BOSC 2022 COFEST!
Status updates / Project reporting
July 2022
OBF Newsletter + blog post
GOAL
Assemble the post-BOSC issue of the OBF newsletter (which goes out through the bosc-announce mailing list) and a blog post
STATUS
NEED !!!
More BOSC participants to contribute your favorite moments/takeaways in the Google doc
NEXT STEPS
Flesh out newsletter and blog text based on group input
Project Proposer:
Geraldine Van der Auwera
Stakeholders (if any):
All of OBF/BOSC
Interested developers:
Everyone can contribute a short note calling out highlights of BOSC
Adding GA4GH TES on top of Arvados Crunch
Status: proof of concept able to start a container, but ran into problems collecting output. Peter is now in contact with Kyle Ellrott & ELIXIR experts about GA4GH TES
https://github.com/arvados/arvados-tes
https://dev.arvados.org/issues/19272
Goal: Implement a GA4GH TES endpoint on top of the Arvados Crunch compute system. Test with the S3 endpoint of Arvados Keep.
Possible users of this include:
Project Proposer:
Peter Amstutz
Stakeholders (if any):
GA4GH, workflow users, other workflow engines with a TES backed
Interested developers:
Michael R. Crusoe
Tazro Ohta
[Add your name here]
EDAM ontology, optionally also Bio.tools
Project Proposer:
Matúš Kalaš
Participants:
Matúš Kalaš
Tom Madden
Hervé Ménager
Bhavesh Patel
Slack: #2022-cofest-edam
NCBI Datasets, a new way to access genome data at NCBI
NCBI Datasets is a new resource for accessing genome sequence and metadata directly from NCBI. This data can be retrieved through our new web interfaces, command line tools and OPEN API. This resource has been built with the help of our users. We invite the BOSC community to try Datasets and give feedback.
Please join us to try out Datasets
Resources
Please contact me if there is a Datasets related project you want to explore!
Project Proposer:
Nuala O’Leary
olearyna@ncbi.nlm.nih.gov
Stakeholders:
Interested Participants:
FAIRshare, a Tool for Making Biomedical Research Data and Software FAIR
FAIRshare is an open-source and free cross-platform desktop software that combines intuitive user interface and automation for streamlining the process of making biomedical research data and software Findable, Accessible, Interoperable, and Reusable (FAIR). In our current phase of development, we have implemented a workflow for making biomedical research software FAIR according to the guidelines established by our team called the FAIR-BioRS guidelines. We are now working on implementing workflows for making infectious disease related research data (immunology, genomics, etc.) FAIR according to applicable guidelines.
Cofest outcomes: We got some great inputs from Michael Crusoe, Hervé Ménager, and Hilmar Lapp about improving the FAIR-BioRS guidelines. Michael has also submitted a PR to include recommendations for documenting CLIs in the FAIR-BioRS guidelines. Hilmar is providing suggestions for publishing the guidelines and we may collaborate on the manuscript. We will keep exchanging with them! Tazro Ohta tested FAIRshare with one of his software located on GitHub and provided very useful feedback as well. All in all, this was a wonderful opportunity for us to get our work in front of experts!
Resources
Project Proposer:
Bhavesh Patel (bpatel@calmi2.org),
Sanjay Soundarajan (ssoundarajan@calmi2.org)
Stakeholders:
Interested Participants:
Laura Gorrell (lgorrell@deloitte.com)
Tazro Ohta (t.ohta@dbcls.rois.ac.jp)
ElasticBLAST - Accelerating Alignments in the Cloud
ElasticBLAST makes it simpler to run BLAST on the cloud (AWS or GCP).
It is relatively new, and we’d like to make it more accessible and a good place for collaboration.
This is a good project both for python developers as well as non-coders.
We will have a Jupyter notebook that you can use to try out NCBI datasets, then use ElasticBLAST with the results of that work.
Topics:
We will be on-line Friday only., so don’t miss us.
Links:
Project Proposer:
Tom Madden
Stakeholders (if any):
Greg Boratyn
Interested Participants:
YOUR NAME HERE!
Contact with any questions
Email: tschlapp@broadinstitute.org
Slack: Same as above! Thomas Schlapp