the participants were excited to explore careers in bioinformatics and data science, including access to advanced training. This workshop allowed my colleagues and me to share our broad knowledge of data science and inspire students to carry on with collaborative, open, and reproducible research in the future.

I want to thank the instructors and helpers who worked tirelessly with me through the five days of the workshop. I appreciate the Laikipia University administration’s support during the preparation and workshop. A big shout out to the OBF event fellowship for the award; without your support, the workshop would not have succeeded.

The next step includes applying for funding from other organizations to facilitate sharing of knowledge around data science and open and reproducible research practices in Kenya and Africa.

Below is a photo of the workshop in progress, a screenshot showing virtual participants, and a group photo at the end of the workshop.

Ruth Nanjala: My experience attending and participating at the ICHG 2023 conference hosted in the Mother City

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 21 Mar 2023 16:32:05 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Ruth Nanjala, a DPhil student in Cellular and Molecular Medicine at the University of Oxford, was awarded an OBF Event Fellowship to attend the International Congress of Human Genetics (ICHG) 2023 conference.

Earlier in 2022, I received the Open Bioinformatics Foundation (OBF) Event Fellowship for participating and promoting open science at the American Society of Human Genetics (ASHG) 2022 conference in Los Angeles. However, I could not travel to ASHG due to unavoidable circumstances. Fortunately, OBF gave me a second chance by facilitating my travel to the International Congress of Human Genetics (ICHG) 2023 conference hosted at home (Africa is considered the cradle of humankind) between the 22nd and 26th of February.

Image: First day of poster presentations at the Cape Town International Convention Centre

My research focused on evaluating different programs, reference panels, and genotyping arrays used to predict HLA alleles from the highly polymorphic human Major Histocompatibility Complex region. The workflow was written using the open-source software, Nextflow and published on GitHub https://github.com/nanjalaruth/MHC-Imputation-Accuracy. For those interested in learning more, the preprint can be accessed at the link: https://pubmed.ncbi.nlm.nih.gov/36747714/.

Aside from presenting a poster of my work, I was able to attend and engage in other conference sessions. Below, I highlight take-home messages from each day:

Day 1 The keynote on Genomics and anthropology set the tone for the day as insights were shared on human settlement patterns and migration patterns in Africa. The continent is widely considered the birthplace of modern humans. During this day, Prof. Nicola Mulder proposed the setup of a network of Genomic Centres of Excellence in Africa with the aim of reducing the access gap for genomic technologies.

Day 2 Karoline Kuchenbaecker from University College London showed that diversity in genetic investigations promotes gene prioritization, causal inference, precise mapping, and locus identification. Andrew Morris from the University of Manchester demonstrated the effectiveness of heterogeneous populations for Genome-Wide Association Studies discovery and application.

Day 3 A captivating session was chaired by Athena, which focused on overcoming obstacles to studying diversity in global genetics. The session presenters, Adebowale, Krystal, and Lerato pointed out strategies that can be adopted to improve diversity.

Day 4 An interesting session was on the “Southern African Population structure, Admixture and Adaptation,” as I got insights on the changes in skin color in southern Africa, Khoisan gene flow and its significance for genetic research, and the intricate patterns of mixing and population migrations during the Bantu expansion.

The conference was then closed by the ICHG conference team led by Prof. Michele Ramsay, who handed over the planning for the next conference in 2026 to the Mexico team.

Image: Aerial view of Cape Town. Table Mountain (left), Lion’s head (right)

Attending my first ICHG conference has been an incredible experience and an excellent opportunity to network with diverse scientists in human genetics. As a researcher interested in enhancing diversity in human genetics research and promoting open science, I found most talks enlightening. I am extremely grateful to OBF and the team members that made it possible for me to attend the ICHG conference, which is hosted every four years.

Call for applications for the first round of OBF Event Fellowship 2023 & overview of the second 2022 round

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 20 Feb 2023 03:09:06 +0000

The call for applications for the OBF Event Fellowship 2023, round 1, is now open. The deadline for this round is 1 April 2023. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling the form – make a copy of this template.The OBF Event Fellowship program aims to increase diverse participation at events that promote open source bioinformatics and/or open science. We invite applications from candidates who are seeking financial support to attend or host relevant scientific events from May 2023 to April 2024. These events can be conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Screenshot of our application form information section

Overview of the round 2 of OBF Event Fellowship 2022

The Open Bioinformatics Foundation (OBF) Event Fellowship program is now in its 8th year. In the last year, we had two calls for applications, with deadlines on 1 April and 1 October in 2022. Starting in 2023, we will open three calls for applications with the following deadlines: 1 April, 1 August, and 1 December.

In 2022 round 2 (October 2022), we received 23 applications, of which three applicants were awarded this fellowship for various events they were participating in. Congratulations to Winfred Gatua, Luise Rauer, and Ruth Nanjala.

Nehemiah Ongeso Mosioma was also approved to attend Vienna BioCenter PhD Program Symposium “Pushing Boundaries”, but due to admin oversight, they could not attend the event. The OBF Fellowship Award chairs are discussing how we can redirect this award towards another event the awardee might be able to attend.

We have recently published a blog post from one of our latest awardees summarising their experience attending a conference with help from an OBF Event Fellowship:

Luise Rauer: Microbiome (k)nights

Congratulations to all of our awardees! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 April 2023.

Microbiome (k)nights

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 29 Dec 2022 20:21:04 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Luise Rauer, a PhD student at the Technical University of Munich, was awarded an OBF Event Fellowship to participate virtually in the 9th International Human Microbiome Consortium (IHMC) conference in November 2022.

What do a total lunar eclipse and the 9th International Human Microbiome Consortium (IHMC) conference have in common? While they are both exciting and rare events that started in Kobe, Japan, on 8th November 2022, they also happened in the very early morning for any spectator from Europe. With the IHMC conference starting at 1 a.m. for me as a virtual participant based in Central Europe, my very unique preparation for this conference included changing my sleeping rhythm to become a nighthawk for 3 days and nights. But it was worth it!

Lunar eclipse during the IHMC conference in Kobe, Japan. Copyright: IHMC2022Kobe on Twitter: https://t.co/fcZmwRyDXr / Twitter

IHMC conference venue in Kobe, Japan. Copyright: IHMC2022Kobe on Twitter: https://t.co/gyksCdOLuK / Twitter

The great selection of talks at the IHMC conference showed that microbiome research is really starting to fulfill its expectations. Kjersti Aagaard summarized a decade of her research on preterm birth in Malawi, which is prevented by supporting beneficial bacteria in the mouth microbiome with a specific chewing gum at the other end of the body. Similarly, Eran Segal reported successful stool transplants in atopic dermatitis – or in simple words, receiving other people’s poop treats your skin disease. Isn’t that amazing?

While we learned that stool transplants are working in relieving some diseases, it is still unclear which bacteria are actually doing the job. An alternative idea – and probably a more appealing solution to patients – is using defined bacterial communities without the attached dark matter, as presented by Bernat Olle. The prospect of treating bacterial infections with pro biotics ( = living bacteria) instead of anti biotics ( = killing bacteria) is the way of positive thinking that I like.

As a methodology enthusiast, I particularly enjoyed the talks by Ami Bhatt, promoting absolute abundance data and investigating how sample storage affects microbiome results, and by Jun Terauchi, presenting recent harmonization efforts in the microbiome field. In the same vein, I presented my two posters on methodological challenges in microbiome research, and how to tackle them using open-source software for quality control and the power of FAIR data and research. Therefore, one of my personal highlights was the keynote presentation by Rob Knight, impressively summarizing his long-standing contribution to the field, starting from early methodological work on diversity measures to the more recent development of open science data platforms.

Rob Knight’s keynote presentation at the IHMC conference in Kobe, Japan. Copyright: IHMC2022Kobe on Twitter: https://t.co/0nJwbV4rg5 / Twitter

While microbiome researchers have been caring a lot about microbial diversity ever since, geographic and ethnic diversity of the sampled humans have only started to be considered, as illustrated earlier in 2022. But science is moving forward: Projects like the Microbiota Vault aim to collect microorganisms across human cultures for sustainable microbiome health, data sharing practices are increasingly enforced by scientific journals, and hybrid events like the IHMC conference allow a wider inclusion of researchers in the scientific exchange through remote participation. While I really enjoyed following the talks from the distance, it would have been great to be able to exchange directly with other remote and onsite participants. Can the just announced next IHMC conference 2024 in Rome further foster interaction between all attendants, e.g. by providing digital sessions or hybrid interaction spaces?

To sum it up, the IHMC conference did not only provide me with an exciting overview on new microbiome research around the globe, but also illustrated the importance of fair, inclusive, open science to me once more. Starting at a small scale, I want to contribute to this development in microbiome research by further providing open-source code on my Github account and by promoting open science practices in my work environment. Therefore, I highly appreciate the work of the OBF, and would like to thank them again for awarding me with the OBF Event Fellowship for attending the IHMC conference.

OBF Community Support Sponsorship scheme funds first pilot project

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 18 Aug 2022 14:30:29 +0000

The OBF Community Support Sponsorship scheme aims to sponsor small open-source-focused events like a scientific meeting, small conference, training workshop, hackathon, or time-limited series like monthly seminars. See details in this post. One application was funded under this program to prototype the workflow, with OBF offering financial support for a seminar series hosted by the Bioinformatics Hub Kenya. Congratulations to Michael Kofia Landi for leading this application and working collaboratively with the BHKi team – Pauline Karega, David Kiragu, Margaret Wanjiku and Festus Nyasimi – and OBF Board including Treasurer Heather Wiencko, to help establish a process for this new type of OBF funding.

Crowdsourced highlights from BOSC 2022

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 16 Aug 2022 00:08:42 +0000

Going home after attending BOSC was a little bittersweet. It’s my favorite conference because it brings together such a welcoming group of people, and the lineup of talks typically offers a great balance of technical learning and community-building insights. So on my flight home, I was coasting on dopamine from the good times, but also getting a little sad that it was over for this year. With the help of a few fellow BOSC enthusiasts (special shout-out to Nomi Harris for the event summary notes, photos and help recruiting contributors), I put together this little recap of the conference, with highlights and personal accounts contributed by a number of other participants. I couldn’t fit everything people shared into the blog post, but you can find the full quotes in the original google doc.

The 4-1-1 on BOSC 2022

If you’re not already familiar with it, BOSC stands for Bioinformatics Open Source Conference, and we just completed the 23rd edition — BOSC 2022 — as a “COSI” track, or Community Of Special Interest, within the ISMB meeting of the International Society for Computational Biology (ISCB). It was a hybrid conference, with the in-person component hosted in beautiful Madison, Wisconsin (USA). Presenters are encouraged to publish their slides and/or posters as part of the BOSC collection on F1000 Research. This year’s BOSC included two joint keynotes with the Education and Bio-Ontologies COSIs, which multiple people highlighted as some of their favorite parts of the conference. Given the overlaps in terms of interests and methodologies between these COSIs, I thought it was especially great that the Education COSI itself took place the day before the BOSC COSI. To my delight I was able to catch a number of their talks without having to make tough track-preference decisions. (I loved to see how many people are creating portable materials using Jupyter Notebooks, in some cases with the explicit goal of distributing them on the cloud.)

Day 1: Education, standards, tools and more

The first day of BOSC proper kicked off with a welcome from chair Nomi Harris and an overview of BOSC’s parent organization, the Open Bioinformatics Foundation, by Chris Fields, who highlighted some opportunities to get involved with the OBF. I may have volunteered to be the new OBF Newsletter editor; you’ll know it’s for real if I ever manage to get the post-BOSC newsletter out!Next was a joint keynote (BOSC/Education COSI) by Jason Williams entitled “Riding the bicycle: Including all scientists on a path to excellence”. Jason discussed principles for making short-format training (aka “bootcamps”) more effective and persistent. Next was a joint keynote (BOSC/Education COSI) by Jason Williams entitled “Riding the bicycle: Including all scientists on a path to excellence”. Jason discussed principles for making short-format training (aka “bootcamps”) more effective and persistent. Let me do you a big favor here and point you to a recorded version of the same talk that Jason posted on Youtube, because googling “jason williams riding the bicycle” will not give you the results you’re looking for (unless you’re into stories about cycling for charity — but it’s a different Jason). You should also check out Jason’s blog post on lifesciencetrainers.org, which summarizes the concept of the “Bicycle Principles” and calls for community involvement. As Hilmar Lapp commented, “Jason Williams set the perfect tone with his keynote: trying to be as professional as you can about whatever your pursuit is matters, for yourself and those who your work affects, and don’t ever forget to regularly laugh and have fun while doing it. A timely reminder after both got increasingly crowded out by a pandemic of other concerns.“After the keynote, BOSC had themed sessions about “Standards and Practices for Open Science”, “Analysis tools & approaches”, “Data access and visualization”, and “Standards for Open Science”. There were too many great talks to mention all of them, but I will say I was excited to see that several talked explicitly about leveraging GA4GH standards. Brian Repko, echoing this sentiment, called out the Phenopackets schema in particular, which provides a human and machine-readable way to structure phenotypic data about a patient or individual. As Monica Munoz-Torres announced joyfully in her talk, Phenopackets version 2.0 was released earlier this year as a major upgrade to the original schema, which represents the culmination of a huge amount of work — so congratulations to the Phenopackets team on their achievement!During the lunchtime poster session, participants checked out 42 BOSC posters and learned about a variety of bioinformatics tools and initiatives. Connections were made, cards and emails were exchanged, and perhaps next year we’ll hear talks about new collaborations that were sparked here.

