# 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 
  * [ ] 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!) 
  * [ ] 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} 

* 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 

* 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 

### 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