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diff --git a/topics/meetings/gn-kilifi-2025-standup.gmi b/topics/meetings/gn-kilifi-2025-standup.gmi new file mode 100644 index 0000000..c20e847 --- /dev/null +++ b/topics/meetings/gn-kilifi-2025-standup.gmi @@ -0,0 +1,177 @@ +# 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 |