WBConfCall 2020.06.04-Agenda and Minutes
Manuel Luypaert - EBI
WS277 up on EBI staging now - files on staging-FTP can be treated as final.
Datomic release next week
WS278 ~1 month after datomic release - July 10 Citaace upload to Hinxton
Hinxton look into release script, could use some updating every decade.
Hinxton: script is called "mailpaulsternberg" and is part of the build
Hinxton will be rationalizing the build and deal with historical stuff
| Cold Spring Harbor | |------------------------|---------+---------+---------+---------+---------+ | LongText | 663417 | 663717 | 301 | 1 | 300 | | Movie | 1539 | 1539 | 0 | 0 | 0 | | Structure_data | 15237 | 15237 | 0 | 0 | 0 | +------------------------+---------+---------+---------+---------+---------+ .... -- The Wellcome Sanger Institute is operated by Genome Research Limited, a charity registered in England with number 1021457 and a company registered in England with number 2742969, whose registered office is 215 Euston Road, London, NW1 2BE."
Place for tools for users
Big question: is it worthwhile to spent time and effort on creating one-off user tools using python/jupyter notebooks and google colab?
Raymond: built gene-mapping tool using python Jupyter notebook and google colab. These are one-off tools made based on user help. This can be thought of as a course--to teach them about bioinformatics. Advantage being users can spin up own notebook and run the code themselves, we wouldn't need to provide notebook space ourselves. Requires Google account.
Scott: the concern is persistent support for storing access to source code. User did not respond.
Sibyl: we could store access to code locally
Todd: can we extend the website to provide this service without having to tinker with the website code itself
Raymond: might not be as good, as they might not be able to adjust things for themselves and start requesting more help. We want them to adapt the tool for themselves
Wen: worth talking with the user to find out how it is working, if they know how to use it, etc. Can they actually use it, not everyone knows python or have a google account
Raymond: will need google account
Paul/Raymond: This is in between offering a tool that we maintain or doing it ourselves to answer a question.
Paul: write the notebook, write it up as a microPublication to publicize it.
Lincoln: loves the idea - encouraging people to write micropublications to publicize them. is there a way to link the notebook or micropub to the gene page. Perhaps index the notebooks
Sibyl: same idea - difficult to link notebooks to pages. Already making index pages based on Raymond's request. People are already starting to write in indexed notebooks. Worth following up with user
Raymond: maybe start with WormMine as there is a list of genes
Paulo: if there is a query you have we could precompute the query and add the index.
Paul: it's good, a good light-weight solution to help people with bioinformatics.