Bosc

We are seeking a diverse list of potential BOSC keynote speakers. We invite you, our community, to nominate people you think would be appropriate (and at least somewhat likely to accept the invitation – for example, it is extremely unlikely that we would get a ‘yes’ from a recent Nobel Laureate). Please submit your nominations here (as many as you like; you can fill out the form more than once to submit additional suggestions) by the end of the day on Wednesday 2024-01-17.

Dear Biopythoneers,

Our first release of 2024 is now out, sooner than planned as this is purely to revert the removal of the .strand, .ref, and .ref_db attributes of the SeqFeature which was done in Biopython 1.82 without a deprecation period. They are again aliases for .location.strand etc, but now trigger deprecation warnings. See our deprecation policy. We apologize for any inconvenience, and thank you to those reporting this.

This release of Biopython supports Python 3.8, 3.9, 3.10, 3.11 and 3.12. It has also been tested on PyPy3.9 v7.3.13. Python 3.8 is approaching end of life, our support for it is now deprecated.

CollaborationFest, CoFest for short, is a collaborative work event that has been held each of the past 13 years as a satellite event of BOSC. At these free events, held right before or after BOSC, participants  gather in small groups to exchange ideas and work together on projects including but not limited to hacking. Participants were encouraged to submit their project ideas in advance to facilitate collaboration.

CoFest 2023 took place during the two days just before BOSC, which was part of ISMB/ECCB 2023 in Lyon and online. It was the first in-person edition after several online-only CoFests, due to Covid pandemics. It was hosted by Jérémy Just at the nearby École Normale Supérieure de Lyon, which provided space and infrastructure, with funding from Complex Systems Institute for lunches and coffee breaks. Free virtual machines were made available by the French Institute for Bioinformatics and the Pôle scientifique de modélisation numérique.

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.

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.

Date and Time: Tuesday, March 14, 11am EDT/ 15:00 (not 16:00!) UTC Location: Online webinar hosted by ISCB and free to the public. (Video now available at https://youtu.be/M2vAotWKd_Q)  Speaker: Hannah Wei, co-founder and technologist at the Patient-Led Research Collaborative Topic: Re-Thinking the Patient’s Role in a Learning Health System: Lessons from the Patient-Led Research Collaborative

The ISCB, which runs the annual ISMB conference, is offering a series of ISCBacademy webinars hosted by the Communities of Special Interest (COSIs), which include BOSC/OBF. These webinars are now open to the public; you’ll just need to create an ISCB Nucleus account to register for the webinar.

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We asked the community to nominate potential BOSC keynote speakers, and we were pleased with all the great suggestions! Now it’s time for the next phase of our process: we’re giving the community a chance to let us know if there is anything that makes any of the nominated individuals NOT appropriate as BOSC keynote speakers.

Our invited speaker process and rubric gives examples of some possible reasons for exclusion. If you have concerns about any of the people on our list, please let us know (with as much specificity as you feel comfortable providing) via this anonymous form no later than February 16, 2023.

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.

We are excited to announce that BOSC and Bio-Ontologies will join forces for part of a day at ISMB 2022. The joint session will include talks chosen from abstracts submitted to BOSC or Bio-Ontologies, plus a keynote speaker who is well known in both the ontology and open science communities!

BOSC and Bio-Ontologies are two of the longest-running COSIs (Communities of Special Interest) at ISMB: BOSC started in 2000 and Bio-Ontologies in 1998. Bio-Ontologies focuses on the FAIR development and application of ontologies and other Linked Open Data resources and the organization and dissemination of knowledge in biomedicine and the life sciences; BOSC covers the full spectrum of open source, open science, open data and open standards in the life sciences.

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 announced today that the conference will be virtual. This news may be disappointing to some, but for others it offers an opportunity to participate in a conference that they would not have been able to travel to attend.