ISMB CollaborationFest 2025 will be a collaborative work event at which participants work together to contribute code, documentation, training materials, and challenging analysis problems and use cases. If you are interested in learning and contributing in an intensely collaborative environment, then CollaborationFest is for you. Bring your own project ideas or come ready to collaborate with others on their projects!
BOSC has organized CollaborationFests (aka CoFests) every year before or after ISMB since 2010 (see, for example, the 2024 CoFest page.). This year, we are excited to hold CollaborationFest as part of ISMB/ECCB, opening it to all registered ISMB/ECCB participants. The organizers are affiliated with four different COSIs: BOSC, Bio-Ontologies and Knowledge Representation (BOKR), Function COSI, and 3DSIG.
Dates
Wednesday July 23 to Thursday July 24 (the last two days of ISMB/ECCB 2025).
How to sign up
Due to space constraints, participation in CollaborationFest is limited. To indicate your interest, register for ISMB/ECCB 2025 by June 20 and sign up for CollaborationFest as an “add-on” during the registration process. We will contact you by June 23 to gather additional information to help organize the event. Last-minute walk-ins may be possible if space allows.
Limited remote participation will be possible, but engagement opportunities will depend on the people and projects active on the day. A video feed from the room will be available, but joining will require you to be a registered (virtual or in-person) ISMB/ECCB participant.
CollaborationFest News and Activities
As we get closer to ISMB/ECCB 2025 and the CollaborationFest, we will add relevant news and activities here. Note that some of these activities are on dynamically updated Github pages, and will only be fully ready “the day of”, or shortly before.
1. Genomic Safe Harbor Sites in Zebrafish
This challenge invites participants to identify potential genomic safe harbor (GSH) sites in the zebrafish genome using an integrative omics approach.
https://github.com/parnaljoshi/gsh-zebrafish-hackathon
2. How much funding per protein?
Quantifying the financial investment in specific areas of biomedical research is challenging. While NIH funding is extensive, directly attributing grant dollars to individual proteins studied is non-trivial. Approximating the dollar amount of funding allocated to the proteins help us to:
- Assess funding distribution across different biological targets.
- Identify potentially under-funded or over-concentrated areas of protein research.
- Track the financial trajectory of research on specific proteins over time.
- Provide researchers and funding agencies with data about financial resource allocation at the protein level.
https://github.com/anphan0828/funding-per-protein-hackathon
3. Enhancing Protein Knowledge Curation using Gene Ontology Annotations and Large Language Models for Community Literature Submissions
Data-driven biomedical discovery depends on effective data curation - a time-consuming process that involves identifying relevant literature, extracting experimental knowledge, and validating information into structured formats suitable for databases like UniProt.
The emergence of generative AI and large language models (LLMs) presents new opportunities to assist human-driven data curation workflows. These technologies can support curators in searching ontologies and extracting knowledge from scientific literature, potentially streamlining the entire curation process.
Objective
Learn how to manually assign Gene Ontology terms or develop innovative approaches using LLM tools to enhance the curation workflow, enabling efficient and accurate extraction of experimental data from scientific literature.
https://github.com/anphan0828/ISMB_CollaborationFest_EBI
Code of Conduct
As part of ISMB/ECCB 2025, CollaborationFest 2025 is covered by the ISCB Code of Ethics and Professional Conduct.