GNSoC 2023

GN Summer of Code

Introduction

We are running a GN Summer of Code in small teams.

• Runs July + August 2023
• Weekly plenary where projects present progress - Thursday 9am EU, 10 am EAT.
• Projects should be (slightly) out of comfort zone
• Use gemtext documentation
• Option for publishing on progress by then end as a BLOG or BioHackrXiv

CI for guix-bioinformatics (guix pull)

• lead: Arun
• team: Efraim, Pjotr, Sarthak

Making GN deployment rock solid

git repo genenetwork-machines, guix-bioinformatics

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?)

Week 2

• RISC-V port progressing with node and zig 0.10
• 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

Week 4

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

More

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

Nextgen databases

lmdb+RDF

• lead: Bonface
• team: Fred, Alex
• contact: Pjotr

git repo genenetwork3

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

Week 2

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

Week 3

• Bonface demoes new documentation & code

Week 4

• 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

LLMs & metadata (RDF)

• lead: Shelby
• team: Priscilla
• contact: Bonface, Pjotr, Rupert

Tracking progress

Week 1

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

Week 2

• Open AI API is working
• 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

Week 4

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

API to access data from GN

• lead: Rupert
• team: Flavia
• contacts: Bonface, Zach, Fred

Documentation and adding endpoints

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

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

Examples for synteny

Week 3

• Rupert proposes endpoints and metadata traversing

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

Week 4

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

Editing data

• lead: Fred
• team: Arthur, Rupert, Zach
• contacts: Rob

Week 1

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

Week 2

• Fixing issues
• Meeting on requirements from Arthur and Zach

Week 4

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

Guix parametrization

• lead: Sarthak
• team: Pjotr, Gabor
• contacts: Ludo

Week 1

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

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

Week 2

• Looking into GeneNetwork3 service
• Enumerated types

Week 3

• Preparing for BLOG on S-exp

Week 4

• BLOG in a stage that we discuss naming conventions

Links

• Matrix room is GNSoC2023

Arun's talk on our issue tracker

Git repo on issues/tasks/topics

This page

For more info contact pjotr.public912 at thebird.nl