• 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?)

• RISC-V port progressing with node and zig 0.10
• guix-bioinformatics now has CI!
• ~700 packages, 240 are broken ;)

• 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

• Arun added channels to CI
• localhost
• cgit
• Efraim: gn2 -> channel; Arun tested

• Added Klaus server for git
• Fixed channels to work wit Python 3.9 instead of 3.10

• Towards a new workbench with cgit support

• Arun has cgit running on his own server - soon bringing up tux02 after resolving https

• cgit deployment at https://git.genenetwork.org/
• guix forge

• Discussion on importers for guix forge
• Talked about propagator networks - part of Seattle presentation

• https://ci.genenetwork.org/jobs/guix-bioinformatics

• CI/CD is up and running again (and broken)
• Rethink: channels and pull channels are used for CI/CD
• Move unused packages elsewhere

• 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

• RDF structure to markdown dump
• Fred is running SPARQL queries
• Alex is adding lmdb phenotype API endpoints

• Bonface demoes new documentation & code

• Settled on prefixes terms and id
• Updated man pages

• https://github.com/genenetwork/gn-docs/tree/master/rdf-documentation

• Started work on lmdb+guile:

• https://github.com/BonfaceKilz/gn-data-vault

• Metadata - renamed prefixes
• Short names gn: gnt:
• Updated virtuoso
• parsing geno files - lmdb support

• Improvements on RDF

• RDF improvements with ontology
• Inconsistencies and privacy discussion today

• Transformed most tables now
• guile-lmdb started by Alex

• New renaming and modelling
• GeneRif
• Working on unique IDs
• SKOS

• Created issue page
• Downloading publications (Priscilla)
• Flask server
• Next: Connecting OpenAI
• Create matrix room

• Open AI API is working
• Shelby is integrating into a Flask interface for GeneNetwork
• Using a pubmed UI style

• Shelby shows code
• Plan to host
• Priscilla is working on SLA and document acquisition
• Hosting GN Q&A

• working on container
• fetched 1000 publication
• JSON documentation on references

• Guix container for LLM
• Expose container to Rupert
• Add a password

• Very close to a working flask app Rupert can try next week

• Working FLASK app ready for testing - Rupert will have a go

• Working prototype!
• references as JSON

• Shelby showed working references and challenges
• System is ready for viewing by Rob

• 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

• 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

• Examples for synteny

• Rupert proposes endpoints and metadata traversing

• https://github.com/genenetwork/gn-docs/blob/master/api/alternative-API-structure.md

• Start working on endpoints
• R api - reference GN/API
• synteny

• Added back-end support for wikidata - finding inconsistencies

• API ready for running in a production environment
• Using latest RDF

• Test version of API is running at https://luna.genenetwork.org/api/v2.0/
• We'll continue building up facilities

• R script to parse API by Rupert
• Move forward with populations/strains and datasets

• Progressed API software to include groups

• Edit phenotype metadata works
• Next: phenotype values and testing on live

• Fixing issues
• Meeting on requirements from Arthur and Zach

• Editing works!
• Discussed the approval procedure and edit button for everyone

• Editing has gone on production - fixing issues
• Discussion on REST API

• Progress on authorization and editing

• Fred has moved code into a new repo for https://github.com/genenetwork/gn-auth

• gn-auth is building locally and needs to go on the forge
• case attributes

• gn-auth continuation
• case-attribute editing progress and challenges

• https://blog.lispy.tech/parameterized-packages-an-update.html

• Next: focus on statically built packages optimized for arch.

• Looking into GeneNetwork3 service
• Enumerated types

• Preparing for BLOG on S-exp

• BLOG in a stage that we discuss naming conventions

• Proposed DSL for parameters

• Posted BLOG and started implementation

• Agreed on final deliverables for GSoC

• Milestone on dependencies!

• Sarthak showed us the working prototype