diff options
| -rw-r--r-- | tasks/alexm.gmi | 20 | ||||
| -rw-r--r-- | tasks/bonfacem.gmi | 19 | ||||
| -rw-r--r-- | tasks/felixl.gmi | 6 | ||||
| -rw-r--r-- | tasks/pjotrp.gmi | 6 |
4 files changed, 28 insertions, 23 deletions
diff --git a/tasks/alexm.gmi b/tasks/alexm.gmi index c39cf70..2c1b129 100644 --- a/tasks/alexm.gmi +++ b/tasks/alexm.gmi @@ -19,19 +19,17 @@ You can refine the search by constraining the checks some more, e.g. to get high ## This week * [ ] 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 +* - [X] Got all transcripts +* [+] Correlations - Fred is having issues - Rust updated on Guix +* - also take a look at long running SQL statement and large LIMIT value (check prod!) * [ ] 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 +* [+] Disable spinner on production (check prod!) * [+] 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 +* - [X] DO mice family file - children are heterozygous - family file contains parents->child +* - [ ] DO GN2 compatible by generating .geno files * [ ] Minor refactorings - Rqtl2 is hacky -* [ ] Work in system container and document +* [ ] Work in development 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) @@ -44,6 +42,10 @@ You can refine the search by constraining the checks some more, e.g. to get high ## Done +* [X] Rqtl1 - ITP output - 3K individuals - family file +* [X] When bonz is ready wire up GNQA +* + balg-qa.genenetwork.org +* [X] Don't support new PIL - stick to the old one in guix-bioninformatics * [X] Make GNQA reliable (with @fahamu) * [X] Improve UX for GNQA (with @shelbys) -- Adrian wants to use our AI UX for their setup * [X] GNQA add abstracts pubmed (with @shelbys) diff --git a/tasks/bonfacem.gmi b/tasks/bonfacem.gmi index 8fc1e81..0fb1317 100644 --- a/tasks/bonfacem.gmi +++ b/tasks/bonfacem.gmi @@ -10,8 +10,15 @@ ### This week -* [ ] Set up meeting with ILRI - - Zasper https://news.ycombinator.com/item?id=42572057 - Alan +* [ ] 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 +* - 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 +* [+] 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 w. Fred @@ -22,17 +29,11 @@ * 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 +* 6. Get docs from Shelby/Brian * [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) -* - base line with GN1 search - add tests -* - 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 * [ ] 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 97001c2..dab1466 100644 --- a/tasks/felixl.gmi +++ b/tasks/felixl.gmi @@ -16,14 +16,16 @@ #### This week +* [ ] Restless Legs Syndrome (RLS) - 'Traditional Phewas' - AI aspect - Johannes * [+] 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 +* [.] 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 +* [+] 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 * [ ] Uploader - setting up code with @fredm +* - [ ] Concrete improvement to work on * - [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 diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi index f19b919..5f8a620 100644 --- a/tasks/pjotrp.gmi +++ b/tasks/pjotrp.gmi @@ -14,13 +14,14 @@ * Mempig * [+] create backup server with @fredm +* [+] RAG with Shelby and Bonz * [+] Moni builds 1U01HG013760 * [+] test framework wfmash - vertebrate tree and HPC compute? * - wfmash - wgatools -> PAF + FASTA to VCF * - wfmash arch=native build * [ ] gbam - data compression with Nick and Hasithak -* [ ] accelerate wfmash with @santiago and team -* [ ] package wfmash and Rust wfa2-lib +* [X] accelerate wfmash with @santiago and team +* [+] package wfmash and Rust wfa2-lib * [ ] add Ceph for distributed network storage 1U01HG013760 * [ ] Work on pangenome genotyping 1U01HG013760 * [ ] update freebayes into Debian (version #) @@ -29,7 +30,6 @@ * - [ ] static build and prepare for conda * [ ] pangenome as a 1st class input for GEMMA * kilifish pangenome with Paul and Dario -* RAG with Shelby and Bonz ## Systems |