diff options
| -rw-r--r-- | tasks/alexm.gmi | 19 | ||||
| -rw-r--r-- | tasks/bonfacem.gmi | 21 | ||||
| -rw-r--r-- | tasks/felixl.gmi | 13 |
3 files changed, 37 insertions, 16 deletions
diff --git a/tasks/alexm.gmi b/tasks/alexm.gmi index 15dc72b..c39cf70 100644 --- a/tasks/alexm.gmi +++ b/tasks/alexm.gmi @@ -18,15 +18,26 @@ You can refine the search by constraining the checks some more, e.g. to get high ## This week -* [X] Rqtl2 - BXD output work on CD -* [X] Rqtl2 - ITP output - 3K individuals - family file -* [ ] Minor refactorings -* [ ] Accelerate Xapian functionality * [ ] Start application - Pwani +* [ ] Correlations - Fred is having issues - Rust updated on Guix +* - also take a look at long running SQL statement and large LIMIT value +* [ ] Friend of UTHSC - Pjotr needs to send forms +* [ ] Disable spinner on production +* [ ] When bonz is ready wire up GNQA +* + balg-qa.genenetwork.org +* [ ] Don't support new PIL - stick to the old one in guix-bioninformatics +* [+] Rqtl2 - BXD output work on CD +* - [ ] should go to production w. fredm +* - [ ] DO mice family file - children are heterozygous - family file contains parents->child +* [X] Rqtl1 - ITP output - 3K individuals - family file +* [ ] Minor refactorings - Rqtl2 is hacky +* [ ] Work in system container and document +=> https://git.genenetwork.org/gn-machines/commit/?h=gn-local-development-container&id=589dcf32be90f5ec827cb6976d3cb5838d500ac0 * [+] 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) +* [ ] Accelerate Xapian functionality - needs Aider key from Pjotr * Check and fix CTL? * [+] 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 diff --git a/tasks/bonfacem.gmi b/tasks/bonfacem.gmi index 7514e5b..8fc1e81 100644 --- a/tasks/bonfacem.gmi +++ b/tasks/bonfacem.gmi @@ -10,15 +10,22 @@ ### This week -* [ ] Describe Generif/wikidata access for Rob in an email with test account on CD +* [ ] Set up meeting with ILRI + - Zasper https://news.ycombinator.com/item?id=42572057 - Alan +* [+] 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 +* 2. Work on production w. Fred +* [+] 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. Try ingestion and prompt (REST API) +* + Pjotr gives API key - OpenAI - model? +* 2. Read the code base - Elixir is plumbing incl. authentication, Python processing text etc. +* 3. Try ingestion and prompt (REST API) - check out postgres tables * 4. Backup state from production Elixir * 5. Assess porting it to Guix (don't do any work) - minimum version Elixir +* [X] With Alex get rqtl2 demo going in CD (for BXD) + +### Later + * [ ] 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) @@ -26,10 +33,6 @@ * - Fix missing search term for sh* - both menu search and global search * - Use GN1 as a benchmark for search results (mechanical Rob?) * - Xapian ranges for markers -* [ ] 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 * [+] Use aider - give a presentation in the coming weeks diff --git a/tasks/felixl.gmi b/tasks/felixl.gmi index b39ff7b..97001c2 100644 --- a/tasks/felixl.gmi +++ b/tasks/felixl.gmi @@ -8,9 +8,18 @@ ## Tasks +### Goals + +1. Write papers for PhD +2. Load data into GN - serve the communities +3. Get comfortable with programming + #### This week -* [ ] Finalize the slide deck - so it can be read on its own +* [+] Finalize the slide deck - so it can be read on its own +* [ ] Review paper: one-liners for @pjotrp - why is this important for GN and/or thesis +* - [ ] list of relevant papers with one-liners - the WHY +=> https://pmc.ncbi.nlm.nih.gov/articles/PMC3294237/ * [ ] Analyse and discuss BXD case attributes with Rob --- both group level and dataset level * [ ] Sane representation of case attributes in RDF with @bonfacem * [X] Present C.elegans protocol and example mappings with GEMMA/Rqtl @@ -18,8 +27,6 @@ * - [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 -* - [ ] list of relevant papers with one-liners - the WHY * [ ] Sort @alexm application with Pwani = this week ### Later weeks |