From 3447970a7ce8fc7848c14ea31aeec3d4b9faad65 Mon Sep 17 00:00:00 2001
From: Lisso_
Date: Wed, 24 Sep 2025 16:27:02 +0300
Subject: Fetche lab patch 1 (#61)

* Adding a new file on progress in gn learning team

* Update progress-hurdles-lessons-learned-journey.gmi

My first commit to the file

* Update progress-hurdles-lessons-learned-journey.gmi

* A new issue on updating strain names to the GN database

* updated an issue on uploading genetype names

* Update hurdles_updating_names_to_GN.gmi

* added my name, fixed the typo, and updated the keyword value

* new updates on my learning journey

* Create Case_Attributes_GN2

* Update felixl.gmi

* Update felixl.gmi---
 tasks/felixl.gmi | 31 ++++++++++++++++++++++++++++++-
 1 file changed, 30 insertions(+), 1 deletion(-)

(limited to 'tasks')

diff --git a/tasks/felixl.gmi b/tasks/felixl.gmi
index 22e0d96..7a472a1 100644
--- a/tasks/felixl.gmi
+++ b/tasks/felixl.gmi
@@ -41,7 +41,7 @@
 
 * 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} 
+  * [+] 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!) 
@@ -187,6 +187,35 @@
 *       - request bonz/alex's help on this (to save time) 
 
 
+* ## this week (30-06-onwards)  
+* [X] - 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)
 
-- 
cgit 1.4.1