Day 2: Workflows, ontologies and inclusion

The second day of BOSC started with a session about “Workflow Management Systems”, including a number of talks related to CWL, aka the Common Workflow Language that grew out of a BOSC CodeFest in 2014. In that same session, I gave a talk about WDL, the Workflow Description Language that grew out of the Broad Institute’s GATK pipeline engineering group and is now stewarded by the OpenWDL community project. Check out my blog post and recording (+ slides on F1000) if you’re interested in a method for deciphering any WDL workflow handed to you by a perfect stranger. The workflows session was delayed by some technical issues, but session chair Hervé Ménager kept his cool throughout the back and forth with the local A/V team. Hervé himself commented “Despite the many technical issues we had with running the Workflow Management Systems session of BOSC, I was really impressed with the patience and understanding of the audience and the speakers, who all went out of their way to try and keep us on track, so that every presenter could get the opportunity to speak.” And it’s true, the BOSC crowd stayed pretty chill when things went, uh, pear-shaped. Ahem. The session after lunch was a joint session with the Bio-Ontologies COSI, featuring a keynote by Melissa Haendel, “The open data highway: turbo-boosting translational traffic with ontologies.” Melissa discussed ways to bridge the translational divide by leveraging semantics and robust ontologies — with the caveat that in most cases, if you think you need to invent a new ontology, you actually don’t. Her talk was very well received and highlighted by multiple people as a conference favorite; though for my money, Brian Repko said it best: “My internal notes for Melissa’s keynote literally says ‘HOLY COW THIS IS GREAT’". BOSC ended with a panel entitled “Building and Sustaining Inclusive Open Science Communities” moderated by Jason Williams, with a fantastic roster of panelists known for their work advancing diversity and inclusion. Being themselves members of groups that are underrepresented in our field, they spoke eloquently of challenges and opportunities that we can all tackle as a community. As Nicole Vasilevsky noted, “Jason did a great job facilitating and the discussion was very thought provoking”. Among key takeaways, “the panel reminded us that we all have much more agency than we think in making spaces welcoming to everyone who wants to enter,” reflected Hilmar.The high level of enthusiasm for the panel was palpable both during the event and in the comments we collected afterward. I read this as a clear sign that the majority of the participants genuinely care about inclusion, which in itself suggests that this community is on the right track. As a long-time community member, Nomi commented, “I’m pretty sure this was the first BOSC, maybe even the first ISMB, where one of the attendees was a [service] dog. Which of course is great regardless, but more seriously, it represents tangible progress in our efforts to make BOSC more inclusive and accessible.” Early feedback from newcomers certainly seems encouraging. “As someone who got into bioinformatics just before the pandemic, it was great to finally be around ‘my people’” wrote Bhavesh Patel, first-time BOSC participant, adding “All the talks were great, but I especially loved the panel discussion on diversity and inclusion. It is a wonderful initiative and I hope it becomes a frequent occurrence at all conferences.“And that is a really nice note to end a conference on, isn’t it?

Add-on #1: Scheduled dinners

But wait, there’s more! BOSC folks are a surprisingly social group, for a bunch of bioinformatics nerds (no offense y’all). So in addition to the daytime conference programming, the organizing committee had organized (as they do) two outdoor dinners for BOSC participants to get together and keep the conversations going. Just about everyone who attended the dinners raved about how great they were, to a point that might be borderline obnoxious to anyone who didn’t go; but I can tell you from first-hand experience it’s all justified. And to be clear, it was “pay-your-own-way” (aka BYO wallet), so the enthusiasm wasn’t about getting a free meal on the dime of some corporate sponsor — it was all about the friendly company and congenial atmosphere. “The dinner was […] a great opportunity to interact with other participants in a laid-back setup,” wrote Bhavesh. As Nomi noted, we were very lucky with the weather, so we were able to hang out, dine and socialize on the outdoor patios until well after nightfall. There was definitely a sense that this felt especially good because we had all been deprived of this kind of interaction for over two years. Nomi shared that for her, “the best moments [of the conference] were not the talks (though of course those were great!) but the personal interactions that I have missed so much the last few years.” As Hilmar pointed out, “The BOSC socials and CoFest showed how much it is worth even to just be together again. Not that we didn’t know, but knowing and understanding are not always the same thing.” This sentiment, which almost everyone who was there in person echoed in some way, does raise the question of how we can provide quality social interaction for those in our community who cannot yet come back to in-person events — or for those who have never been able to do so due to the circumstances of their lives or their geography. As Tazro Ohta remarked eloquently, “What I learnt during the pandemic was: The power of online meetings that connect people and the power of time differences that prevents me from attending them helding in a western time zone.” That is a topic I expect we will have to explore as we iterate on the hybrid event models that are likely to shape the future of scientific gatherings.

Add-on #2: Collaboration Fest (CoFest)

Ok we’re almost done, but I still have to tell you about CoFest, a two-day “collaboration fest” that takes place informally after the conference, in which a subset of BOSC participants stick around for a couple of days to work together on some projects. Those projects can involve coding, but also documentation or other non-coding activities, so anyone can contribute regardless of their technical background. In fact, for my CoFest project, I started working on the upcoming OBF newsletter issue. You can see the full set of projects that were undertaken at this year’s CoFest in the status update slide deck. Out of the six projects that were proposed this year, three were worked on by remote CoFest participants while the other three were worked on by the in-person group. Those of us who attended CoFest in person worked at the Madison Public Library on the first day, and we had ourselves a nice little sunset social on the waterfront with beer and brats. On the second day, we relocated to the airport to accommodate the group’s wide range of departure times, and “cofested” variously from the pre-security lounge, from our respective gates, and from the air, because sometimes it’s just that hard to let a good thing go. In-person CoFesting from the Madison airport lounge. Don’t judge me, I only took off my mask for the photo! In my experience, CoFest is as much about community building as it is about making progress on a project. As Bhavesh, our BOSC first-timer who also attended CoFest, observed, “The cofest was my favorite part as it provided a very informal setting to get to know all the participants on a personal level. It also gave me a unique opportunity to discuss personally with experts of the field and get one-on-one feedback on my work.” In fact, he added, “I would highly recommend anyone new to BOSC to join the cofest!“So don’t miss your opportunity to get in on the fun, and make sure to add BOSC to your must-go list of conferences for next year (whether remotely or in-person). BOSC 2023 will be part of ISMB/ECCB 2023 and will be held in Lyon, France between July 23-27 (exact dates TBD).I hope to see you there/onscreen!

Call for the second round of OBF Event Fellowship 2022 & overview from the first round

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 12 Aug 2022 05:27:23 +0000

The call for applications for the OBF Event Fellowship 2022, round 2 is now open. The deadline for this round is 1 October 2022. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling the form – make a copy of this template.

We invite applications from candidates who are seeking financial support to attend or host relevant scientific events from late October 2022 to April 2023. These events can be conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. For more details, please read our OBF Event Fellowship policy document.

Screenshot of our application form information section

Overview of the round 1 of OBF Event Fellowship 2022

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to support and encourage diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. Each year we open two calls for applications, the deadlines for which are 1 April and 1 October.

In 2022 round 1, we received 17 applications, of which six applicants were awarded this fellowship for various events they were participating in. Congratulations Jemima Becker, Furkan M. Torun, Xi Zhang, Festus Nyasimi, Omar Ahmed, Emmanuel Adamolekun.

Confidence Goji Vandu was also granted their application to attend BOSC 2022, but due to admin oversight, they could not attend the event. The OBF Fellowship Award chairs are discussing how we can redirect this award towards another event the awardee might be able to attend.

Here, we have recently published blog posts from a few awardees summarising their experience from attending these conferences:

Furkan Torun: Furkan M. Torun: Highlights of my participation at PyCon IT 2022
Jemima Becker: My trip to the EMBO neural stem cells workshop
Festus Nyasimi: Festus Nyasimi: Journey to the ISMB/BOSC 2022 conference

Congratulations to each of them! We are delighted to support their participation with OBF Event Fellowships, and we wish them all the best for their future work.

Please share this post and apply for the fellowship before 1 October 2022. Also, read the updates from the OBF Event Fellowship chairs.

Festus Nyasimi: Journey to the ISMB/BOSC 2022 conference

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 01 Aug 2022 15:45:40 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Festus Nyasimi, A co-founder and lead of the Bioinformatics Hub of Kenya Initiative (BHKi), attended the ISMB/BOSC conference 2022, supported by this fellowship granted to him in the first round of 2022.

In mid-May, I attended a different conference where I shared my experience with community building in the bioinformatics space with one of the attendees. I had a chance to brief them about the BHKI community we are building and growing in Africa. Immediately they suggested I should check out the ISMB/BOSC conference happening on July 11th - 14th, 2022.

I looked into it immediately, and I was lucky to find the late abstract submission round was still on. I sent in an abstract on our community, its activities, and the progress we have made in the region. A few weeks later, our abstract was strongly accepted for poster presentation and iced up with free registration. Bam!!! This felt like a Lebron James slam dunk or Steph Curry swish three point shot. Never felt this happy to go share our work with a larger bioinformatics community.

In the happy moment, the rush to plan for the conference set in; this included travel, accommodation and misc stuff. The rest of the team and I worked on the presentation alongside our training activities; this is one amazing team. Considering we are a young and growing community mostly running training through volunteering and small grants to cater for the training, we had to find a source of funding to cater for the conference fee and that’s where the OBF Event fellowship showed up perfectly. Honestly, I least expected this but I didn’t discount myself and gave it a shot; I always tell myself, “ if I don’t knock, I will never know the answer”.

Fast forward, here I am at the conference; I got to attend some sessions i.e. BioInfo Core, NetBio, Varl, MLCSB and Educational COSI, where I learnt many new skills in Bioinformatics the BOSC track started. Some of the things I learned I will propose to the organizing team we develop tutorials for the community to learn from. The opening day of BOSC was the peak of the conference for me; I had an opportunity to learn more about open-source software, how to efficiently contribute to ongoing projects and how to help communities grow. I also had a chance to join the GA4GH VRS hackathon at the conference. I had a good opportunity to represent the BHKI community on what we are doing and received great responses from attendees who visited my poster. The light was shining on our community; I hope the spotlight will be on and attract more collaborators to help us achieve our mission of a collaborative and inclusive hub.

Some of the cool people I meet at BOSC: panelist Jenea Adams and keynote speaker Jason Williams.

I learned how to advocate for our community to grow well towards achieving Diversity, Equity and Inclusion (DEI) goals; these are necessary for a strong, welcoming and collaborative community. Interacting with attendees at the conference provided me with an opportunity to learn more about leadership and how to be a good leader from a different perspective. I look forward to keeping in touch with other communities to grow further collaborations, especially in community empowerment.

Generally, the whole conference turned out to be the best one I have attended in many months through the pandemic, and I am so thankful to OBF, all organisations and team members who made it possible for me to attend the conference. Looking forward to more of these sweet moments.

This Twitter post got my notifications blowing a trumpet! While you are here, check out the BHKI website and Twitter we have some cool stuff. :)

Reflections from my 3 years on the OBF Board - Malvika Sharan

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 25 Jul 2022 19:34:37 +0000

Thank You. Photo by Aaron Burden on Unsplash

I have reached the end of my term after working with the OBF board members since 2019 and have stepped down from the board. It is bittersweet! I will miss seeing my colleagues from OBF in monthly calls, but also, this comes with an opportunity to make space for new voices to come into the leadership role of the Open Bioinformatics Foundation.

Over the last years, one of my main focuses has been the OBF Event Fellowship, previously managed by Nomi Harris and Farah Zaib Khan ( previously called travel fellowship). Having benefited from this programme, I personally value the opportunity for small funding that researchers with low or non-existent travel budgets can use for attending international conferences. Scientific events are extremely valuable for researchers to build new connections, share their research and often find their next career opportunities. You can see my post-event blog from 2019 here: /2019/08/27/tips-for-informal-discussions/.

Since joining, I managed and coordinated the programme (see the task list) and built rubrics to review applications ensuring fair evaluation and avoiding biases that unexplicit scoring can lead to (see review process). Primarily motivated by the travel restrictions experienced due to the pandemic, in collaboration with the OBF board members, I revised the travel fellowship documents to adapt to the need for supporting online participation. So far, I have managed six rounds of Event Fellowships (over three years) and supported one OBF-BOSC Event Support Fund, which together was awarded to 28 individuals (see all announcements). Of course, none of this could be possible without the timely review and thoughtful advice given by Bastian Greshake, Chris Fields, Hilmar Lapp, Nomi Harris, Peter Cock, Yo Yehudi and our wonderful treasurer Heather Wienco.

Earlier this year, I onboarded two newly elected members, Caleb Kibet and Hilyatuz Zahroh, as co-chairs of the Event Fellowship. They will continue in this position and will take forward the programme. I am really excited for the OBF community to see further improvement in the Event Fellowship programme supporting our commitments to open science and strengthening the participation of diverse researchers in bioinformatics events ( see discussion).

Since the event fellowship is an individual award, we received many applications from event hosts asking for financial support for their attendees. This was unfortunately not in scope for this scheme. However, it led to many internal discussions with the OBF Board members to build pathways for the grassroots communities and identify support for their ongoing activities. I contributed to drafting the OBF Community Support Fund proposal, which is being led by Peter Cock.

I also drafted a Code of Conduct adopted from The Carpentries for the OBF community in collaboration with the board members, especially Bastian Greshake and Yo Yehudi, who along with me are listed as the members for report handling. Started in 2020, the Code of Conduct was approved in January 2022. This was a long process for a good reason, as we could reflect on the scope, extent and enforcement procedure carefully. The complete Code of Conduct document is available on the OBF GitHub repository and applies to the OBF community including the board.

OBF’s annual conference, Bioinformatics Open Source Conference (BOSC) was my entry into the open science community in bioinformatics in 2012 ( mentioned in the third paragraph). This community has a special place in my heart and I was grateful to be involved in the BOSC 2021 planning committee, which was chaired by Nomi Harris. At that conference, we featured the first bilingual keynote lecture, discussed the rubrics and honoraria for invited speakers to align our workflow with the intention to build an inclusive community and facilitated an OBF-BOSC Event Support Fund for BOSC attending from underrepresented communities. See the full report: Harris, N. L., Cock, P. J. A., Fields, C. J., Hokamp, K., Maia, J., Munoz-Torres, M., Sharan, M., Williams, J. (2021). BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference. F1000Research, 10(1054), 1054. DOI: 10.12688/f1000research.74074.1.

