WBConfCall 2020.06.04-Agenda and Minutes

Agenda

New Starter

Manuel Luypaert - EBI

Release updates

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

release notes

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.

Help Desk

Karen just started helpdesk, nothing outstanding - things dealt with by Faye