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Tasks for Felix

Tasks

Goals

1. Write papers for PhD 2. Load data into GN - serve the communities 3. Get comfortable with programming

#### Previous week(s)

[x] Restless Legs Syndrome (RLS) - 'Traditional Phewas' - AI aspect - Johannes
[+] Finalize the slide deck - so it can be read on its own
[.] Review paper: one-liners for @pjotrp - why is this important for GN and/or thesis
- [ ] list of relevant papers with one-liners - the WHY

https://pmc.ncbi.nlm.nih.gov/articles/PMC3294237/

[+] Analyse and discuss BXD case attributes with Rob --- both group level and dataset level
[ ] Sane representation of case attributes in RDF with @bonfacem
[X] Present C.elegans protocol and example mappings with GEMMA/Rqtl
[ ] Uploader - setting up code with @fredm
- [ ] Concrete improvement to work on
- [X] run small database mysql locally
- [X] aider with Sonnet + code fixes
- [ ] document - add to code base - merge with Fred's tree - share changes with Pjotr & team
[ ] Sort @alexm application with Pwani = this week

This week (07-04-2025 onwards)

GN2 tasks

* [ X ] Progress on Kilifish - meet with Dennis (send him an email with all the queries needed) - progress to format and upload data to gn2 (to be ready by latest Friday!) * [ X ] Make a milestone with genotype smoothing

PhD tasks

* [ X ] Complete and share concept note and timeline to supervisors, have a meeting for progress * [ ] Make a milestone on chapter one manuscript (deep dive into the selected papers){THE BIG PICTURE; a complete draft by early May}

Programming

* [ ] Make a milestone with the uploader (really push and learn!) - documentation (use ai); add to the code base of the uploader - utilise the hurdles to learn programming priniciples in action

This week (14-04-2025 onwards)

gn-uploader programming

* [X] - Resolve the config file issue with your local uploader * [ ] - Run the uploader locally, then break the system, see how components connect to each other * [ ] - document your findings

genotype smoothing

* [ ] - resolve errors with plotting, document your findings

This week (21-04-Onwards)

genotype smoothing

* [ ] - haplotyping tools for smoothing (plink,., etc) - see what it can offer with smoothing. See what others say about this.

gn-uploader programming

* [ ] - Run the uploader locally, then break the system, see how components connect to each other (ask help from Bonz) * [ ] - document your findings

This week (28-04-Onwards)

gn-uploader programming

* [X] - Run the uploader locally, then break the system, see how components connect to each other (ask help from Bonz) * [X] - document your findings {Get help from your teammates/AI to jump start this!, swallow your pride! :(}

genotype smoothing

* [X] Keep refining the following: * [X] filtering power adapted from plink * [X] the xsomes mix up in the plot (probably the phenotype data?) * [X] Update findings and push to github

This week (05-05-Onwards)

programming (gn-uploader)

* [ ] - pick one file each day, review it, understand it * [ ] - pair programming with Alex on test runs

HS rats scripts

* [ ] - prepare/refine scripts to quickly process HS rats file * [ ] - assist alex with hs rats cross info

AOBs

* [ X ] Weekly meetings * [ X ] follow up with Paul on his progress * [ X ] follow up on the MSc bioinformatics project * [ X ] follow up on Alex's application with Pwani

(12-05-onwards)

* [X] - HS genotypes scripting

(19-05-onwards)

* [X] - HS genotypes debugging (memory issue) * [X] - pair programming with Bonz to improve the script

this week (26-05-onwards)

* [X] - process the genotype file for hs rats * [X] - approach by tissues categories * [X] - adipose and liver - test by Xsomes for memory capture - run the working commands * [X] - the rest 10 other tissues (in progress) * [X] - *.bed file vs the updated vcf files from the website?

this week (02-06-onwards)

[X] - process the genotypes for the rest of the 10 tissues for HS rats
[X] - document the new findings about smoothing using bcftools and plink

## this week (09-06-onwards)
[+] - identify start and end points for haplotypes in hs genotype files
[+] - upload the final updates to gn2, test and see the results
[-] - gn-uploader/uploader folder, explore

## this week (16-06-onwards)
[X] - hs rats proximal and distal haplotype edges
[+] - uploading kilifish using the backend route

## this week (23-06-onwards)
[X] - hs rats recombination counts
[+] - kilifish to gn2 via backend

## this week (30-06-onwards)
[ ] - mapping offsprings to founders (hs rats)
[ ] - upload kilifish to genenetwork
[ ] - revise celegans smoothing (genotypes)

## this week (07-07-onwards)
[X] - generate haplotypes for offsprings and founders combined; intepretation next..,
[+] - keep improving the uploader via data uploading and error solving
[-] - close smoothing revision for celegans, as left before
[X] - why should people read my paper on improving genotyping methods?
- on smoothing (low density genotypes for mapping, high density genotypes for fine mapping.,)
- liftovers due to reference versions (currently, a challenge to be looked upon)
- founders and their offsprings in genotyping
- pangenomics and machine learning for improved genotyping

** keys (+; in progress, X; done, -; not yet)

## this week (14-07-onwards)
[+] - map founders to offspring, work with only pure recombiantions

[+] - tools available? (plink, rqtl2, beagle, etc) [+] - custom pipeline, to reflect gaps in the existing tools? (dealing with multiparent species) [+] - documentation for the paper write up