My path has diverged – I no longer work in bioinformatics. Over the last years, I moved countries, changed jobs, co-launched Open Life Science, transitioned to co-leading The Turing Way, became involved in various open science communities and established a team of Community Managers at The Alan Turing Institute. My limited time and energy are now being directed towards building people-centric resources and community infrastructure, which I am sure will continue to cross paths with OBF, even beyond my time on the OBF board.

With immense gratitude towards all members of the OBF board, previous member Yo Yehudi who nominated me for election, and various collaborative projects I was involved in, I am bidding my farewell to the OBF board. Please look out for the call for the next election and nominate yourself, or someone who would like to give back to the open source communities in bioinformatics through an opportunity to support the ongoing projects or propose new ideas for the OBF.

You are very welcome to find details about my work and connect with me: https://malvikasharan.github.io/.

With best wishes,

Malvika

My trip to the EMBO neural stem cells workshop

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 23 Jun 2022 22:04:41 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Jemima Becker, DPhil student at Merton College, University of Oxford, attended the EMBO workshop: “Neural stem cells: From basic understanding to translational applications", supported by this fellowship granted to him in the first round of 2022.

This June, I had the opportunity to travel to the EMBO workshop: “Neural stem cells: From basic understanding to translational applications”. There, I presented a poster documenting the first six months of my PhD work on long noncoding RNAs (lncRNAs) in the postnatal ventricular-subventricular (V-SVZ): “Long noncoding RNAs in the Ventricular-Subventricular zone: what have we learnt from single cell transcriptomics?”.

Images: My supervisor Francis Szele and I after the end of the first poster session (left). Sunset on the first evening at the conference (right).

This work was a broad meta-analysis of single cell RNAseq papers, in conjunction with ChIP-seq data in order to identify candidate genes for functional studies into the role of V-SVZ lncRNAs. I presented my computational logic and workflow for this study, linking back to how open access data and code can be used to construct a robust prediction of regulatory genes. I made the argument that, particularly in the stem cell field, a lot of redundant data is generated; during the process of this project I found many overlapping studies – by making use of online data to identify candidates for further study we can save time, expense, and resources by narrowing down the pool of molecules to investigate in vitro or in vivo. Through the results of this analysis, I have started mechanistic investigations into two select lncRNAs and the role they may be playing in V-SVZ neurogenesis in vivo.

The conference was an invaluable experience, as it provided me with not only the opportunity to meet and discuss my work with others working in high resolution’ omics, but also allowed me to network with researchers tackling similar problems using divergent approaches.

Day 1

The first day of the conference began with an early flight from London to Athens, followed by a coach journey to a beautiful venue on the coast. The first keynote talk of the conference was given by Malin Parmar, discussing the applicability and translational capacity of stem cell studies in treatment of human neurodegenerative disease. A fascinating aspect of this talk was the use of scRNAseq to analyse the survival and development of tissue grafts, linking high resolution molecular description to gross changes in motor performance.

Day 2

On my second day in Kyllini, I attended four sessions totalling 15 talks and was able to present my poster in the evening. Of great excitement to me was a talk from Ana Martin-Villalba regarding a single cell triple-omics approach to analyse stem cell trajectories. The first of two poster sessions took place this evening from 8:30pm, and I found enough people interested in discussing my approach that I stayed at the session until midnight! It was incredibly valuable to be able to talk to other people, as many approaches to finding novel regulatory genes in the V-SVZ (or other tissues) take into account a limited amount of data; by comparing different datasets to identify consistent trends I had been able to find a large number of candidate genes, and was able to discuss the strengths and difficulties of my strategy.

Day 3

The third day focused on bioengineering of neural stem cells and 3D human models of neural stem cells. One talk that I found particularly interesting was from Marisa Karow, which focused on the utilisation of SNP maps to identify the allelic origin of individual transcripts in sequencing data. I have previously worked on this with mouse-derived tissue, although I found difficulties with my approach when examining low-abundance transcripts such as lncRNAs, so hearing about Professor Karow’s strategy was very useful.

Day 4

The fourth and final day of the conference consisted of three sessions, with a focus on translational capacity and patient care. I enjoyed a talk from Noelia Urban Avellaneda examining the spectrum of stem cell states within the V-SVZ. This was particularly relevant to my work, as something I have noticed in the papers whose scRNAseq data I have examined is that the number of and criteria for different V-SVZ stem cell states is apparently defined on a paper-by-paper, rather than universal basis. Dr Urban Avellaneda proposed a fluid model in which stem cells exist within a complex topology, rather than a single trajectory, of developmental potential.

Overall, my first conference has been an unforgettable opportunity and a fantastic introduction to the wider world of neural stem cells. An especially valuable element, for me, was the chance to meet more women working in bioinformatics – the bulk of my interactions within local computational biology as an undergraduate consisted of male-dominated classes, a trend which has persisted through my classes and workshops as a graduate student. The combination of meeting a greater diversity of scientists alongside the chance to share and discuss my ideas was highly rewarding, and I look forward to taking up more opportunities like this in the future.

I would like to express my gratitude to the Open Bioinformatics Foundation for making this experience possible, and thank them for their support.

Furkan M. Torun: Highlights of my participation at PyCon IT 2022

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 17 Jun 2022 16:34:35 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Furkan M. Torun, Data Scientist at OmicEra Diagnostics & Computational Biologist, attended the PyCon Italia 2022, supported by this fellowship granted to him in the first round of 2022.

Background

As it is shown in the surveys of the programming languages used and the latest publications in the field of bioinformatics/computational biology, Python has experienced unprecedented growth. Meanwhile, to spread knowledge, learn from each other, and make new networks for Pythonistas, several Python conferences (“PyCon”), are held annually by the international communities worldwide.

A while ago I came across the PyCon Italia 2022 and I hoped to attend this conference as it is fairly close to me and easy to travel. Moreover, I was thrilled to see the speakers and titles of the talks when I reviewed the schedule of the conference. Personally, I have been using Python for several years to develop bioinformatics pipelines, machine learning projects, and other data analyses for my computational biology research. Then, I decided to attend the conference and make it for my first PyCon. However, unfortunately, due to my nation’s currency meltdown against foreign currencies, I was facing a tough problem of finding enough financial support for myself to attend such an event in Europe that unites many developers and scientists from a wide range of disciplines. I applied to the Open Bioinformatics Foundation and was awarded the Event (Travel) Fellowship! So, this opportunity provided by OBF enabled me to afford my expenses including conference ticket, traveling, and accommodation! Excellent news!

Now, let’s focus on the talks!

When I entered the hotel where the conference was hosted, it started to excite me as all attendees were already chatting! After 2 years of pandemics without any in-person conference, we all looked forward to such events! Then, I learned that more than 700 participants were at the conference. So, after getting my badge, I had a chance to get to know people, including another bioinformatician, share my skills and experiences, and learn from them!

The schedule of the first day was so exciting. I had already planned what talk to attend as there were several talks going in parallel. The first talk I participated in was “Building data pipelines with Apache Airflow” since I am interested in creating repeatable and reliable workflows in Python, which is an emerging problem in bioinformatic pipelines. Then, I followed the Data Science and Machine Learning tracks as I would like to pursue my future career in those domains. So, overall the talks I attended inspired me and enabled me to make my future work better!

Also, I listened to the keynote talk entitled “Pro tips for writing great unit tests” by Raymond Hettinger and it emphasized the test concepts and writing of unit tests in a readable, fast, clear way.

Afterwards, I joined the next keynote talk entitled “Inclusive community leadership” delivered by Jessica Greene which gave insights into how a community can continue growing and evolving by staying true to its principles.

In the next days, I was also inspired by another talk namely “Python’s Life of the Brain”. In this talk, several open-source Python libraries developed by brain research enthusiasts were presented to analyze, process, and visualize the data coming from the neurons and simulate the whole brain in silico, even in a Jupyter notebook!

Also, another really exciting talk was about source code optimisation and code efficiency where I learned how to write faster code in Python 3, which will help me a lot while developing new pipelines for my future projects!

Last but not least, there was another fabulous talk delivered by the CEO of Jina AI, Dr. Han Xiao, with the title “DALL·E Flow: when neural search meets generative art”. We all know that the use of deep learning has become ubiquitous in almost every area. But, how about generating an image based on the text user provided? Yes, in this talk, it is demonstrated with examples and here are the some of them (the text on the left-hand side of the image was given and the image on the right was generated based on that text provided):

To sum up…

Overall, I really enjoyed the conference and had a chance to meet and socialize with developers, engineers, and scientists while listening to their experiences and challenges!

I was very lucky that I had a chance to meet with the creator of the project that I contributed to last month by sending a Pull Request for a bioinformatics application!

So, again, I am thankful to both the organizers of the PyCon Italia 2022 and the Open Bioinformatics Foundation for awarding me this Event (Travel) Fellowship!

For the next steps, I will advocate open-source software development (especially in bioinformatics/computational biology fields) and open science over my social media channels! Moreover, I will be applying my new learnings to the future open-source projects I publish on my GitHub account.

Call for applications for OBF Event Fellowship, Round 1 of 2022

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 07 Feb 2022 16:56:29 +0000

Announcement drafted by Malvika Sharan, Caleb Kibet and Hilya Zahroh, with the OBF Board’s input.

The call for applications for the OBF Event Fellowship 2022, round 1 is now open. The deadline for this round is 1 April 2022. Applications should be submitted via this Google Form. We have provided a Word template to help you draft the application locally before filling the form – make a copy of this template.

We invite applications from candidates who are seeking financial support to attend or host scientific events in 2022. These events can be conferences, workshops, code fests, hackathons, training courses, collaborative sprints, informal meet-ups or other skill-building and networking events. The selected awardees can use the OBF Event Fellowship to cover conference registration fees and potentially additional expenses associated with attending or hosting the event. Please read details about what this fellowship award will and will not cover. For instance, group applications are not in scope, but if multiple members of the same group would like to attend the same event, each member should send their application separately. If members of an organising committee would like to apply for support for hosting an event, the application should be sent by one person (preferably the lead organiser). More details regarding the fellowship application, review, and reimbursement process can be found on our website: /event-awards/.

Your application with required details allows reviewers to make informed decisions!

Our efforts with this fellowship are to support members from underrepresented demographic groups including but not limited to diverse ethnic backgrounds, career stages, sexuality, gender identity and expression, people with disabilities and members from low-income backgrounds (such as from developing nations). The goal is to create opportunities for exposure to open science practises in bioinformatics and enhance collaboration among diverse researchers by covering participation costs for attendees from underrepresented groups.

In the previous rounds, we received many applications that did not provide us with sufficient information to allow us to make informed decisions about what applicants hoped to gain from the conference they selected to attend, and how their participation contributes to the overall goals of the OBF Event fellowship programme. We encourage all applicants to read our review process before drafting their applications. We have also added our rubrics for review to keep the process transparent and supportive for our applicants, read them here.

We have recently announced that Caleb Kibet and Hilyatuz Zahroh will join Malvika Sharan as co-chairs of the OBF Event Fellowship ( read details). We have also announced a round-up from the 2021 fellowship.

If you have questions, please contact the OBF board by emailing board@open-bio.org.

C over photo by Brett Jordan on Unsplash.

Round-Ups from 2021 OBF Fellowship Awardees

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 07 Feb 2022 16:55:38 +0000

In 2021, we received 15 applications, of which three applicants, Sona Charles (Indian Institute of Spices Research, India), Anshika Sah (Institute of Home Economics, India) and Rupesh Gelal (Nepal Engineering College, Nepal) were awarded funding across the two open calls.

In addition, in the spirit of the OBF Event Fellowship, we made it easier to attend our own conference with the BOSC-OBF Event Support Fund, which received 9 applications, all of which were granted fee waivers for their participation in BOSC 2021, which took place online as a part of ISMB 2021. These awardees are David Twesigomwe (Sydney Brenner Institute for Molecular Bioscience – South Africa), Gemma Turon (University of Arkansas, USA), Ariel Mundo (University of Arkansas, USA), Paula Roxana Reyes Pérez (UNAM, Mexico), Fortune Ogo-ndah Awala (University of Port Harcourt, Nigeria), Wishah Mohammednour Ahmed Mohammednour (Omdurman Islamic University, Sudan), Menegbe Zibo (Université Félix Houphouët-Boigny, Ivory Coast –NH), Priyanka Sarkar (Deen Dayal Upadhyaya University, India) and Gloria Umutesi (EDAM Ontology Intern, Rwanda).

Here, I have compiled blog posts from a few of these awardees summarising their experience from attending these conferences:

Sona Charles: Summary of my participation at the GLBIO-2021 conference
Rupesh Gelal: My virtual participation at the RISC-V 2021 summit
Gemma Turon: Highlights of my participation at the BOSC-2021
David Twesigomwe: My BOSC 2021 Experience
Ariel Mundo Ortiz: My participation at BOSC 2021

Congratulations to each of them! We are delighted to support their participation as the OBF Event Fellowship and BOSC-OBF Event support fund awardees and wish them all the best for their future work.

We have receently opened the call for the first round of applications for 2022; read details and apply before 1 April 2022. Also, read the updates from the OBF Event Fellowship chairs.

Cover photo by Brands&People on Unsplash

Updates from the OBF Event Fellowship Chairs

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 07 Feb 2022 16:51:54 +0000

We are delighted to announce that Caleb Kibet and Hilyatuz Zahroh, two members who recently joined the OBF board, will be joining Malvika Sharan as the co-chairs of the OBF Event Fellowship program. Inviting contributions from the OBF board members, as well as bringing insights from their lived experiences, Caleb, Hilya and Malvika will re-evaluate how we can manage the OBF Event fellowship more effectively going forward.

There is a growing body of evidence, including the report from BOSC 2021, that virtual events are indeed more equitable for our colleagues from the Global South (see references: [1] & [2]), who were inadvertently excluded from most international events which required expensive travelling before the pandemic. However, in 2021, we saw a decline in applications to the Event Fellowship where we specifically accepted applications requesting funding for online conferences. We suspected that, after a year of the pandemic, most people working remotely must have managed the basic setup to attend virtual events. It is also possible that many potential applicants might consider the expense for participation trivial enough that they didn’t want to spend time writing proposals or dealing with the admin workload of requesting fee assistance, and instead pay it out of their own pockets. Furthermore, online events are often free and/or provide free recordings to watch after the event – removing the need to pay a registration fee.

