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# Stand-up Notes
## 25-8-2025
### Felix
* Completed first draft of the abstract
* HS genotyping; polishing founders vcf file:
* - sorting xsome order
* - remove duplicate markers
### Johannnes
* Extending the rag system, make it more of an agent:
* - fixing bugs
* - reduce runtime
### Bonface
* CD went down!
* revert it to last commit
* set it up locally (not very easy)
* coordinate with Fred and Aarun for help
## 27-8-2025
### Felix
* updating the abstract: meeting with Kauthar, for more tips and insight
* HS rats genotyping
* still no significant output
### Bonface
* fixed GN3, GN guile, and GN auth
* reproduce GN2 error, not yet fixed though
### Johannes
* LLM transformer is taking too long to run
* change input documentations to observe results
## 29-8-2025
### Felix
* Still on the abstract
* Errors with hs genotyping script
### Johannes
* Still on the rag system: experimenting with documents as input
### Bonface
* CD down again, tux02 is the calprit
* Running gn2 outside container in meantime
## 1-9-2025
### Felix
* improving the smoothing scripts for hs: building a snakemake pipeline; redrafting the abstract introductory part
### Bonface
* looked on deployment to fix...,
* install gpu drivers for penguine 2 with alex
* it has gpu drivers tesla k8, but hardware installation is important for the meantime
### Alex
* rqlt2/lmdb runs and rebooted
* dumping bxd phenotype dataset for testing
### Johannes
* no big updates
* literature review on rag systems and how they work
## 3-9-2025
### Felix
* Improved the inferring script
* Abstract on hold first
### Johannes
* fix documents using agents: the issue is parallelization
* reviewing fahamu AI (the python part)
### Bonface
* Gn2 finally runs
* Documenting the progress and steps
* Gn-auth is broken; Fred to solve it
* Updated tesla k8 gpu drivers
### Alex
* Rqtl-wrapper for BXD is done
* focusing on cross-information;lmdb
## 5-9-2025
### Felix
* managed to generate haplotype blocks for hs rats
### Johannes
* RAG experimentation script: balg01, running slow; prepare for msc defense
### Alex
* dumping phenotypes to lmdb
### Bonface
* install drivers on tesla k8
* review Johannes scripts
* fixing gn2
* review alex's patches, {pull requests via emails}
* AOB;
* API tokens for RAG and coding
## 10-9-2025
### Felix
* Managed to run gemma and generate plots for the original hs genotype data and hs smoothed genotype data
* Still working on fine-tuning the statistical metrices to suite the plots
### Bonface
* All the GN machines are up and running, expect GN Auth
* Sent documentations to Pjotr on the progress with troubleshooting GN machines
### Alex
* writing queries to move phenotypes matrices from gn2 db to lmdb
### Johannes
* defense
## 17-9-2025
### Felix
* Completed abstract writing
* Working on generating genotype files for hs in gn2 format
### Bonface
* Gn machines are up and running
* Still some issues with manually restarting the container
* Worked with Alex to set up an external bootable ssd for Johannes
### Alex
* Succeeded dumping phenotypes to lmdb
* Been reading literature around phenotypes in gn2
* Assisted Bonz in setting up external bootable ssd for Johannes
### Johannes
* Managed to get access to bux01 server for the llms work
## 19-09-2025
### Felix
* Finalized HS genotypes/haplotypes
### Bonface
* GN machines are running on CD
* troubleshooting assisted by Aaron
### Johannes
* Experimenting with RAG systems
### Alex
* Writing LMDB scripts to dump phenotypes to LMDB from the common gn DB
## [Review] MONTH OCTOBER, 2025
*** Metric wise, plans and goals to achieve
### Bonface
Thoughts: Good start after relocation.
* CD/CI: Make sure that tests/infra is super stable
* Look at suggested forge/guix-bioinformatics upgrades that affect prod
* Support work for GNQA: sane gn-qna(fahamu)/AI deploys; Review Johannes' work; Help with tuning models; play catch up (cover up knowledge gap); figure out how to compare the different models.
* Follow up on my phd
### Alex
Thoughts: very productive
* Rqtl2 lmdb adapter running on production; depends on traction with Rqtl2 upstream by karl Browman to gn-bioinformatics
* Collaborate with Felix on his scripts
### Johannes
Thoughts: Not very productive, barely, looking forward for more improvement
* Experimenting on the qtl data with the AI system being currently built; also in need of optimization
* Comparing LLMs/GNQA agents; getting assistance from Shelby's work
### Felix
* HS genotypes to be fully supported in GN2
* Poster presentation
* PhD: ML objective (ML fundamentals); Complete 1st manuscript draft; Process my student pass
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