• Completed first draft of the abstract
• HS genotyping; polishing founders vcf file:
• - sorting xsome order
• - remove duplicate markers

• Extending the rag system, make it more of an agent:
• - fixing bugs
• - reduce runtime

• CD went down!
• revert it to last commit
• set it up locally (not very easy)
• coordinate with Fred and Aarun for help

• updating the abstract: meeting with Kauthar, for more tips and insight
• HS rats genotyping
• still no significant output

• fixed GN3, GN guile, and GN auth
• reproduce GN2 error, not yet fixed though

• LLM transformer is taking too long to run
• change input documentations to observe results

• Still on the abstract
• Errors with hs genotyping script

• Still on the rag system: experimenting with documents as input

• CD down again, tux02 is the calprit
• Running gn2 outside container in meantime

• improving the smoothing scripts for hs: building a snakemake pipeline; redrafting the abstract introductory part

• 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

• rqlt2/lmdb runs and rebooted
• dumping bxd phenotype dataset for testing

• no big updates
• literature review on rag systems and how they work

• Improved the inferring script
• Abstract on hold first

• fix documents using agents: the issue is parallelization
• reviewing fahamu AI (the python part)

• Gn2 finally runs
• Documenting the progress and steps
• Gn-auth is broken; Fred to solve it
• Updated tesla k8 gpu drivers

• Rqtl-wrapper for BXD is done
• focusing on cross-information;lmdb

• managed to generate haplotype blocks for hs rats

• RAG experimentation script: balg01, running slow; prepare for msc defense

• dumping phenotypes to lmdb

• 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

• 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

• All the GN machines are up and running, expect GN Auth
• Sent documentations to Pjotr on the progress with troubleshooting GN machines

• writing queries to move phenotypes matrices from gn2 db to lmdb

• defense

• Completed abstract writing
• Working on generating genotype files for hs in gn2 format

• 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

• Succeeded dumping phenotypes to lmdb
• Been reading literature around phenotypes in gn2
• Assisted Bonz in setting up external bootable ssd for Johannes

• Managed to get access to bux01 server for the llms work

• Finalized HS genotypes/haplotypes

• GN machines are running on CD
• troubleshooting assisted by Aaron

• Experimenting with RAG systems

• Writing LMDB scripts to dump phenotypes to LMDB from the common gn DB

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

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

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

• HS genotypes to be fully supported in GN2
• Poster presentation
• PhD: ML objective (ML fundamentals); Complete 1st manuscript draft; Process my student pass