The goal of the OBF Event fellowship programme is to create opportunities for exposure to open science practises in bioinformatics and enhance collaboration among diverse researchers by covering participation costs for attendees from underrepresented groups. Considering the recent evolution of scientific events, there is a need to assess how we continue to support participants who represent their local research, exchange knowledge and benefit communities more widely through their participation in international scientific events.

With the new co-chairs on board, we will reflect on changes we can make in this programme that benefits members from marginalised groups and low-income backgrounds through learning, sharing and networking opportunities – potentially helping them advance their careers and impact the directions of bioinformatics research at the international level. We encourage you to participate in the discussion via this GitHub issue: https://github.com/OBF/obf-docs/issues/88.

We have just opened the call for the first round of Event Fellowship applications for 2022; read details and apply before 1 April 2022.

References:

[1] Harris, N.L., Cock, P.J.A., Fields, C.J. et al. BOSC 2021, the 22nd Annual Bioinformatics Open Source Conference [version 1; peer review: not peer reviewed]. F1000Research 2021, 10(ISCB Comm J):1054. https://doi.org/10.12688/f1000research.74074.1

[2] Skiles, M., Yang, E., Reshef, O. et al. Conference demographics and footprint changed by virtual platforms. Nat Sustain (2021). https://doi.org/10.1038/s41893-021-00823-2

New Code of Conduct, Community Support Sponsorship approved by OBF membership vote

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 27 Jan 2022 23:08:50 +0000

As previously described, during the November 2021 public Board meeting, the OBF announced two new initiatives to be voted on by the OBF membership. Both of these received a large majority of votes:

OBF Community Support Sponsorship (53 for, 3 against, 2 abstaining)
OBF Code of Conduct (54 for, 2 against, 1 abstaining)

The work to set up the new Community Support Sponsorship is underway. The new Code of Conduct is now available on the OBF website.

OBF Membership Referendum

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 04 Jan 2022 21:44:00 +0000

During our last public Board meeting, the OBF announced two new initiatives that are being proposed for approval by the OBF membership in a formal votes.

1. OBF Community Support Sponsorship: a proposed new grant programme, based on the OBF Event Fellowships but aimed at supporting grassroots projects running events in their own communities. For details see: - /2021/05/11/obf-community-support-sponsorship/ - https://github.com/OBF/obf-docs/issues/86

2. Code of Conduct: BOSC has a code of conduct, as part of the parent conference, but OBF does not yet have its own code of conduct. This pull request lays out a Code of Conduct for the OBF that, if approved by a membership vote, will replace the content on /code-of-conduct/. For details see: - https://github.com/OBF/obf-docs/pull/78

The deadline to vote is January 10, 2022 (NOTE: later extended to January 17.). All active OBF members should have received an email ballot on December 28 from Helios Voting with “OBF Membership Referendum” in the subject line. If you didn’t receive a ballot (and you’ve already checked your junk/spam mail folder), please contact us (board atsign open-bio.org).

My virtual participation at the RISC-V 2021 summit

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 17 Dec 2021 16:04:58 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Rupesh Gelal, a student from Nepal Engineering College, Nepal, attended the 2021 RISC-V Summit, supported by this fellowship granted to him in the second round of 2021.

The pandemic has made attending conferences and events more accessible for full-time students like me, who often can’t travel internationally to attend in-person events. These days everything is possible remotely — there is no need to travel halfway across the world. Still, the cost of small hardware (headphones, webcam, speaker, and/microphone) for attending remote events can be a hindrance sometimes. Fortunately, I came across the Open Bioinformatics Foundation Event Fellowship while researching the 2021 RISC-V Summit. I applied immediately for the fellowship. After a month, I received an email notifying me about my successful application. In this post, I provide an overview of my participation at this conference.

Day 1 of RISC-V Summit

The first day of the event was really exciting. I bonded with other RISC-V community members, which helped extend my professional network. I had an opportunity to share my skills, ideas, and views with fellow participants regarding the present and future of technology and learn from them. After the initial bonding and introduction phase, I attended a lightning Talk session and enjoyed the demo session “How to Extend RISC-V to Accelerate AI/ML” given by Veronia Iskandar from TU Dresden & Dr. William Jones from Embecosm. I learned the internal working of RISC-V architecture and how it can be extended to improve performance. This session was one of the reasons why I wanted to attend this year’s RISC-V summit.

Day 2 of RISC-V Summit

On day two, I attended a couple of sessions. First, I attended the “Efficient Issue Scheduling for Hardware Multithreaded RISC-V Pipeline” session by Dr. Shlomo Greenberg, Ben Gurion University of the Negev & Sami Shamoon College Engineering, Beer-Sheva, Israel. This is where I learned about the importance of an effective scheduling algorithm as well as other multithreading techniques. Second, I listened to the talk “AI-RISC - Custom Extensions to RISC-V for Energy-efficient AI Inference at the Edge of IoT” by Vaibhav Verma from the University of Virginia. In this session, I dived deeper into the AI-RISC hardware/software co-design methodology. The session gave me better insights into the AI integration on the RISC-V-based processor.

Day 3 of RISC-V Summit

On the final day of the RISC-V event, I attended the “Quantitative Methods for Continuously Improving RISC-V Compilers” session by Philipp Tomsich from VRULL. Through this session, I learned how quantitative methods can be used to assess the quality of code generation and identify and prioritize potential improvements based on hot-block analysis, dynamic instruction count metrics, and instruction histograms.

To conclude, I feel the RISC-V summit was a great learning experience. I learned a lot about the RISC-V architecture and its open-source community. The skills learned from this conference, such as collaboration, open communication, and open source best practices, will directly help me achieve my professional and academic goals. All data recordings of the conference will be available as an open source resource on YouTube on the RISC-V International channel.

I would like to thank the OBF board again for selecting me for the fellowship. I will make sure to promote and advocate open-source software development and/or open science in the biological research community as well as in my community.

Event Fellowship deadline extended to October 4, 2021

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 30 Sep 2021 18:37:41 +0000

The deadline for applying for an OBF Event Fellowship has just been extended to October 4, 2021! The OBF Event Fellowship program is aimed at increasing diverse participation at events relating to open source bioinformatics. You can read blog posts by previous Event Fellowship recipients.

See more details on our webpage, and submit your application at https://forms.gle/7ocmgvypiFHeFNfy7!

Ariel Mundo Ortiz: My participation at BOSC 2021 sponsored by the BOSC-OBF Event Support

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 08 Sep 2021 02:43:46 +0000

The BOSC-OBF 2021 Event Support Fund was awarded to Ariel Mundo Ortiz, a researcher from the University of Arkansas, to participate in BOSC 2021, an annual conference hosted by the Open Bioinformatics Foundation (OBF). Based on the OBF Event Fellowship program, this fund aimed to facilitate the participation of diverse researchers from historically underrepresented groups at BOSC to help wider awareness and adoption of open source bioinformatics practices in the biological research community. Find more information here.

A while ago I came across a Twitter post that mentioned the Bioinformatics Open Source Conference (BOSC). A quick Google search took me to the BOSC website, and I was thrilled to see that one of the core concepts of the conference was to promote open science. Personally, I have been working over the last year to make my work reproducible and accessible, and the fact that BOSC provided talks and workshops focused on open science sparked my interest; I decided that although I did not have material for a presentation, I still wanted to attend the conference.

Fortunately enough, BOSC offered this year the BOSC-OBF 2021 Event Support Fund, with the aim of increasing the participation of members from groups otherwise underrepresented in BOSC. I suspected the number of applications for the Support Fund was going to be high, but nonetheless, I decided to submit my own application.

On July 10th, I received an email notifying me about my successful application! That was excellent news, and now I was sure I would be able to attend the event. One personal challenge with the Conference this year was the time zone; all the sessions started at 5:30 am! (In my time zone).

Day 1

The challenge of time zones quickly became a minor thing after attending the first keynote session by Dr. Christie Bahlai (from Kent State University) on July 29th. Her keynote was titled “Significant heterogeneities: Ecology’s emergence as open and synthetic science” and it covered the historical background of Ecology, and how significant changes over the last two decades have moved the focus of the field, enabled Dr. Bahlai and other researchers to conduct research that is grounded in collaboration and openness.

Her keynote resonated deeply with me; I could see how her path was similar to my own academic path. For instance, trying to analyze noisy data gathered through my research (that never looks like the “example data” from statistical books) was challenging. I was inspired by her talk, and it reinforced in me the desire to make my future work open and to continue to refine my statistical armamentarium.

Day 2

The keynote for the second day of BOSC 2021 was delivered by Dr. Thomas Hervé Mboa Nkoudou (from the African Institute of Open Science and Hardware) titled “Contribution of the maker movement to biotechnology in Africa: An open science perspective”. This keynote covered the democratization of biotechnology in Africa, and how the maker movement (a community-based movement that democratizes access to tools and technologies) has proven successful by promoting Biomakerspaces where African researchers can replicate existing protocols and locally produce enzymes, for example. This keynote was very interesting to me because it allowed me to appreciate a different perspective of the open science movement and the impact that reproducible research has in other parts of the world.

That day I was also able to attend the Sessions on Visualization and Translational Bioinformatics. The talk “Robust variant interpretation in precision oncology using a graph knowledge base” by Caralyn Reisle (UBC) was a talk I enjoyed very much, as it emphasized the use of graph-based knowledge to enable the discovery of molecular pathways in cancer; this talk made me better understand the importance of the use of big data to treat and diagnose cancer, which I think will become extremely important in the future.

Despite the challenges of 2021, and not being able to travel much, I feel BOSC 2021 was a wonderful experience. It allowed me to interact with people from around the world that believe that openness is a central theme in science, and I was able to learn about new tools, statistical analyses, and to get a better understanding of where the open science movement currently stands. I look forward to a (hopefully in person) rewarding and motivating experience for BOSC 2022!

David Twesigomwe: My BOSC 2021 Experience

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 07 Sep 2021 10:24:48 +0000

The BOSC-OBF 2021 Event Support Fund was awarded to David Twesigomwe, a PhD student based at the Sydney Brenner Institute for Molecular Bioscience (SBIMB) - South Africa, to participate in BOSC 2021, an annual conference hosted by the Open Bioinformatics Foundation (OBF). Based on the OBF Event Fellowship program, this fund aimed to facilitate participation of diverse researchers from historically underrepresented groups at BOSC to help wider awareness and adoption of open source bioinformatics practices in the biological research community. Find more information here.

Attending the Bioinformatics Open Source Conference (BOSC) has definitely been one of my highlights for 2021 so far. I am so grateful to have received a registration fellowship as part of the global initiative supported by the BOSC-OBF 2021 Event Support Fund. From the research point of view, nothing beats getting together (albeit virtually) to talk all things bioinformatics and open science with such a welcoming BOSC community as we continue adapting to new routines and work-life balance during the COVID-19 pandemic.

Pre-BOSC

The first thing that stayed with me about BOSC 2021 was the detailed critique and useful comments we received from the reviewers of our abstract. As an up-and-coming bioinformatics scientist, it was wonderful to get such actionable feedback on our pipeline ( StellarPGx), and suggestions on how we can promote open source contributions to the code. One of the reviewers even went the extra mile and submitted the very first issue in the GitHub repository :)

Overview of the conference

BOSC 2021, which was one of the tracks of ISMB/ECCB 2021, was really exciting despite it being a virtual event – kudos to the organising team for putting the conference together aa nd navigating all the technical issues. In particular, I enjoyed the session on workflow management systems, which included a fascinating talk by Paolo di Tommaso on the evolution of Nextflow – the workflow management system of choice for a number of students and senior scientists at the SBIMB. I also enjoyed the session on analysis tools, where I got the opportunity to present StellarPGx, and I learned a great deal from the other sessions as research reproducibility was rightly championed to all the talks.

Furthermore, it was quite exciting to round off the days with virtual round table and happy hour group meetings with incredible role models (Chris Fields, Nomi Harris, and Geraldine Van der Auwera to mention but a few).

Welcoming community

Even though BOSC 2021 (the first BOSC for me) was held virtually, the warm welcome I received from the community – be it on the remarkably active Slack channel or in the round table meetings – was quite uplifting. Special mention to Nomi Harris and the entire organising team for dedicating a lot of time and effort in organising such an engaging conference.

Next steps

I am looking forward to incorporating the ideas and suggested open source best practices arising from BOSC 2021 in the next phase of development for StellarPGx. I will forever be grateful for being awarded the BOSC-OBF 2021 Event Support Fund which enabled me to attend and present at #BOSC2021. I hope to be an active member of the BOSC-OBF community for years to come and to volunteer in some of the upcoming OBF activities.

Gemma Turon: Highlights of my participation at the BOSC-2021 conference thanks to an OBF Event Fellowship

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 31 Aug 2021 09:46:12 +0000

The BOSC-OBF 2021 Event Support Fund enabled awardees to register for free for BOSC 2021, an annual conference hosted by the Open Bioinformatics Foundation (OBF), which promotes and facilitates the open source bioinformatics development and open science. Based on the OBF Event Fellowship program, the BOSC-OBF support fund aimed to facilitate participation of diverse researchers from historically underrepresented groups at BOSC, helping to spread wider awareness and adoption of open source bioinformatics practices in the biological research community. One of the BOSC-OBF awardees was Gemma Turon, a researcher from the Ersilia Open Source Initiative (EOSI), who writes here about her experience at BOSC 2021.

When we started our small non-profit, the Ersilia Open Source Initiative (EOSI), to strengthen the research capacity against neglected diseases using open-source AI/ML tools, we were not aware of the large number of resources and community back-up we would encounter. I first heard of the BOSC conference in February, and quickly realized it would be a great opportunity to present our newly founded initiative and the software we were trying to develop. What interested me mostly of the BOSC was the openness and inclusion of a broad range of topics of interest, many of which are aligned with EOSI’s mission, namely Open Science and Reproducible Research, Open Biomedical Data, Open Approaches to Translational Bioinformatics and Inclusion, Outreach and Training.

