# 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 * [ ] - approach by tissues categories * [X] - adipose and liver - test by Xsomes for memory capture - run the working commands * [ ] - the rest 10 other tissues (in progress) * [ ] - *.bed file vs the updated vcf files from the website? ### this week (02-06-onwards) * [ ] - process the genotypes for the rest of the 10 tissues for HS rats * [ ] - document the new findings about smoothing using bcftools and plink ### Later weeks * [ ] 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