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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

* [ ] 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} * [ 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

* [x] 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

AOBs

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

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

* [X] - haplotyping tools for smoothing (plink,., etc) :IN PROGRESS: - see what it can offer with smoothing. See what others say about this. - [X] check the original genotypes and compare with the ones in gn2 {done} - [x] inspect the Xsome column order in comparison with the snp positioning {done} - [x] adapt the plink algorithm to fit your dataset format {done} - consider inspeting the phenotype file too. {in progress}

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

Previous 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) - start simple, read the script files (one at a time, take your time to understand how it flows) - In running the uploader, consider pair programming to save time with solving issues that your teamates can solve in hours, as they take you days to solve

* [ ] - 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 - the low the r2 value, the strictier the filtering.., * [X] the xsomes mix up in the plot (probably the phenotype data?) - individual ids in phenotype data was not in sync with the genotype 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

* [X] - prepare/refine scripts to quickly process HS rats file (in progress) [ ] - memory hurdles, goal to simplify running script * [X] - assist alex with hs rats cross info

(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 (09-06-onwards)
[+] - identify start and end points for haplotypes in hs genotype files
- checked the rembination densities first, still need more comprehension (arrange a meeting with Rob)
[ ] - 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
[+] - mapping offsprings to founders
- examining founders
[-] - kilifish to gn2 via backend

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

## this week (21-07-onwards)
[X] - HS rats smoothing continues
[+] - documenting the milestones
[+] - see the possibility to write a tool from it
[-] - Pushing kilifish to genenetwork2/learn the source code build up
[-] - resmoothen celegans genotypes with the new knowledge

## this week (28-07-onwards)
[-] - predict genotype probabilities with rqlt2 functions

- problems with control setup to load in the needed files for the functions

[+] - comparison models for @individual rat vs 8 founders (similarities and percentage composition)

[+] - ongoing discussion with alex, there's progress

## this week (04-08-onwards)
[+] - Testing the logic to infer Hs outbred genotypes with the founders

- Managed to identify parents of origin for each snp on each rat per position, corresponding to the 8 founders - Still, need to filter in the disntictive snps, then generate haplo blocks.,

## this week (11 - 08 - onwards)
[X] - generate final haplo file and document
[+] - testing on local gemma and in gn2

## this week (18-08-onwards)
[+] - push for the file to be in gn2, and feedback from the team
[X] - complete the local gemma run, interpret the results
[+] - process the rest of the Xsomes for a ready file to go to gn2
- issues: over filtering snps, neglecting the one parent of origin, takes long to run.
[+] - prepare an abstract for CTC conference in Barcelona

## this week (01-09-onWards)
[+] - finetune abstract
- include more of what i achieved: main focus; genotype smoothing on models with complex traits
- thought map: generate plots, compare before and after smoothing, check for overlaps, and whether or not the peaks in traits are same before and after smoothing
[X] - troubleshoot inferring scripts for all Xsomes
- request bonz/alex's help on this (to save time)

## this week (08-09-onwards)
[X] - generate hs haplotype final file
- push it to gn2 (with Zach and Arthur's help)
[X] - Mapping experiments with the original vs smoothed genotype file on all phenotypes selected
[X] - Abstract write up on the results

## this week (15-09-2025)
[+] - Arabidopsis is next after HS rats, then Kilifish: Bigger picture, publications..,
[X] - Getting HS genotypes and phenotypes to gn2
[+] - Mapping experimentation with gn2 tools, share results
[+] - Prepare metadata corresponding to the hs data in gn2
[X] - refine scripts used for analysis for reproducibility purposes

## this week (23-09-2025)
[X] - hs metadata
[+] - Arabidopsis dataset

## this week (30-09-2025)
[+] - Arabidopsis phenotypes; gemma plots
- testing the prepared data with gemma, see what the plots communicate
[+] - hs to genenetwork2 testing

methods to bonferroni:

- compute against randomized data; 1000 permutation (Gary Churchill); LOD score of 4.0 (p- value 10^4) - precompute, by Pj, check on this.., - qtl results, more suggestive than absolute..,