# 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

=> ../../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?)

### Week 2

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

=> 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

=> ../../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

### Week 2

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

## LLMs & metadata (RDF)

* lead: Shelby
* team: Priscilla
* 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

### Week 2

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

## 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
=> https://issues.genenetwork.org/topics/xapian-search-queries Examples for 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

## 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

## Links

* Matrix room is GNSoC2023

=> https://fosdem.org/2023/schedule/event/tissue/ Arun's talk on our issue tracker
=> https://github.com/genenetwork/gn-gemtext-threads Git repo on issues/tasks/topics
=> https://issues.genenetwork.org/topics/biohackathon/GNGSoC2023 This page

For more info contact pjotr.public912 at thebird.nl