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Diffstat (limited to 'topics/biohackathon')
| -rw-r--r-- | topics/biohackathon/GNGSoC2023.gmi | 36 |
1 files changed, 36 insertions, 0 deletions
diff --git a/topics/biohackathon/GNGSoC2023.gmi b/topics/biohackathon/GNGSoC2023.gmi index 0019271..2bdeaef 100644 --- a/topics/biohackathon/GNGSoC2023.gmi +++ b/topics/biohackathon/GNGSoC2023.gmi @@ -33,6 +33,14 @@ git repo genenetwork-machines, guix-bioinformatics - once built they are shared * And create a GN3 channel (Efraim?) +### Week 2 + +* RISC-V port progressing with node and zig 0.10 +* guix-bioinformatics now has CI! +* ~700 packages, 300 are broken ;) +* CI/CD is up and running again (and broken) +* Rethink: channels and pull channels are used for CI/CD + ## Nextgen databases lmdb+RDF @@ -55,6 +63,12 @@ git repo genenetwork3 * Next week: guile bindings for lmdb - improving RDF +### Week 2 + +* RDF structure to markdown dump +* Fred running SPARQL queries +* Alex lmdb phenotype API endpoints + ## LLMs & metadata (RDF) * lead: Shelby @@ -71,6 +85,11 @@ git repo genenetwork3 * Next: Connecting OpenAI * Create matrix room +### Week 2 + +* API is working mostly +* Shelby is integrating into a Flask interface for GeneNetwork +* Pubmed UI style ## API to access data from GN @@ -97,6 +116,13 @@ git repo gn-docs & genenetwork3 & SPARQL - settle on form of API - create example URLs for mouse +### Week 2 + +* GraphQL Arun gives a mumi demo - schema allows for (partial) queries and querying the schema itself +* Pjotr convenience API demo - add endpoints in results +* Flavia added questions in gn-doc - e.g. for synteny search +=> https://issues.genenetwork.org/topics/xapian-search-queries Examples for synteny + ## Editing data * lead: Fred @@ -108,6 +134,11 @@ git repo gn-docs & genenetwork3 & SPARQL * Edit phenotype metadata works * Next: phenotype values and testing on live +### Week 2 + +* Fixing issues +* Meeting on requirements from Arthur and Zach + ## Guix parametrization * lead: Sarthak @@ -120,6 +151,11 @@ git repo gn-docs & genenetwork3 & SPARQL * Next: focus on statically built packages optimized for arch. +### Week 2 + +* Looking into GeneNetwork3 service +* Enumerated types + ## Links * Matrix room is GNSoC2023 |