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# 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 ;)
### 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
=> ../../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
### 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
=> ../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
### 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
=> 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
### 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
=> 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
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