diff options
| -rw-r--r-- | tasks/alexm.gmi | 25 | ||||
| -rw-r--r-- | tasks/bonfacem.gmi | 37 | ||||
| -rw-r--r-- | tasks/felixl.gmi | 26 | ||||
| -rw-r--r-- | tasks/pjotrp.gmi | 1 |
4 files changed, 69 insertions, 20 deletions
diff --git a/tasks/alexm.gmi b/tasks/alexm.gmi index 88d3927..a66de6b 100644 --- a/tasks/alexm.gmi +++ b/tasks/alexm.gmi @@ -1,4 +1,4 @@ -# Tasks for Fred +# Tasks for Alex ## Description @@ -16,11 +16,20 @@ You can refine the search by constraining the checks some more, e.g. to get high # Tasks -* [ ] Make GNQA reliable (with @fahamu) -* [ ] Improve UX for GNQA (with @shelbys) -* [ ] GNQA add abstracts pubmed (with @shelbys) -=> ../issues/fetch-pubmed-references-to-gnqa +## This week + +* [ ] Rqtl2 - BXD output work on CD +* [ ] Rqtl2 - ITP output - 3K individuals - family file +* [ ] Start application + +## Next week(s) -* [ ] Edit markdown/gemtext pages through web UI (with @bonfacem) -* [ ] GNQA add GN metadata with @bonfacem -* [ ] Create terminal output for external processes (WGCNA as a pilot, with @bonfacem and @pjotrp) +* [+] Create terminal output for external processes (Rqtl1, Rqtl2, pair-scan are done --- WGCNA as a pilot, with @bonfacem and @pjotrp) + +## Done + +* [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) +=> ../issues/fetch-pubmed-references-to-gnqa +* [X] Edit markdown/gemtext pages through web UI (with @bonfacem) diff --git a/tasks/bonfacem.gmi b/tasks/bonfacem.gmi index bd930a0..5445eeb 100644 --- a/tasks/bonfacem.gmi +++ b/tasks/bonfacem.gmi @@ -8,16 +8,32 @@ ## Tasks -* [X] Indexing generif data / Improve Local Search -* [ ] lmdb publishdata output and share with Pjotr and Johannes -* [ ] Add lmdb output hashes to RDF metadata -* [ ] https://github.com/genenetwork/genenetwork2/blob/testing/scripts/sample_count.py -* [ ] Describe Generif access for Rob -* [ ] Add case attributes to RDF and share with Felix +### This week + +* [ ] Describe Generif access for Rob in an email +* [ ] 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 + +### 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 -* [ ] Rest API for precompute output +* - 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) + +### Even later + +* [ ] Rest API for precompute output (mapping with GEMMA) +* [ ] GNQA add GN metadata (to RAG) +* - Focus on RIF +* - triple -> plain text +* - bob :fatherof nancy -> Bob is the father of Nancy. ## Later @@ -45,3 +61,6 @@ Should something in one of these closed issues be amiss, we can always and shoul Currently closed issues are: => https://issues.genenetwork.org/search?type=closed-issue&query=assigned%3ABonfaceKilz%20AND%20type%3Aissue%20AND%20is%3Aclosed Closed Issues + +* [X] Indexing generif data / Improve Local Search +* [X] lmdb publishdata output and share with Pjotr and Johannes diff --git a/tasks/felixl.gmi b/tasks/felixl.gmi index 209e8c9..8e8bfe8 100644 --- a/tasks/felixl.gmi +++ b/tasks/felixl.gmi @@ -1,4 +1,4 @@ -# Tasks for Munyoki +# Tasks for Felix ## Tags @@ -6,12 +6,32 @@ * assigned: felixl * status: in progress -## October +## Tasks + +#### This week + +* [ ] 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 +* [ ] Uploader - setting up code with @fredm +* - run small database mysql locally +* - aider with Sonnet + code fixes +* - document +* [ ] Review paper: one-liners for @pjotrp - why is this important for GN and/or thesis +* [ ] Sort @alexm application with Pwani + +### Later weeks +* [ ] Review paper on genotyping +* [ ] HS Rat +* [ ] Prepare others for C.elegans * [ ] Upload Arabidopsis dataset * [ ] Upload Medaka dataset -## Tasks +### Done + + + ### On going tasks => https://issues.genenetwork.org/search?query=assigned%3Afelixl+AND+is%3Aopen&type=open-issue All in-progress tasks diff --git a/tasks/pjotrp.gmi b/tasks/pjotrp.gmi index b284c46..87e9a69 100644 --- a/tasks/pjotrp.gmi +++ b/tasks/pjotrp.gmi @@ -18,6 +18,7 @@ Generally work applies to NIH/R073237482 and other grants. ## Systems +* [ ] synchronize git repos for public, CD, fallback and production using sheepdog and document * [ ] make sure production is up to scratch (see stable below) * [ ] backup tux04 * [ ] add Ceph for distributed network storage 1U01HG013760 |