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| -rw-r--r-- | topics/biohackathon/GNGSoC2023.gmi | 49 |
1 files changed, 48 insertions, 1 deletions
diff --git a/topics/biohackathon/GNGSoC2023.gmi b/topics/biohackathon/GNGSoC2023.gmi index 07918c2..11b025f 100644 --- a/topics/biohackathon/GNGSoC2023.gmi +++ b/topics/biohackathon/GNGSoC2023.gmi @@ -23,6 +23,16 @@ git repo genenetwork-machines, guix-bioinformatics => ../../issues/gnsoc-ci-rethink Tracking progress +### Week 1 + +* Proposal written + - guix pull on guix-bioinformatics + - updated guix is broken gemma (Pjotr) +* Efraim guix GN2 - so we can have a channel +* Next step build substitutes for guix-bioinformatics + - once built they are shared +* And create a GN3 channel (Efraim?) + ## Nextgen databases lmdb+RDF @@ -35,14 +45,33 @@ git repo genenetwork3 => ../../topics/next-gen-databases/design-doc Design doc +### Week 1 + +* RDF dumps +* Parsing S-exp -> markdown +* Hashing tables (Fred) + - automated updates +* Some progress on sample data from SQL -> lmdb (Alex) +* Next week: guile bindings for lmdb + - improving RDF + ## LLMs & metadata (RDF) * lead: Shelby * team: Priscilla -* contact: Bonface +* contact: Bonface, Pjotr, Rupert => ../lmms/llm-metadata Tracking progress +### Week 1 + +* Created issue page +* Downloading publications (Priscilla) +* Flask server +* Next: Connecting OpenAI +* Create matrix room + + ## API to access data from GN * lead: Rupert @@ -55,12 +84,30 @@ git repo gn-docs & genenetwork3 & SPARQL => https://github.com/genenetwork/gn-docs +### Week 1 + +* Mapping out the API + +=> https://github.com/genenetwork/gn-docs/blob/master/api/questions-to-ask-GN.md + +* Ideas on structuring +* Questions on GN +* Next: unify access to information + - collecting questions from users + - settle on form of API + - create example URLs for mouse + ## Editing data * lead: Fred * team: Arthur, Rupert, Zach * contacts: Rob +### Week 1 + +* Edit phenotype metadata works +* Next: phenotype values and testing on live + ## Links * Matrix room is GNSoC2023 |