BOSC 2021 COFEST!
Project Proposals
July 2021
What is this!?
This is CoFest! This is a celebration of innovation and collaboration open to all Bioinformatics Open Source Conference (BOSC) participants.
Come and sponsor an idea on a slide here.
Share what you plan to work on, learn something new, and maybe discover new friends (or at least people with the same interests).
As part of ISMB/ECCB, BOSC CoFest 2021 will be covered by the ISMB/ECCB Code of Conduct.
COPY THIS SLIDE! Project Title Goes Here
Put a brief description of your project here, including why you’re proposing it and why you think it’s valuable, fun, or otherwise awesome.
If you are looking for people with specific skills to join your team, call that out.
If your project benefits a particular lab or scientist or class of users, mention that as well!
Project Proposer:
Your name here
Stakeholders (if any):
House Lannister�Goonies Lab
Arrakis Sandworm
Interested developers:
Someone else!
Biopython
In previous CoFest meetings we’ve often had several regular Biopython contributors physically present which had let us have some in person discussions (e.g. flake8 styles) and help new people get involved.
Peter will only be available intermittently but has plenty of things on his mental to-do list, and might attempt one or two:
Project Proposer:
Peter Cock
Stakeholders (if any):
End users
Interested developers:
Brad Chapman
Spencer Bliven
Vimalkumar Velayudhan
Ian Simpson
Antoine Lain
ElasticBLAST - using the cloud to speed up science
ElasticBLAST is a cloud-based tool to perform BLAST searches faster. It is ideal if you have a large number (thousands or more) of queries to BLAST. Under the hood, it uses AWSBatch and docker on AWS and Kubernetes and docker on GCP.
We’re looking for all kinds of backgrounds and skill sets. This is a new project, and we need your feedback!
Possible Activities:
Read more at our blog:
NCBI Insights : Try out ElasticBLAST at the BOSC2021 CoFest!
Documentation: https://blast.ncbi.nlm.nih.gov/doc/elastic-blast/
GitHub: https://github.com/ncbi/elastic-blast
Poster Video: https://youtu.be/4DVNnwNE9k0
Interested? Please email us at elastic-blast-support@ncbi.nlm.nih.gov
Project Proposer:
Tom Madden
Stakeholders:
Christiam Camacho
Greg Boratyn
Victor Joukov
Interested developers:
Anshika Sah!
Anyone interested!
EDAM for open source communities
How can the EDAM ontology better help FOSS communities that already use it (e.g. CWL, Debian, Galaxy, Tripal, Jalview, ...), and ones that could potentially benefit from using it?
Project proposers:
Matúš Kalaš
Hervé Ménager
Hager Eldakroury
Melissa Black
Interested collaborators:
<your name here 😊>
Junjun Zhang - Can EDAM help WFPM?
Spencer Bliven - Can EDAM help data management & archiving?
This is a project also for TOTAL NEWCOMERS & TOTAL NON-CODERS!!!
👩🏽🔬 👾 🤹🏽♀️ 🦑 🛀🏽
Special thanks to Ivan Kuzmin!
OpenWDL v1.1 to CWL v1.2 conversion
For the current round of the Outreachy internship program, Dinithi Wickramaratne has been creating a dedicated converter that takes OpenWDL 1.1 format documents and produces CWL v1.2 documents at https://github.com/common-workflow-lab/wdl-cwl-translator
The codebase is quite new, so please be mindful of the open issues. We haven’t made an initial release yet; consider this to be pre-Alpha :-)
Those with experience with CWL, WDL, and/or Python are very welcome to participate. If you don’t have experience with those, but enjoy reading technical specifications, then you also might enjoy this project!
Project Proposer:
Dinithi Wickramaratne
Stakeholders (if any):
Michael R. Crusoe
Interested developers:
Hervé Ménager
WFPM - WorkFlow Package Manager
To our knowledge, WFPM is the first full-featured package manager for workflow development. It works much like package management tools in general-purpose languages, such as, NPM, the package manager for JavaScript
WFPM CLI offers a wide range of assistance to the workflow development lifecycle, such as, code template generation, automated continuous integration testing and releasing. Workflow packages developed by WFPM CLI are guaranteed to be reproducible, portable, reusable and shareable.
WFPM is a new project, it’s built out from real world experience to address real world needs. We’d love to hear your feedback. If you are interested in contributing we are even happier.
Possible activities:
Read the blog for the story behind WFPM:
Build workflows collaboratively using reusable and shareable packages
Documentation: https://wfpm.readthedocs.io/
GitHub: https://github.com/icgc-argo/wfpm
BOSC CoFest Slack channel: #2021-cofest-wfpm
BOSC 2021 talk video: https://www.youtube.com/watch?v=kOC6SH0GFPQ
Project Proposer:
Junjun Zhang
Stakeholders:
ICGC ARGO
OICR
Interested developers:
<anyone interested, please add yourself>
Adelaide Rhodes
Scaling assembly and pangenome graphs
Update nf-core/pangenome workflow to DSL2 and bring in latest from pggb
Migrate/refactor graph format support from multiple libraries into a single project
�Other ideas? Please suggest in comments or add additional slide(s)
Project Proposer:
Michael Heuer
Stakeholders (if any):
Human Pangenome Reference Consortium ?
Interested developers:
Ravneet Bhuller
Matus Kalas - add specs to EDAM�<your name here 😊>
I need a team!
A space for anyone who hasn’t joined a team, or doesn’t know what team to join. Please add your name here if you need a team, and team members feel free to reach out.
Project Proposer:
Stakeholders (if any):
Jamboree teams needing members
Interested developers:
Contact with any questions
Email: tschlapp@broadinstitute.org
Slack: Same as above! Thomas Schlapp