diff options
| -rw-r--r-- | tasks/alexm.gmi | 11 | ||||
| -rw-r--r-- | tasks/bonfacem.gmi | 26 | ||||
| -rw-r--r-- | tasks/felixl.gmi | 12 | ||||
| -rw-r--r-- | tasks/fredm.gmi | 4 |
4 files changed, 36 insertions, 17 deletions
diff --git a/tasks/alexm.gmi b/tasks/alexm.gmi index a66de6b..3a4207b 100644 --- a/tasks/alexm.gmi +++ b/tasks/alexm.gmi @@ -18,13 +18,16 @@ You can refine the search by constraining the checks some more, e.g. to get high ## This week -* [ ] Rqtl2 - BXD output work on CD -* [ ] Rqtl2 - ITP output - 3K individuals - family file -* [ ] Start application +* [X] Rqtl2 - BXD output work on CD +* [X] Rqtl2 - ITP output - 3K individuals - family file +* [ ] Minor refactorings +* [ ] Accelerate Xapian functionality +* [ ] Start application - Pwani +* [+] Create terminal output for external processes on *PRODUCTION* (Rqtl1, Rqtl2, GEMMA, pair-scan are done --- WGCNA as a pilot, with @bonfacem and @pjotrp) ## Next week(s) -* [+] Create terminal output for external processes (Rqtl1, Rqtl2, pair-scan are done --- WGCNA as a pilot, with @bonfacem and @pjotrp) +* [ ] GNQA says there are no results, but has them ## Done diff --git a/tasks/bonfacem.gmi b/tasks/bonfacem.gmi index 5445eeb..5c65543 100644 --- a/tasks/bonfacem.gmi +++ b/tasks/bonfacem.gmi @@ -10,20 +10,25 @@ ### This week -* [ ] Describe Generif access for Rob in an email +* [ ] Describe Generif/wikidata access for Rob in an email with test account on CD +* 1. Send email to Rob +* 2. Work on production * [ ] Migrate fahamuai RAG to VPS and switch tokens to GGI OpenAI account -* 1. running AI server using (our) VPS and our tokens -* 2. read the code base -* 3. assess porting it to Guix (don't do any work) -* [ ] Add lmdb output hashes with index and export LMDB_DATA_DIRECTORY -* [ ] Share small database with @pjotrp and @felixl +* 1. Running AI server using (our) VPS and our tokens +* 2. Read the code base +* 3. Try ingestion and prompt (REST API) +* 4. Backup state from production Elixir +* 5. Assess porting it to Guix (don't do any work) - minimum version Elixir +* [ ] xapian search, add dataset size keys, as well as GN accession id, trait id, and date/year +* - Improve xapian markdown docs to show all used fields/keys with examples +* - genewiki search (link in table? check with Rob) +* - base line with GN1 search - add tests +* [ ] With Alex get rqtl2 demo going in CD (for BXD) ### Later * [ ] Sample/individual/strain/genometype counts for PublishData only - ProbeSetData? https://github.com/genenetwork/genenetwork2/blob/testing/scripts/sample_count.py - mirror in RDF and use global search * - search for all traits that have more than X samples -* [ ] xapian search, add dataset size keys, as well as GN accession id, trait id, and date -* - Improve xapian markdown docs to show all used fields/keys with examples * [+] Use aider - give a presentation in the coming weeks * [ ] Add case attributes to RDF and share with Felix (depends on @felixl) @@ -64,3 +69,8 @@ Currently closed issues are: * [X] Indexing generif data / Improve Local Search * [X] lmdb publishdata output and share with Pjotr and Johannes + +## Done + +* [X] Add lmdb output hashes with index and export LMDB_DATA_DIRECTORY +* [X] Share small database with @pjotrp and @felixl diff --git a/tasks/felixl.gmi b/tasks/felixl.gmi index 8e8bfe8..b39ff7b 100644 --- a/tasks/felixl.gmi +++ b/tasks/felixl.gmi @@ -10,15 +10,17 @@ #### This week +* [ ] Finalize the slide deck - so it can be read on its own * [ ] Analyse and discuss BXD case attributes with Rob --- both group level and dataset level * [ ] Sane representation of case attributes in RDF with @bonfacem -* [ ] Present C.elegans protocol and example mappings with GEMMA/Rqtl +* [X] Present C.elegans protocol and example mappings with GEMMA/Rqtl * [ ] Uploader - setting up code with @fredm -* - run small database mysql locally -* - aider with Sonnet + code fixes -* - document +* - [X] run small database mysql locally +* - [X] aider with Sonnet + code fixes +* - [ ] document - add to code base - merge with Fred's tree - share changes with Pjotr & team * [ ] Review paper: one-liners for @pjotrp - why is this important for GN and/or thesis -* [ ] Sort @alexm application with Pwani +* - [ ] list of relevant papers with one-liners - the WHY +* [ ] Sort @alexm application with Pwani = this week ### Later weeks diff --git a/tasks/fredm.gmi b/tasks/fredm.gmi index 5e7e71d..5324285 100644 --- a/tasks/fredm.gmi +++ b/tasks/fredm.gmi @@ -1,5 +1,9 @@ # Tasks for Fred +# Tasks + +* [ ] Fix password weakness + ## Description These are the tasks and issues to be handled by Fred. |