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# Tasks for Felix
## Tags
* kanban: felixl
* assigned: felixl
* status: in progress
## 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
* ## this week (21-07-onwards)
* [ ] - 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
### Later weeks (non-programming tasks)
* [ ] Kilifish into GN
* [ ] Review paper on genotyping
* [ ] HS Rat
* [ ] Prepare others for C.elegans
* [ ] Upload Arabidopsis dataset
* [ ] Upload Medaka dataset
* [ ] Work on improved DO and Ce genotyping
### Done
### On going tasks
=> https://issues.genenetwork.org/search?query=assigned%3Afelixl+AND+is%3Aopen&type=open-issue All in-progress tasks
Rank-ordered list of on-going tasks:
=> https://issues.genenetwork.org/search?query=assigned%3Afelixl+AND+tag%3Ain-progress+AND+priority%3Ahigh+AND+is%3Aopen&type=open-issue High Priority
=> https://issues.genenetwork.org/search?query=assigned%3Afelixl+AND+tag%3Ain-progress+AND+priority%3Amedium+AND+is%3Aopen&type=open-issue Medium Priority
=> https://issues.genenetwork.org/search?query=assigned%3Afelixl+AND+tag%3Ain-progress+AND+priority%3Alow+AND+is%3Aopen&type=open-issue Low Priority
### Stalled (To Be Done/Completed)
=> https://issues.genenetwork.org/search?query=assigned%3Afelixl+AND+tag%3Astalled+AND+is%3Aopen&type=open-issue All stalled taskse that are to be promoted to in-progress
Rank-ordered list of stalled tasks:
=> https://issues.genenetwork.org/search?type=open-issue&query=assigned%3Afelixl%20AND%20tag%3Astalled%20AND%20priority%3Ahigh%20AND%20is%3Aopen%20AND%20NOT%20in-progress High Priority
=> https://issues.genenetwork.org/search?type=open-issue&query=assigned%3Afelixl%20AND%20tag%3Astalled%20AND%20priority%3Amedium%20AND%20is%3Aopen%20AND%20NOT%20in-progress Medium Priority
=> https://issues.genenetwork.org/search?type=open-issue&query=assigned%3Afelixl%20AND%20tag%3Astalled%20AND%20priority%3Alow%20AND%20is%3Aopen%20AND%20NOT%20in-progress Low Priority
### Unclear Issues
Ad-hoc issues that were picked some where some how:
=> https://issues.genenetwork.org/search?type=open-issue&query=assigned%3Afelixl%20AND%20NOT%20tag%3Astalled%20AND%20NOT%20tag%3Ain-progress%20AND%20status%3Aunclear%20OR%20priority%3Aunclear Unclear Issues
### Closed Issues
Should something in one of these closed issues be amiss, we can always and should re-open the offending issue.
Currently closed issues are:
=> https://issues.genenetwork.org/search?type=closed-issue&query=assigned%3Afelixl%20AND%20type%3Aissue%20AND%20is%3Aclosed Closed Issues
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