From 752298ae74fbe033e7e7e20409242ca1eeffd079 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 29 Jun 2023 11:01:14 +0200
Subject: Week 1 of GNSoC2023

---
 topics/biohackathon/GNGSoC2023.gmi | 49 +++++++++++++++++++++++++++++++++++++-
 1 file changed, 48 insertions(+), 1 deletion(-)

(limited to 'topics/biohackathon/GNGSoC2023.gmi')

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
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