WormBase-Caltech Weekly Calls
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November 4 2021
Migrating Paper Pipeline to Alliance
- Meeting abstracts
- Continuing to review what we have and standardize bibliographic info before we migrate
- QC checks highlight some older abstracts with little-to-no data - propose to invalidate these so we don't migrate poor quality paper data to the Alliance
- We can always respond to individual requests to add old meeting abstracts if they arise
November 11 2021
WS284 upload dates for Caltech
- When are files due for the Caltech group?
- WS284 upload-Better to upload before the holidays or in Jan 2022
- Wen will contact Paul D/Hinxton to find out when the WS284 models will be released
November 18 2021
Proposal for upgrading tanzendra/mangolassi computing resources
1. Move them to Chen. (done) monitor stability of network
Old hardware and out of support OS (Ubuntu 14.04)
2. Establish a development environment for Dockerizing services (curation OA, other web forms, postgres DB) (use Valerio's local server/desktop)
3. Establish a local file server for storage and download access (PDFs, dump files)
4. Run dockerized services from AWS
5. Continuous development and integration locally -> AWS
- Daniela contacted ZFIN and FlyBase. ZFIN does curate commercial antibodies only if found in publications. Waiting for FlyBase feedback (Sian out).
- TODO: Contact TAIR and see if they including commercial antibodies and if they charge companies (Daniela sent a message on slack). Tanya: We have not charged for placing the links but have strongly encouraged a corporate subscription for the two companies.
- This can be an Alliance project. Need to contact companies and see who is interested (need to have a price in mind for that).
- Can pilot text mining for commercial antibodies
- GeneCards charges for inclusion of commercial reagents on their website: "Companies that wish to provide deep links to their products (e.g. reagents, assays, antibodies, clones, etc) in the Services and other relevant sections of GeneCards, should contact firstname.lastname@example.org." From https://www.genecards.org/Guide/FAQ