By then, we had all become used to virtual meetings, and despite there might be some drawbacks, global reach is an advantage in these settings, enabling us to participate in international meetings from our home-made offices. Nevertheless, conference registration costs still need to be covered, and they can be unaffordable to limited-resource organizations such as ours. With delight, then, I found out about the BOSC-OBF 2021 Event Support Fund, which encouraged me to continue with my application for a short talk and apply to the Support Fund to cover my registration.

Overview of the conference

The three keynote speakers delivered outstanding talks on the application of open and collaborative science to a broad range of topics, from ecology (Dr. Christie Balai) to the maker movement in Africa (Dr. Thomas Hervé Mboa Nkoudou), and including a great talk on new protocols in data collection, transparency and reproducibility for data-driven biomedical research (Dr. Lara Mangravite). The last two are particularly relevant to the mission of EOSI, which is focused on implementing data-driven technologies for drug discovery research in Low and Middle Income Countries, particularly in Africa, where most of our collaborators are based.

The short talks were organized in topic-based sessions that included short (5 min), medium (8 min) and long (16 min) talks. I would like to highlight the “Tools for Open Science” session (Day 1), which included talks about outstanding tools like the OpenCGA and the GenePattern Notebook, and the “Translational Bioinformatics” session (Day 2) where I introduced the Ersilia Model Hub, and learned about great initiatives such as the target identification in Parkinson disease presented by Dr. Jeremy Yang.

The keynote talks and different sessions were complemented by a large selection of poster presentations and community-engaging events in the form of “Birds of Feathers”.

Learnings and thank you

I first want to congratulate the BOSC organization for an incredible effort in managing such a large online event, I always received prompt answers to all my questions via email and on the conference day the set up of the meeting rooms and the availability of the staff made sure there were no technical issues and the sessions run smoothly and according to the schedule. In addition, the BOSC-OBF organisers set up the Slack channel that enabled the participants to continue on the discussions started live during the conference, a great strategy to further engage the audience and provide more feedback to the speakers and poster presenters.

Finally, as I am writing this short blog post, I have reviewed the aims and objectives of BOSC, as stated on their website:

Provide developers with a forum for displaying their work to the wider research community
Provide a focused environment for developers and users to interact and share ideas about software development, open science, and practical techniques in bioinformatic
Promote Open Science, with its focus on sharing data and tools, transparency, reproducibility, and data provenance
Inform the research community of important developments in Open Source Bioinformatics.

And I believe that they have all been accomplished in the BOSC-2021 edition. As a speaker and participant, I have had the opportunity to learn about open source tools for data sharing and research reproducibility, I have engaged in high-level discussions with other scientists and become part of the BOSC-OBF community and, moreover, I have had the opportunity to present the research we are developing at EOSI thanks to the support of the OBF Event Fellowship. I want to give my deepest thanks for the opportunity, and to encourage all readers to go to the youtube channel where you can find the recordings of the talks, and, if you are interested in reading more about EOSI’s mission, please check out our page and our Medium Blog.

Call for application for the OBF Event Fellowship - second round 2021

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 18 Aug 2021 18:45:01 +0000

The call for application for the second round of this year’s Open Bioinformatics Foundation (OBF) Event Fellowship is open. Please submit your application before October 1, 2021 (save a calendar reminder).

Just announced: deadline extended to October 4, 2021!

Please apply via this Google application form: https://forms.gle/7ocmgvypiFHeFNfy7.

The OBF Event Fellowship program is aimed at increasing diverse participation at events promoting open science practices such as open source bioinformatics resource development and dissemination in the biological research community. These fellowships are available to support both in-person and remote (virtual) participation at events such as conferences, workshops, training courses or collaborative development sprints. See more details on our webpage.

Like the previous three rounds, we are continuing to invite applications from individuals seeking financial support to attend or host virtual events.

In the previous rounds, we have offered fellowships to participants in bioinformatics, open research and life science-related projects or conferences. This fellowship supported their participation as a speaker, poster presenter or new learners of these particular topics. You can read blogposts from their participation.

If multiple members of a group are applying for this fellowship, please send your applications separately as the OBF Event Fellowship is aimed at supporting individual applicants only. For more information, please contact the OBF Event Fellowship chair by emailing: board@open-bio.org.

BOSC-OBF 2021 Event Support Fund

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 11 Jun 2021 12:00:00 +0000

Thanks to funding from our sponsors, we are opening a special call for applications to the BOSC-OBF Event Support Fund. This fund aims to increase participation of members from groups otherwise underrepresented in BOSC or in bioinformatics community events in general, including but not limited to underrepresented demographic groups (country of residence and citizenship), ethnic background (historically underrepresented and other minority groups), career stages, gender identity and expression, people with disabilities and members from low income/resource organisations.

A limited number of qualified applicants will be chosen to receive free registration for ISMB/ECCB 2021. No other financial support (for example, for internet access or headphones) will be included.

The application deadline is 30 June 2021, and decisions will be sent out by 8 July 2021. Apply at https://forms.gle/aDVSHpq7Gs46CNDb6.

We hope you’ll join us at BOSC! For more #BOSC2021 news, follow us on Twitter!

Summary of my participation at the GLBIO-2021 conference funded by OBF Event Fellowship

board@open-bio.org (Open Bioinformatics Foundation) — Mon, 07 Jun 2021 09:16:08 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program supports and encourages diverse participation at events focusing on open source bioinformatics software development and open science practices in the biological research community. Sona Charles, a Scientist (Bioinformatics) at ICAR-Indian Institute of Spices Research, India, was supported to participate in the Great Lakes Bioinformatics (GLBIO) 2021 Conference by this award granted to her in the application round-1 of 2021. Find more information here.

In this pandemic stricken world when all conferences are taking place virtually and don’t require traveling, it has become more accessible for international participants like me. However, the cost for registration, video-conferencing accessories and childcare remain the same. Luckily, I came across the Open Bioinformatics Foundation Event Fellowship, when I was hoping to attend the Great Lakes Bioinformatics (GLBIO) 2021 Conference. I had already submitted a poster entitled “ Sequence-Based Prediction of Phytophthora- Host Interaction Using Machine Learning Methods” to the conference, which was accepted. I went ahead and applied for the event fellowship at Open Bioinformatics Foundation for its first round of 2021. Two weeks later (after the application review phase), I was informed by the Chair of OBF Event Fellowship that I was awarded the fellowship.

Day 1 of GLBIO 2021

The GLBIO conference commenced on 13 May 2021 with the workshops, which is undoubtedly my favourite attraction for attending a conference. Out of all the options for workshops, I chose two: (1) Machine Learning on Microbiome Data: Theory and Practice and Introduction to Deep Learning, and (2) Creating Neural Networks in Python and R. All the code for the workshop as well as the required packages were shared much earlier so that it would be easy for us to follow. As a beginner in Machine Learning, the two workshops enabled me to gain more knowledge on the topics in which I anticipate working in the coming days.

Day 2 of GLBIO 2021

The keynote talk “Variable Selection and Interpretability in ‘Black Box’ Statistical models” took place on 14 May 2021 by Dr Lorin Crawford (screenshot of his title slide below). He introduced the various concepts in Biologically Annotated Neural Networks and their applications in Multiscale genomic inference.

On the same day, I attended four sessions on Knowledge Guided Machine Learning (KGML) in Bio. As a beginner in this area, I really appreciated this session and wanted to learn more about the applications. The session-1 included two talks on predicting the promiscuity of enzymes and Predicting RNA Pseudouridine Sites in Nanopore Sequencing Data. The session-2 included the talks “Knowledge-based Meta-Learning for Cancer Prediction and Survival Analysis” and “Learning to align with differentiable dynamic programming” by Aidong Zhang and Michiel Stock respectively. The session-3 had three informative talks on new machine learning approaches for estimating the functional consequence of mutations in diverse human populations, for diagnostic screening of cardiovascular disease using gut microbiome data and for gut microbiome-based detection of inflammatory bowel diseases. The final session included three talks: (1) Gene signatures of COVID-19 infection severity identified using graph convolutional neural networks on single-cell RNA-Seq data, (2) Machine learning on knowledge graphs and ontologies, and (3) Supervised prediction of ageing-related genes from a weighted dynamic protein-protein interaction network. An EDI panel survey discussion was held between the sessions followed by the poster session. Day 2 of the conference was highly informative and I had a lot of take-home messages and ideas.

Day 3 of GLBIO 2021

Day 3 started with the keynote lecture titled “Methodological advancements to improve metagenomics for surveillance of antimicrobial resistance” by Dr Noelle Noyes (screenshot from her talk).

Metagenomics is one of the areas of interest in my research institute and I attended the Microbiome and Multi-omics analysis sessions. I also attended two sessions on Algorithms and Machine Learning. Another keynote by Michael Osterholm attracted the attention of researchers interested in SARS-Cov2 epidemiology.

It was followed by a session on SARS-CoV2 analysis and a session on proteomics and metadata. The last keynote of GLBIO2021 was on Predicting the evolution of syntenies with closing remarks by Aïda Ouangraoua.

On Day-3, a second poster session was organised where I presented my work titled “ Sequence-based prediction of Phytophthora-host interaction using machine learning” (Sona Charles, & Sreekumar J., 2021, DOI: 10.5281/zenodo.4892738). I got to interact with many researchers and receive feedback from a global audience working in the area of machine learning.

Screenshot of the top section of my poster titled: Sequence-based prediction of Phytophthora-host interaction using machine learning, available on Zenodo under CC-BY 4.0 license, http://doi.org/10.5281/zenodo.4892738

Overall the conference was excellent and all data of the conference will be available as an open source resource on YouTube on the ISCB TV channel. I am extremely thankful to the OBF for funding my participation related cost for the conference. I will be able to cover my registration and connection related costs. Since the conference was conducted during lockdown it would have been practically impossible for me to attend the conference if the childcare grant was not awarded for the entire duration of the conference. Since the time zones were overlapping from 21:30 to 03:00 Indian Standard Time (IST), child care was the most essential resource for me for attending the conference throughout the night.

I express my heartfelt thanks for the opportunity to present my research at a reputed international conference with the support of the OBF Event Fellowship. As part of this fellowship, I will soon be depositing my work in my GitHub repository, developed under a CC-BY license ( GitHub).

OBF Community Support Sponsorship

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 11 May 2021 17:08:35 +0000

The following outlines a potential new grant programme, subject to approval by the OBF membership in a formal vote, which the OBF board would hope to launch this year.

Motivation

In 2016, the OBF introduced a “Travel Fellowship” to help individuals attend meetings, aiming to improve diversity in the bioinformatics community. Awardees were reimbursed (with receipts) after the event in which they participated, with a standard cap of USD $1000. The Travel Fellowship was later renamed the “Event Fellowship” reflecting that with the COVID-19 pandemic (and hopefully longer-term changes in scientific conferences to promote the participation of diverse members in online events and reduce carbon emissions), attending events no longer automatically means travelling in person.

This fellowship and some of the applications to it have drawn our attention to the fact that for similar amounts of money, we may be able to help grassroots projects running event(s) in their own communities. It would be practical if we do not have to handle itemised receipts for reimbursement, as that would be a significant time overhead for volunteer board members. Instead, the proposal is to follow the existing model of sponsoring conferences whereby the organisers of the event OBF has agreed to support to invoice us an agreed amount (e.g. USD $1000) before the event, and in return our logo appears on their event webpages and materials, acknowledging our support. Where appropriate, applicants will be encouraged to become OBF Affiliate Projects.

This mechanism will require the event organisers to have some sort of bank account or fiscal sponsor (e.g. a university staff member’s budget, a local hackerspace) where we can transfer the funds.

The scope explicitly excludes well-established organisations, which are able to solicit donations and sponsorships on their own. Since some of the OBF’s funds are donated to us by other organisations, we can hopefully be a useful intermediary between our supporters and smaller efforts globally.

Scope

Single events like a scientific meeting, small conference, training workshops, hackathon, or time-limited series like monthly seminars. An organisation can receive only one financial award per calendar year, to ensure that we can offer this support to the wider community.

Essential:

Strong bioinformatics component
Strong Open Source / Open Science component
Code of Conduct

Desirable:

Applying for OBF affiliate membership (need indicative time scale). If the group is already an affiliate member, rather than using this scheme, please email the board directly to discuss direct funding.
The event that is not yet well-established or well-funded
Promotes diversity of bioinformatics participants
Organisers largely based in countries on the World Bank’s low or lower-middle-income list
Meeting materials will be shared under an open licence (e.g. talk slides/videos under CC-BY)

What is not in the scope:

Well established groups able to attract their own donors and sponsors directly (e.g. ISCB, The Carpentries)

Budget

An initial commitment of $10,000 over two years as an evaluation period, with an individual grant award cap of USD $1000 per event or $2000 for an event series.

Logo and text

We would need a standard logo/image banner, URL, and perhaps text for the event to use.

Argument For

With this scheme, OBF will be able to offer benefits to community projects that are aligned with OBF’s mission but are working on a low budget or without any organisational support. This will be an opportunity to reach the demographic and communities that are not yet served by OBF but that promote Open Source and Open Science practices. Furthermore, by encouraging new projects to become affiliated members of OBF, we will enhance the representation of diverse bioinformatics projects through the OBF platform. As a volunteer organisation that holds funds earned by volunteer labour (in particular via conference fees and Google Summer of Code), it helps to reassure OBF volunteers that funds earned through their efforts are being put to good use empowering communities that have aligned goals.

Argument Against

This proposal is a deliberate expansion on where the OBF spends its income, the vast majority of which is earned through the volunteer labour of OBF community members, including those helping to organize BOSC and serving as mentors and administrators in the OBF’s Google Summer of Code participation. The OBF’s assets and income are finite, and thus funds given to projects, events, or initiatives outside of the OBF umbrella are no longer available to spend on OBF members or membership projects. In other words, for the funds committed to this program, the assumption is that frequently more meritorious recipients and/or causes can be found outside of the OBF umbrella, in the scope of this program, than within OBF’s umbrella, in the full scope of OBF’s mission. There’s little evidence supporting this assumption, and until there is, income earned through OBF volunteer labour should be disbursed within the OBF community (which, as it includes BOSC and its attendees, is already broadly defined).

