From 6a0e96e12b001e90e154df400e06ab5cb29997b2 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 13 Jul 2023 04:05:54 -0500
Subject: GN SoC progress

---
 topics/biohackathon/GNGSoC2023.gmi | 31 +++++++++++++++++++++++++++++++
 topics/systems/ci-cd.gmi           |  2 +-
 2 files changed, 32 insertions(+), 1 deletion(-)

(limited to 'topics')

diff --git a/topics/biohackathon/GNGSoC2023.gmi b/topics/biohackathon/GNGSoC2023.gmi
index f1377a7..8fe7310 100644
--- a/topics/biohackathon/GNGSoC2023.gmi
+++ b/topics/biohackathon/GNGSoC2023.gmi
@@ -39,6 +39,16 @@ git repo genenetwork-machines, guix-bioinformatics
 * guix-bioinformatics now has CI!
 * ~700 packages, 240 are broken ;)
 
+### Week 3
+
+* Arun gives a presentation on laminar using guix-forge: slides:
+=> https://issues.genenetwork.org/topics/ci-rethink-slides
+* New system is simpler and has reproducibility issues
+* Efraim is doing channels for GN2 and GN3
+* Sarthak will try to run guix-forge
+
+### More
+
 => https://ci.genenetwork.org/jobs/guix-bioinformatics
 
 * CI/CD is up and running again (and broken)
@@ -73,6 +83,10 @@ git repo genenetwork3
 * Fred is running SPARQL queries
 * Alex is adding lmdb phenotype API endpoints
 
+### Week 3
+
+* Bonface demoes new documentation & code
+
 ## LLMs & metadata (RDF)
 
 * lead: Shelby
@@ -95,6 +109,13 @@ git repo genenetwork3
 * Shelby is integrating into a Flask interface for GeneNetwork
 * Using a pubmed UI style
 
+### Week 3
+
+* Shelby shows code
+* Plan to host
+* Priscilla is working on SLA and document acquisition
+* Hosting GN Q&A
+
 ## API to access data from GN
 
 * lead: Rupert
@@ -127,6 +148,12 @@ git repo gn-docs & genenetwork3 & SPARQL
 * Flavia added questions in gn-doc - e.g. for synteny search
 => https://issues.genenetwork.org/topics/xapian-search-queries Examples for synteny
 
+### Week 3
+
+* Rupert proposes endpoints and metadata traversing
+
+=> https://github.com/genenetwork/gn-docs/blob/master/api/alternative-API-structure.md
+
 ## Editing data
 
 * lead: Fred
@@ -160,6 +187,10 @@ git repo gn-docs & genenetwork3 & SPARQL
 * Looking into GeneNetwork3 service
 * Enumerated types
 
+### Week 3
+
+* Preparing for BLOG on S-exp
+
 ## Links
 
 * Matrix room is GNSoC2023
diff --git a/topics/systems/ci-cd.gmi b/topics/systems/ci-cd.gmi
index 9db9885..e9a24a3 100644
--- a/topics/systems/ci-cd.gmi
+++ b/topics/systems/ci-cd.gmi
@@ -26,7 +26,7 @@ periodically, say, once an hour/day):
 * CI: run unit tests
 * CD: rebuild and redeploy a container running GN3
 
-Arun has figured out the CI part. It runs a suitably configured laminar CI service in a Guix container created with `guix system container'. A cron job periodically triggers the laminar CI job.
+Arun has figured out the CI part. It runs a suitably configured laminar CI service in a Guix container created with `guix system container'. A cron job periodically triggers the laminar CI job (note: this is no longer true).
 
 => https://git.systemreboot.net/guix-forge/about/
 
-- 
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