Process

What happens next? This post outlines our vision; next, we will ask the OBF membership if they approve of the idea in principle. We invite feedback via this GitHub issue or emails to the board by Friday 4th June 2021. If the membership approves, the exact policy wording will be drafted as another OBF policy document on GitHub for the board to approve.

Join us at BOSC 2021!

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 24 Mar 2021 21:21:52 +0000

BOSC 2021 will take place July 29-30, as part of ISMB/ECCB 2021 Online.

Key Dates

May 6, 2021 (11:59pm EDT): Deadline for submitting one-page talk/poster abstracts May 27: Talk/poster acceptance notifications June 3: Late poster (and Late-Breaking Lightning Talk) submission deadline June 10: Late poster / LBLT acceptance notifications July 29-30: BOSC 2021 Online (part of ISMB/ECCB 2021 Online) July 31-Aug 1: CollaborationFest (CoFest)

About BOSC 2021

BOSC is returning to ISMB in 2021, after a successful partnership with Galaxy for the first Bioinformatics Community Conference last year (BCC2020 online). Originally slated to take place in Lyon, France, ISMB/ECCB 2021 will be held online, and features over a dozen tracks, including BOSC. As usual, BOSC will include keynote talks, longer and shorter (lightning) talks from submitted abstracts, posters, Birds of a Feather, and more!

Timing

BOSC 2021 will take place the last two days of ISMB/ECCB: July 29-30. Our usual free collaborative work event, CoFest, will be held July 31 - August 1.

The complete ISMB/ECCB schedule is available here. The core hours for talks will be 11:00-15:30 UTC, with poster sessions and ISMB keynotes from 15:30-17:30 UTC. The core hours correspond to:

13:00-17:30 CEST (Europe) 12:00-16:30 BST (UK/Ireland) 7:00-11:30am EDT (East coast of North America) 4:00-8:30am PDT (West coast of North America) 9:00pm-1:30am AEST (East coast of Australia)

Abstract submission

We encourage you to submit abstracts on any topic relevant to open source bioinformatics or open science. After review, some abstracts will be selected for lightning talks, longer talks, or posters. The deadline for abstract submission is May 6th (11:59pm EDT / 03:59 (May 7th) UTC)!

BOSC session topics include (but are not limited to):

Open Science and Reproducible Research Open Biomedical Data Citizen/Participatory Science Standards and Interoperability Data Science Workflows Open Approaches to Translational Bioinformatics Open Science for Global Health Developer Tools and Libraries Inclusion, Outreach and Training Bioinformatics Open Source Project Reports (about new or existing projects)

Requesting registration fee assistance

We realize that the cost of ISMB/ECCB may be prohibitive for some. If you are submitting an abstract to BOSC and would have difficulty covering the cost of registration, you can request registration fee assistance. To make it easy, this request can be made right on the abstract submission form. (Only the conference chairs will see these fee assistance requests – the abstract reviewers will not.) We regret that we will not be able to offer registration fee assistance for those who are not submitting abstracts. (But you should consider submitting an abstract! Even if your work is preliminary, it may qualify for a poster.)

Stay in touch!

Learn more about BOSC: /events/bosc/ Join our BOSC announcements mailing list: https://groups.google.com/forum/#!forum/bosc-announce Chat with us on Slack: https://join.slack.com/t/obf-bosc/shared_invite/zt-n5ur1gsj-z2C~69_4lYTFPg5tbWA8Ew Find us on Twitter at @OBF_BOSC and use #BOSC2021 for this year’s conference.

We hope to see you online at BOSC 2021! Please share this announcement with people or groups who might be interested. We are particularly interested in reaching out to diverse communities who may not yet be aware of BOSC!

Call for applications for OBF Event Fellowship, Round 1 of 2021

board@open-bio.org (Open Bioinformatics Foundation) — Fri, 19 Feb 2021 10:36:38 +0000

The call for applications for the OBF Event Fellowship 2021, round 1 is now open. The deadline for this round is 1 April 2021. Applications should be submitted via this Google Form.

We invite applications from candidates who are seeking financial support to attend or host virtual events in 2021. The selected awardees can use the OBF Event Fellowship to cover conference registration fees and potentially additional expenses associated with attending or hosting the event, such as small hardware (microphone, speaker, webcam), childcare for the duration of the event and high-speed internet. Like last year, in this round, we will consider applications to attend or host virtual events only. This decision has been made due to the ongoing Coronavirus pandemic induced lockdown and restricted travels. Expenses that will be incurred by remote participation have to be justified in the application and will be evaluated on a case-by-case basis.

Group applications are not in scope, but: if multiple members of the same group would like to attend the same event, each member should send their application separately. If members of an organising committee would like to apply for support for hosting an event, the application should be sent by one person (preferably the lead organiser).

Planning to attend BOSC 2021 ? You can request a registration fee waiver/reduction when submitting your abstract for a talk or poster directly via the BOSC abstract submission form. If you would like to participate without a talk or poster, please fill the OBF Event Fellowship application form providing your motivation and expected outcomes from attending BOSC 2021.

More details regarding the fellowship application, review, and reimbursement process can be foundon our website: /event-awards/. If you have questions, please contact the OBF board by emailing board@open-bio.org.

Learn about the OBF Event Fellowship Awardees from 2020!

Round 1 (1 April 2020)

As part of the fellowship process, all OBF Event Fellowship awardees write blog posts that are posted on the OBF website ( see here). Below are the blog posts by the awardees from 2020 application rounds.

Using his OBF Event Fellowship Award, Armando Blondel Djiyou Djeuda hosted the H3ABioNet‘s Introduction to Bioinformatics course (IBT) in Cameroon for the first time. Read his report in this blog post.

Gigi Kenneth and Edidiong Etuk attended the Bioinformatics Open Source Conference (BOSC) track at the Bioinformatics Community Conference 2020. It was a first-time opportunity for them to attend bioinformatics and open science workshops at an international conference. Read their posts: A Software Engineer’s Experience at BCC 2020 (by Edidiong) and Getting introduced to Bioinformatics and Open Science through BCC 2020(by Gigi).

Pengfei Fan from Queen’s May College in London attended the Conference on Lasers and Electro-Optics 2020 and shared his experience in this blog post: Smart computational imaging.

Round 2 (1 October 2020)

Siddhant Sharma, an undergraduate student from India, received the OBF Event Fellowship to participate in the International Student Conference 2020 (IEEE, EMBS). A post will be shared soon.

MetaDocencia: Teaching to Teach (Bioinformatics and more) Online in Spanish

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 13 Jan 2021 18:26:38 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open-source bioinformatics software development and open science practices in the biological research community. Dr. Laura Ación , a researcher at the Instituto de Cálculo, University of Buenos Aires, Argentina . She is also one of the co-founders of MetaDocencia , which she could partly support with the OBF Event fellowship granted to her in the December 2019 application round.

What was supposed to happen

I applied to OBF Event Fellowship to attend CarpentryCon 2020 (June 29 – July 1 in Madison, WI) and useR! 2020 (July 7-10 in St. Louis, MO). Plans were going perfectly because shortly after receiving the fellowship, CarpentryCon 2020 organizers invited me to give a keynote talk. It was a once in a lifetime event alignment! My first international keynote talk for a beloved community with extensive ties to Bioinformatics education. Plus, useR!, the primary academic conference about R, a language widely used in open-source bioinformatics projects. Traveling from Buenos Aires to North America to participate in international meetings is usually unaffordable. I was ecstatic. However, as you know, nothing happened as expected in 2020!

What happened

Having the OBF fellowship award repurposed to host or attend online events was one of the 2020 silver linings because it enormously facilitated my work towards the advancement of MetaDocencia.

On March 16th, 2020, all in-person classes and training opportunities were canceled in Argentina due to the pandemic, with no clear indication of when they will resume. That afternoon, it was already clear that we all had to stay home for a while (thus my WhatsApp avatar “Yo me quedo en casa,” meaning, “I stay at home”). That afternoon I sent two audio messages to a group of friends.

The two audio messages with the idea that sparked MetaDocencia

These audios said:

“Girrrrrrrrrlsssssss, how are you? I hope you are fine! I think I just found my way of helping in the midst of all that is going on! (…) I just got the idea of using all we know on how to teach online to help train teachers that will be having to take their classes online immediately.

I am all ears about your thoughts. To me, this seems like THE opportunity [to put out there all we know about active teaching].

These past days, I had no idea what my role could be amid this pandemic. (…) Today, when I saw the Ministry of Education press conference, I realized it is a crucial moment. Everyone will be switching their content to online delivery mode. Maybe we need to teach one workshop very fast; one, two, three, as many as needed. What do you think?”

First time I shared my idea for MetaDocencia project with my colleagues and friends

The answers of this group of academics, researchers, and teachers with deep ties to the Latin American research and teaching community were immediate. That is how the MetaDocencia ride started.

MetaDocencia is ‘meta teaching’ in Spanish. Our mission is to nurture a community of Spanish-speaking educators by teaching concrete, evidence-based, and student-centred educational methods. We collaboratively develop open, reusable, and accessible resources to foster effective training practices.

THE opportunity

You may wonder why in March 2020 I thought we had ‘THE’ opportunity and how MetaDocencia connects to Open Bioinformatics. Despite open educational communities exist worldwide, most of them speak in English and hence, language is an enormous barrier in Latin America. Translations of contents are necessary but not enough for culturally-responsive teaching. Furthermore, “meeting our learners where they are” in Latin America means not making assumptions about the knowledge of technologies such as Zoom, Slack, or Google docs and being conscious about internet access and accessibility inequalities.

A lot of terrain levelling work is needed before meaningful international integration is feasible. ‘Communities of Practice’ are still a new concept in our region. Tools like active classrooms powered by minimal technology such as peer-instructions, shared note-taking, or a Code of Conduct are far from being standard in (online) classrooms and events, even among the most tech-savvy professionals in our region.

MetaDocencia helps bridge this gap by empowering Spanish-speaking educators from countries that are under-served in the area of Open Science. Several participants of MetaDocencia are bioinformaticians. Hence, advancing bioinformatics knowledge in Latin America is included in our overall goals, which also require the teaching of open source practices. The coronavirus pandemic forced all classes and events to run online, which meant that all bioinformatics educators, among others, needed to learn how to teach online effectively.

Consequently, MetaDocencia has focused mainly on the 3-hour workshop ”Introduction to Online Teaching Essentials.” This hands-on workshop builds on open educational resources to teach how to run synchronous events. It includes practical, evidence-based tips for delivering an engaging online workshop, class, tutorial, panel, or another event type. We learned these techniques mostly from The Carpentries and RStudio Education. In these workshops, we introduce our teaching philosophy (e.g., Code of Conduct, open licensing, community building, active teaching). Participants experience each of our tips and advice starting at pre-registration and staying in touch afterward through our Slack.

Since March 27th, 2020, we taught this workshop 41 times (yes, a lot more than my initial thoughts of “one, two, three”! 😍) to more than half of the 1,300 Spanish-speaking educators from 20 countries who registered their interest (as of January 2021). Despite unstable internet connections and many other staying-at-home circumstances, more than 90% of workshop attendants stayed engaged throughout the workshop and completed our end-of-workshop survey. Among these educators and researchers, there are bioinformaticians, biologists, school teachers and professors.

Ana Julia Velez Rueda, a bioinformatician who is also a part of the leadership team of the First Congress of Women in Bioinformatics and Data Science Latin America. She attended one of our first workshops, recommends MetaDocencia in this tweet.

Community stewardship and outreach

MetaDocencia also fosters a community through a 100% Spanish-speaking Slack workspace, where everyone is welcome and must follow our Code of Conduct. It currently hosts almost 400 members encouraged to share material, resources, and experiences. In MetaDocencia, we believe that the best support for teaching during this pandemic comes from others who also experienced teaching online during these challenging times. We are also active tweeps and asynchronous content creators.

In 2020, we also presented MetaDocencia in Spanish and English in over a dozen communities and events. We spearheaded the first R-Ladies Global event in Spanish, taught at LatinR Conference, and presented our experience in different formats at Open Life Science, Carpentry Con, Open Education Conference, IEEE International Conference on Imaging Processing, PyCon Argentina, and Open Source Community Call, among several other events related to Open Science and Open Education. We also collaborated with PyLadies El Alto (Bolivia) and nedear.la.

Everything MetaDocencia achieved in 2020 is detailed in our bilingual end-of-year report.

Team effort

From my initial WhatsApp audios in March 2020, MetaDocencia has come a long, long way. Since its very inception, MetaDocencia was not a one-woman effort. Indeed, all MetaDocencia´s accomplishments took the deeds of a fast-growing group of volunteers with experience in teaching technical skills, delivering online classes, and working remotely, locally, regionally, and globally. Our team is geographically-spread, including eleven collaborators in Argentina, France, and the United Kingdom. In Argentina, we make MetaDocencia from six different cities (i.e., Buenos Aires, Rosario, Resistencia, Corrientes, Balcarce, and La Pampa). We are Carpentries-certified instructors and instructor trainers, RStudio certified instructors or regionally-knowledgeable accessibility experts. An international advisory team of education experts also guides us in our vision of thinking globally while acting locally.

All of our activities at MetaDocencia are free, open, and executed through 100% volunteer work. Thus, the fellowship award offered to me by the Open Bioinformatics Foundation helped me pay for tools (such as Zoom and Calendly subscriptions and a desk microphone) were crucial for MetaDocencia´s infrastructure. As per the OBF board members, email discussions with me about repurposing my fellowship allowed them to improve their fellowship plans during the pandemic in 2020. Indeed, the OBF Event Fellowship was previously called OBF ‘Travel’ Fellowship.

More silver linings coming in 2021

I did not dare to envision in 2020 anything about 2021. However, 2021 looks bright for MetaDocencia as it will continue expanding its training activities to incorporate technical skills relevant to open and reproducible research computing, bioinformatics, and data science. With the support of other funding opportunities offered to MetaDocencia’s sustainability, we also seek to build capacity to further our reach to more under-served Latin American regions. We envision generating more accessible materials (e.g., free, in Spanish, welcoming, and safe for everyone) to lower as many barriers as possible for as many people as possible. To achieve this, in addition to pursuing further funding, we will work on furthering or creating partnerships with alike-spirited communities and organizations.

Would you like to join us on this beautiful and exciting ride? You (yes, you!) are welcome! Please check out ways to participate in MetaDocencia. You can also join our Slack workspace or follow us on Twitter.

Endlessly thankful

Endless thanks to the Open Bioinformatics Foundation for being part of the MetaDocencia journey and helping me realize my most impactful vision yet, while I have the chance to add my two cents to open bioinformatics education!✨🌈

H3ABionet’s Introduction to Bioinformatics Training (IBT) 2020: a report of the first iteration hosted in Cameroon

board@open-bio.org (Open Bioinformatics Foundation) — Thu, 24 Sep 2020 08:06:10 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Armando Blondel DJIYOU DJEUDA, a researcher from University of Douala, Cameroon, set up and host H3ABioNet‘s Introduction to Bioinformatics course (IBT), supported by this fellowship granted to him in application round 1 of 2020.

Due to the rich biodiversity of sub-Saharan African countries, bioinformatics and data management are crucial in helping to advance biomedical research. While many African countries are emerging in those specific fields, Cameroon and Central African countries in general, are still lagging behind. Based on this observation, in 2019, we created Bioinformatics and Biostatistics Hub (B2Hub) at the Biotechnology Center of the University of Yaounde I. Our aim through this platform is to promote bioinformatics and biostatistics among graduate students and young researchers from Central Africa.

After successfully organizing a first Bioinformatics workshop in 2019, this year I set up a virtual classroom for the H3ABioNet‘s Introduction to Bioinformatics course (IBT) at the Laboratory for Public Health Research Biotechnologies, Biotechnology Center, University of Yaounde I. I decided to host this event because no other host was selected in Cameroon (even in Central Africa) last year and as a result, I and most likely many other interested Central African candidates were unable to attend this course.

The workshop ran from May to August 2020 (see full curriculum). In this blog post, I have provided a monthly summary of how this workshop was conducted. I have also provided the demographic distribution of our attendees, their learning process, personal and COVID-19 related challenges experienced by them, and the overall impact of this event.

Training Format

The training was carried out using a distance-based learning model where classrooms were set up at different sites (a total of 47 sites with more than 1000 participants this year) and linked to the trainer via Zoom conferencing software during biweekly contact sessions. The trainers used a combination of theoretical and practical sessions for participants to gain practical experience in using various tools and resources. Initially, the course was supposed to run from 10:30 am to 2:30 pm every Tuesday and Thursday for 3 months (12th May 2020 to the 27th August 2020) at the Biotechnology Center, University of Yaounde I, Cameroon. However, due to the current Covid-19 pandemic, it was no longer possible to have contact sessions and the training was then shifted entirely online. In our classroom, we decided to keep in contact with our participants through online meetings every week and we created a WhatsApp group to allow participants to ask questions directly to our teaching assistants and exchange each other.

As a consequence, the course was highly demanding particularly in terms of internet connection and other basic equipment to conduct online meetings (such as webcam, headsets, small hardware needs, or a TV screen for practicals), especially in our context where it is not yet widely accessible. Thanks to the support of the Open Bioinformatics Foundation (OBF) through the OBF (travel) fellowship, I was able to get those equipment and successfully host our first IBT course.

May: Introduction to Bioinformatics Resources

We started our journey in May with a short introduction about Bioinformatics and its relevance in biomedical research, before moving to module 1: Introduction to databases and resources. In this module, we learned with Dr Shaun Aron how to navigate through biological databases and resources (like NCBI or EBI), perform basic protein and DNA analysis (sequence features, start sites, restrictions sites and so on), and conduct a more efficient search using PubMed.

June: Unix Command-line and Sequence Alignment Theory

After a promising first month, we covered two exciting modules in June. We started with an introductory workshop to the Linux/UNIX command-line, which was delivered by Dr. Amel Ghouila. Using an emulator called Cygwin (for Microsoft users) or Ubuntu (for MAC OS users), we got useful commands and tips to manipulate files and directories. Most of the participants were afraid because it was their first time working on Linux and its command-line environment. However, Dr. Ghouila was able to ease the learning process of beginners to command line computing. We then moved to the third module: Sequence alignment theory and application. In this module, after describing the most popular algorithms used for both global and local alignment, Dr. Jonathan Kayondo then taught us how to use BLAST and other pairwise sequence alignment tools (such as EMBOSS water and EMBOSS needle) to answer some biological questions.

July: Multiple Sequence Alignment and Genomics

In July, we deepened our knowledge and skills in sequence alignment, especially using multiple sequence alignment (MSA) tools and software. We learned the main characteristics of the most popular programs for building MSA and how to select the appropriate one to use. Indeed, we saw the differences between Cobalt, ClustalW, MUSCLE, and Tcoffee, and we used mainly online tools during our practical sessions. Besides, we had an initiation to Jalview, an exceptional multiple sequence alignment viewer, editor, and analysis tool. Dr. Ahmed M. Alzohairy showed us how to use Jalview for editing and analyzing MSAs produced with the most popular MSA programs we saw before.

We then continued during the same month with one of the most attractive modules in my opinion: Genomics. We started with a short overview of sequencing technologies and NGS and further proceeded with more complex topics such as genome annotation, comparative genomics, and human variation. During this module, we used the Ensembl genome browser, an amazing platform that allows access to publicly available reference genomic data such as genes (through tools and a visual interface), variation data, and annotation of your variants through the Variant Effect Predictor (VEP) tool. We closed this module by applying some basic Linux command-lines we learned in module 2, to visualize our data and retrieve some basic information from our sample sequences.

August: Molecular Evolution and Phylogenetics

Finally, we entered into our last month (August) with the last module: Molecular evolution and phylogenetics. This module, entirely taught by Dr. Anna Zhukova, was full of new skills, tools, and resources. Briefly, we were introduced to the components of a phylogenetic tree, discussed the basic principles of building a tree, different types of methods (Distance method, max parsimony, and Max likelihood), and how to interpret a phylogenetic tree. During practical sessions, we build our trees using both an online tool ( NGPhylogeny) and a downloadable software tool ( Seaview). We also used iTOL for tree visualization and manipulation tools and SMS for the selection of the best evolutionary model. We end up training with tree dating and phylogeography. During this session, we used TempEst, a downloadable software tool to check for temporal signals in the tree, LSD/LSD2, an online tree dating and rooting tool, and PastML for ancestral character reconstruction.

Demographic Distribution of Workshop Attendees

A total of 44 participants were selected in our classroom (41% were female), mainly coming from Cameroon. We also enrolled 3 participants coming from neighboring countries, especially Chad. They were mostly MSc and PhD students (87.5%) but also post-doc or young researchers (10%). At the end of the training, we build a post-training evaluation form using a Google forms questionnaire to obtain feedback from participants. The majority (82%) of our participants found the information and/or skills gained during this training highly relevant and useful in their daily activities, 86% of them were satisfied with the course design and methodology and will therefore highly recommend this training course to their classmates and/or colleagues. The dark point of our training was the low completion rate.

Indeed, only 15 participants out of 44 have completed the entire training and obtained a certificate. The most evocated reason among those who did not complete the course was the lack of internet connection at home to complete their assignments and they had not enough time to complete the training. However, even those who did not complete the training admitted having improved their bioinformatics skills and will be happy to complete the training during the next edition as long as we maintain contact sessions as initially planned.

Positive Feedback

I would also like to end up by sharing with you some general comments and appreciation by our participants:

“ This training was as I expected. This allowed me to use many tools and computer software to analyze and annotate different types of biological data as well as to retrieve information from databases and more… This gave me the level I needed to start my own analyzes related to my PhD research.” Brice Fonkou NATCHEMA SOH, PhD candidate, Faculty of Sciences, University of Yaoundé I, Cameroon.

“ The training was great and understandable for a beginner like me. Haven’t done that before, it was really challenging but finally relevant.” Nelly Ornelle ONANA ATEBA, PhD candidate, Faculty of Sciences, University of Yaoundé I, Cameroon.

“ It was a good experience. I loved being part of it. I will do it again if the opportunity comes to me.” Pacome Valery TCHUENKAM KOM, PhD candidate at the Dschang School of science and technology, University of Dschang, Cameroon.

“ The course was very enlightening and instructive, with great insights that will definitely be helpful in my current and future research avenues.” Willy Leroi TOGNA PABO, PhD candidate at the University of Buea, Cameroon.

To conclude, I would like to acknowledge the OBF for providing a fellowship to host an IBT classroom here in Cameroon. Thanks to this fellowship, we will now be able to offer an Introduction to Bioinformatics course to interested students and young graduates every year. This is a great step in the process of expanding bioinformatics skills and knowledge in an underrepresented region like Central Africa. Encouraged by the success of this year’s workshop, we are now considering hosting intermediate courses and building an open learning circle in our classroom. Feel free to get in touch if you would like to stay updated on this activity (email: armando_djiyou@yahoo.fr).

Smart computational imaging: a report from CLEO 2020

board@open-bio.org (Open Bioinformatics Foundation) — Tue, 25 Aug 2020 12:23:51 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Pengfei Fan, a researcher from Queen Mary University of London, was supported to participate in CLEO 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information here.

During the last two decades, we are witnessing a fascinating growth of computational imaging (CI) methods, e.g. tomography, compressive sensing and 3D/super-resolved/lensless microscopy, and artificial intelligence (AI) algorithms, mainly machine learning and deep learning, both from the theoretical (mathematical) and practical (experimental) point of view. New computational capabilities in terms of, e.g., big data, large scale optimisation, neural networks and highly parallel computing, are facilitating further improvements in numerically enhanced imaging surpassing the limitations imposed by ‘classical’ all-optical information processing systems. It is joyful to observe how CI and AI merge to innovatively address challenging tasks fuelled by wide-spreading applications in 3D imaging, biomedicine, microscopy and general physics of light propagation in scattering media, to name just a few. When designing a computational imaging technique, one needs to originally link the applicable data acquisition scheme with the capable image reconstruction algorithm, often aided by learning-based frameworks employed not only for image classification and interpretation but also for image formation and final outcome restoration. As the AI stimulatory development continues to flourish, open-source tools and software, especially deep learning framework and platform, have become a key ingredient of modern science. Hundreds of software packages, libraries, and applications have become essential tools.

We count on open-source software and tools in almost every research project, and it is also our responsibility to maintain and develop them. I have been engaging in a research project on deep learning for optical imaging and sensing, and our group at Queen Mary University of London are developing a robust ultrathin multimode fibre based endoscope. Progress in bioinformatics relies on new techniques for investigating the complex dynamics of biological systems. This research theme will develop the crucial role for Data Science and Artificial Intelligence in answering many fundamental questions in genomics and biology regarding the structure and function of genomes, the molecular interplay within cells and organs, the role, shape and functions of proteins as well as advancing imaging techniques.

An All-virtual Presentation of CLEO 2020 Technical Conference (Screenshot from the event, shared with permission)

CLEO is the world’s premier international forum to learn about innovative advances, research and new technologies from the optical science industry. Biomedical imaging and sensing is always an essential part of CLEO every year. The CLEO 2020 Technical Conference was held as scheduled in a first-ever, all-virtual format. The conference reached almost 20,000 registrants from 75 countries. By the end of the conference, 33,322 minutes of programming was presented. 248 Technical, Poster and Dynamic ePoster Sessions equated to more than 2,000 scientific presentations — all delivered in a combination of live and pre-recorded sessions and demonstrating a wide breadth of advancements and discoveries. The session recordings are now available on the conference website for individuals who registered for CLEO.

The first day of the conference started with an exciting symposium on Integrated Photonics for Neural Networks and Deep Learning, which was presided by Ozdal Boyraz from University of California Irvine. After the symposium, participants started travelling to different virtual ‘rooms’ to attend their favourite sessions. I presented our current research results at Fiber Based Imaging session, and our software, code and datasets have been published and were highlighted again. We were happy to share the datasets at the conference to catalyse the impact of data science and AI across the world. Specifically, these interesting datasets could be made the focus of a data study event or an impactful long-term project. As data owners, we have been given an opportunity and support to form a data science and bioinformatics community around our data and kick-start interdisciplinary or translational project collaborations.

The second day of the conference was kicked off with ‘Meet the OSA Editors’ talk, which was followed by two content-rich plenary sessions. The first one is on Intelligent Optical Synthesizer by Professor Kaoru Minoshima from University of Electro-Communications. Another is on Silicon Photonics by John Bowers, Director of the Institute for Energy Efficiency and Professor, University of California Santa Barbara. On the third day, there was also one plenary session on Advanced Resources for Optical Quantum Information Processing by Paul Kwiat from University of Illinois at Urbana-Champaign. I also participated in one Special Symposium on Artificial Intelligence for Photonics Imaging and Sensing, where Lei Tian, from Boston University, gave an invited talk about Deep learning-based computational biomedical microscopy with uncertainty quantification. On the fourth day and fifth day, I went through the fantastic Joint Poster Sessions: Micro- and Nano-Photonic Devices, and Photonic Innovations for Biological Sciences respectively.

To conclude, I would like to thank the OBF for providing me with the OBF Event Fellowship to cover the presentation fee to participate in CLEO 2020. This fellowship was an excellent opportunity to connect with open source and open science enthusiasts, and I firmly believe that this community will ideally promote open-source software development and advocate diversify in the years to come.

Call for applications for OBF Event Fellowship, Round 2 of 2020

board@open-bio.org (Open Bioinformatics Foundation) — Sat, 22 Aug 2020 15:46:50 +0000

We are glad to announce that the call for applications for the OBF Event Fellowship is now open. The deadline for this round is 1 October 2020. Applications should be submitted via this Google Form.

Renaming from “OBF Travel Fellowship” to “OBF Event Fellowship”

One of the goals of the OBF fellowship is to increase the participation of members from traditionally underrepresented groups at events or communities that promote Open Source software development and/or open science practices in the biological sciences. Since so many scientific meetings have been or are now run online, and we wish to explicitly support remote participation for this year, we are renaming ‘OBF Travel Fellowship’ to ‘OBF Event Fellowship’.

The OBF Event fellowship now supports participation in virtual events. Image reference: The Turing Way Community, & Scriberia. http://doi.org/10.5281/zenodo.3695300

This year, the COVID-19 pandemic has compelled research communities to move all in-person meetings to online. Although this situation has limited our ability to freely travel and meet each other in person, we have seen more diverse participants than ever attend and benefit from scientific conferences and training events. Financial burden, visa issues, and general lack of equitable support prevent many of our community members from participating in conferences that often take place far from their home countries. Therefore, virtual events have proven to be more accessible by allowing researchers to attend conferences for a small fee or for free, listen and learn from the experts from their fields, share their work with others and represent their communities. Taking this aspect into account, OBF will continue to offer OBF Event Fellowships for our community members to attend both in-person events and virtual events after the COVID-19 pandemic is over.

Inviting applications to attend virtual events

For the OBF Event Fellowship Round 2 of 2020, we are inviting applications from candidates who are seeking financial support to attend virtual events. At the time of launching this call, we don’t foresee any scientific event taking place in person in 2020 or the first half of 2021. We encourage our community members to follow the guidelines provided by WHO and as recommended by their local authorities, and plan their participation in online scientific events accordingly.

The selected awardees can use the OBF Event Fellowship to cover conference registration fees and the costs of small hardware (such as a microphone, speaker, and webcam), childcare for the duration of the event, and other supporting materials.

Reimbursement for expenses incurred by remote participation will be evaluated on a case-by-case basis. For example, we are aware that due to the load-shedding issues in many developing countries, our applicants might need to pay for the fuel for a generator to keep their electricity running for the duration of the event. Similarly, the cost of high-speed internet may vary across countries and may also be requested by applicants from some developing countries.

More details regarding the fellowship application, review, and reimbursement can be found on GitHub (current draft in pull request 79 on OBF’s GitHub repository).

Since we are in the process of finalizing the guidelines for this fellowship, we invite feedback and suggestions on the draft on GitHub from our community members to help us make the OBF Event Fellowship truly beneficial. For additional information, please contact OBF board members by emailing board@open-bio.org.

Getting introduced to Bioinformatics and Open Science through BCC 2020

board@open-bio.org (Open Bioinformatics Foundation) — Wed, 19 Aug 2020 18:56:33 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Gigi Kenneth, a biochemistry undergrad and a bioinformatics enthusiast from Nigeria, was supported to participate in Bioinformatics Community Conference 2020 by this fellowship granted to her in the application round-1 of 2020. Find more information here.

I’m a biochemistry undergraduate, in my final year from the University of Port Harcourt, Nigeria. I started learning about artificial intelligence and machine learning last year (2019), which I found really interesting and was really amazed by its applications in various fields. I found myself wondering about how these related to my graduate program, so I did some digging and was awed by the incredible work being done in this field.

A couple of months into my tech journey, I realized there are several buzz words in the computational field that I am not completely aware of. One of them that stood out the most was Open Source. I did some googling and barely understood what I read and hoped that I would learn about it along the way. Bioinformatics was another new word I came across a couple of times. I must admit that it intrigued me as I went through the list of organizations in Google Summer of Code (GSoC 2020), several of which had listed interesting bioinformatics projects.

Bioinformatics Community Conference (BCC) 2020 opened my eyes to the amazing ongoing work in both Bioinformatics and Open Source, and I’m really grateful that I got to be a part of this conference through the OBF Event Fellowship.

When I found out my application got accepted and that my registration fee for BCC 2020’s virtual conference had been waived, I happily signed up for a lot of sessions. I attended the pre-conference sessions about Nextflow, Intermine, Open Life Science and Galaxy. I missed out on the sessions on introduction to machine learning but it was interesting going through the shared notes that were shared with everyone. The session I enjoyed the most was about handling biological data using Python, Jupyter and Intermine that Yo Yehudi hosted. I’ve since taken a deeper look into Intermine, explored HumanMine a bit more, and shared what I was able to grasp with some friends. It was a lot of fun trying to get the hang of the online platforms like Shed(for schedule), Discord(for chat) and Remo(for virtual participation) as the conference progressed.

There were several interesting talks during the conference about research and a variety of open source tools. It was also fun switching between the Galaxy and BOSC sessions (the two parallel community tracks) when topics got a little complicated in one of the sessions.

Abigail Cabunoc Mayes’ keynote was really amazing where she talked about understanding bias and discrimination in research data and code, and how to combat them in our work. Lincoln Stein’s keynote about how open source has changed the world was also really insightful and I got to understand a bit about the processes involved in the research. The keynote about how open minds bring open collaborations by Prashanth Suravajhala was also very interesting.

In between sessions, I enjoyed joining different virtual tables and going to different virtual floors on Remo where I got to interact with really cool people during the conference.

I learned a lot, and also realized that there’s a lot more out there that I don’t know. I’m encouraged to continue pursuing my goals in bioinformatics and soon enough, be able to contribute to open source as well.

A Software Engineer's Experience at BCC 2020

board@open-bio.org (Open Bioinformatics Foundation) — Sun, 16 Aug 2020 11:55:53 +0000

The Open Bioinformatics Foundation (OBF) Event Fellowship program aims to promote diverse participation at events promoting open source bioinformatics software development and open science practices in the biological research community. Edidiong Etuk (Eddie), an open-source lover and a software engineer from Nigeria, was supported to take part in Bioinformatics Open Source Conference 2020 by this fellowship granted to him in the application round-1 of 2020. Find more information here.

TL;DR This post is about my experience at Bioinformatics Community Conference 2020.

Before attending the Bioinformatics Community Conference (BCC) 2020, I had zero experience with Bioinformatics. But, after the conference, I am more confident in my ability to tackle bioinformatics-related tasks, challenges and discussions. I enjoyed every moment of BCC2020 virtual conference, hung out with a lot of cool folks through the Remo conference platform, and got introduced to new concepts in bioinformatics through workshops, keynotes, short talks, poster sessions and community interactions. In this post, I am summarising my experiences and lessons learned from this conference.

BCC Pre-Conference Workshops

I registered for two workshops: Dockstore Fundamentals: Introduction to Docker and Descriptors for Reproducible Analysis and I must say I found them easy to understand as a beginner. I had an idea of what Docker was but the tutors made working with Docker so easy. They also switched up and explained Descriptors (focus was on Workflow Description Language). It was a good introduction to Dockstore.

Next, I attended Reproducible Analysis in the Cloud with Dockstore and Terra, where I got introduced to Terra, Anvil, and learned more about Dockstore. The ability to access data, run analysis, and use the cloud all from Terra while fostering collaboration is what this training was about. All experiments I toyed with, worked and results could be seen easily and tracking bugs or experiment failure was seamless.

One regret I had during the workshops is the number of sessions I missed. All the sessions were so interesting that I wished I could attend all training and workshops. All the training materials and notes were made available, so I guess I’d have enough resources to start with when learning them on my own.

Main Conference

I attended the West sessions of the 3-day main conference as this favored my timezone. As a volunteer for BOSC, I spent a lot of my time in the BOSC building (yes a virtual building). There were several interesting talks during the conference about research and a variety of open-source tools which I can’t point to, but some of those I describe below.

Day 1

Day 1 started with a keynote from Lincoln Stein who showed us how Open-Source has improved the biomedical world.

The presentations were all short and precise and though some were very technical, I got a thing or two from them. The most memorable presentation was Streamlining accessibility and computability of large-scale genomic datasets with the NHGRI genome data science Analysis, Visualization, and Informatics Lab-Space (ANVIL).

It was very relatable and I applaud the creativity behind the presentation, bravo Michael!!

Poster sessions were cool and were held in a different virtual building from Galaxy and BOSC tracks. This was a good opportunity for me to see innovative work by the researchers in various bioinformatics communities. I also had a chance to chat with the representatives of the sponsors at the sponsor tables.

Day 2

On Day 2, Prashanth N Suravajhala gave the keynote on the importance of mentoring students. It was sad to hear that the building he was delivering his keynote from had some emergency situation during the presentation, but kudos to him for delivering an excellent keynote.

Another memorable session was Building open source communities and empowering new contributors by Yo Yehudi. This talk was important as without Yo’s mentorship from Outreachy, I wouldn’t be here (Thanks Yo!). Although that session clashed with a Galaxy session, luckily the recordings were made available so I got to watch The cloud-native Galaxy: Galaxy on Kubernetes. I’m interested in everything Kubernetes so the session, of course, interested me.

Day 3

Day 3 hit closer to home due to my work at Popper, everything about workflow management seemed understandable. Although I gotta add, there are a lot of workflow engines out there for reproducibility in research.

It would make a lot of sense if they all came together to do a conference to ensure we’re all going in the same direction and not competing with each other. Of course, there were a lot of interesting posters which I got to check out.

Welcoming Community

Everyone at BCC 2020 was very welcoming, Birds of a Feather session at the virtual-bar was a great addition to the event. I had my drink with me, and of course, we all drank responsibly (lol!). I enjoyed switching tables and going to different floors on Remo where I got to interact with warm and friendly people during the conference.

The Bioinformatics community is the most welcoming out there! Special shout out to everyone who made me feel welcome, Michael R. Crusoe, Dave Clements, Emmy Tsang (who pronounced my name very well), Nomi Harris, and others! You were all fun to hang with and I hope next year I can meet y’all in person!

BCC exemplified diversity in tech and I loved it. BOSC Happy Hour West was thrilling as we had 18 people on the stage (please don’t try this on Remo! 😬).

Next Steps

Due to my interest in Bioinformatics, I am working to dockerize DoBlastzChainNet and popperize it to make it reproducible. This is going great and I’ll appreciate any help.

Thanks to OBF for this amazing opportunity! Till next time!

Event-Fellowship on Open Bioinformatics Foundation

Undergraduate to Best Poster Awardee: My experience at BITS2026 and BioHackathon

The BioHackathon

The Conference

The Poster Session: The turning point

Not only Science

Conclusion: A message to other Undergraduate students

Call for the second 2026 round of the OBF Event Fellowship & overview of the first round of 2026.

Call for the first 2026 round of the OBF Event Fellowship & overview of the awards made in 2025

Overview of the overall 2025 rounds of OBF Event Fellowship

Bridging Learning Gaps Through Open-Source Tools

Introduction

Poster Presentation

Final Thoughts

BioHackathon Europe 2025: BUSCO genes, lakeside hacking, and open workflows

A hackathon by the lake

Project #03: benchmarking BUSCO genes for phylogenomics

My role: testing and debugging

Community and mid‑week reporting

Take‑home messages

What comes next

Acknowledgements

Elixir BioHackathon Experience

My BioHackathon Experience: Contributing to Open Science in Proteomics

Why I Joined

My Contribution: Making Sense of Quality Metrics

What Open Source Contribution Feels Like

Beyond Technical Skills

Why This Matters

Want to Explore More?

BioHackathon Europe 2025: A Week full of Brainstorming, Coding & Collaboration

Background on the Hackathon

Brief information about my project

Social events

Learning experiences

2025 ESIIL Innovation Summit: Collaborative and Open Environmental Data Science in Boulder

Introduction

Acknowledgements

Call for the third 2025 round of the OBF Event Fellowship & overview of the second round of 2025

Overview of the Second 2025 round of the OBF Event Fellowship

ISMB/ECCB 2025: Liverpool, LLMs and Lessons in Open Science

The Journey to Liverpool

Navigating a Massive Conference

Posters, Serendipity and Collaboration

Lessons Learned and Reflections

Acknowledgements

Links and Resources to Open Science

ISMB 2025: A Week of Learning, Teaching, and Connecting in Liverpool

Day 1: Teaching and Kicking Things Off

Day 2–4: Talks, Posters, and Conversations

Exploring Liverpool

Final Thoughts

Call for the second 2025 round of the OBF Event Fellowship & overview of the first round of 2025

Overview of the First 2025 round of the OBF Event Fellowship

The 2025 International Statistical Genetics Workshop - a goldmine of open-source genetic analysis tools and tutorials

Call for the first 2025 round of the OBF Event Fellowship & overview of the last round of 2024

Overview of the third 2024 round of the OBF Event Fellowship

Jacqueline Wahura: experience at the Royal Entomological Society Conference 2024

Erin (Rin) Krichilsky: Leveraging Open Data to Address the Bee Biodiversity Crisis

Masturina Binti Md Mansor: My experience at the first APBJC2024 in Naha city, Okinawa, Japan

Discovering Okinawa at APBJC 2024: Tanakamol Mahawan's First Conference Back in Asia

Falling in Love with Okinawa

Building Quality Connections

Embracing Open Science and Representing Thailand

Exploring Open Science in Computational Virology: Li Chuin Chong's Journey at ECCB2024

Jacob González Isa: Bioinformatics, Spain and I

Call for the third 2024 round of the OBF Event Fellowship & overview of the second round.

With a little help from your friends! -Learning bioinformatics online.

Zehra Köksal: My unforgettable experience presenting accessible software to 1000 forensic experts

My Amazing BOSC 2024 Experience

Urszula Włodkowska: Building Brains in Canada

Call for the second round of OBF Event Fellowship 2024 & overview of the last round of 2023.

Open Data, Open Doors

A PhD student’s perspective on attending the 17th Annual International Biocuration Conference in Faridabad, India

Call for the first round of OBF Event Fellowship 2024 & overview of the last round of 2023

My Journey at the nf-core Hackathon and Nextflow Summit 2023: Coding and Community

Yvonne Walburga: Journeys across oceans

Call for the third round of OBF Event Fellowship 2023 & overview of the second 2023 round.

Michell Salcan: My Wonderful Experience at LANET 2023 in Cusco, Peru

Embracing Science and Culture: My Memorable Conference Experience at SMBE23 in Ferrara, Italy