- Variant Browser seems to be using mm9
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
Variant Browser seems to be using mm9
## Tags
* assigned:
* priority: unclear
* type: bug
* status: stalled
* keywords: variant browser, mm9, from github
## Members
* acenteno
* robw
* pjotrp...
- Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
issue opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
...a UCSC genome browser link to the corresponding human region as a track for the mapping figure.
# TODO
[X] Display track showing homology across mouse/human/maybe rat (done for mouse, won't be hard...
- CD is slow
issue opened 13 days ago by Pjotr Prins, last updated 9 days ago by Pjotr Prins; 2 of 8 tasks done
...curl, try
```
curl -G https://query.wikidata.org/sparql -H "Accept: application/json; charset=utf-8" --data-urlencode query="SELECT DISTINCT * where {
wd:Q158695 wdt:P225 ?o .
} limit 5"
{
"head"...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...exists)
* [ ] synchronize between queues using a dump
* [ ] sheepdog_expect.rb - expect PINGs
* [ ] sheepdog_rsync.rb - test for 'total size is 0'
* [ ] sheepdog_list tag and filter switches improve...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...rm --cached --ignore-unmatch \
MouseTissuesRWWMay08.xls' --prune-empty --tag-name-filter cat -- --all
git reflog expire --expire=now --all && git gc --prune=now --aggressive
```
Note this rewrites...
- Fix Broken Global Search UI
issue opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
...search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox Version 128.3.1** ESR Version.
The root cause of the problem is unclear,
but after reviewing...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...help wanted
* closed
the keyword statement may have aliases, such as tag and kanban. To undo a keyword simply remove them from the file.
Can't think of anything more to add to make it really useful...
- Slow query
issue opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
...query.
## Indices
ProbeSet has a large number of columns, indices and full text indices(!)
## Nailing it down
The obvious thing to try is to reduce the query and see what speeds it up again. So, let's...
- Fallback issues
issue opened on Mar 22 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins; 3 of 6 tasks done
...I created them outside a container
```
-rw-r--r-- 1 root root 10M Apr 2 07:03 4OJCzmGV.cross
-rw-r--r-- 1 root root 10M Apr 2 07:03 6cExgwkd.cross
```
# Purescript browser buttons not showing...
- Slow query
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Slow query
## Tags
* assigned: Uditgulati
* priority: high
* status: stalled
* keywords: slow query, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/419...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
...GN searched for the term(s) "shh" in 754 datasets and 39,765,944 traits across 10 species
and found 1210 results that match your query.
You can filter these results by adding key words in the fields...
- GN1 annotation page broken
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
...Ember
```
Turns out that lily URLs were hard-coded in the source. So, that was an easy fix. There are still some complaints about CSS links missing in the browser console, but until someone sees...
- rewrite sampledata fetching with genofiles using scheme
issue opened on Jul 19 2023 by Alexander_Kabui, last updated on Jul 26 2023 by Alexander_Kabui; 2 of 6 tasks done
.../data-vault-2
### TODOS
* [x] reading the genofile
* [x] parsing the genofile to obtain the sample names,metadata
* [] adding unit tests for the module
* [] query statements fetch sampledata...
- Global search does not close connections properly (and is slow)
✓ issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
...[Warning] Aborted connection 45219 to db: 'db_webqtl' user: 'webqtlout' host: '127.0.0.1' (CLOSE_CONNECTION)
```
generating 6Mb of log file info.
In fact, every row in the table has a SQL query...
- Fetch trait names for phenotypes
issue opened on Mar 22 2022 by Frederick Muriuki Muriithi
.../564 From GitHub
The 'Fetch Trait Info' query returns detailed information for transcript expression traits, but not for traits from the 'Publish' database.
### Describe the solution you'd like
For...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated on Mar 23 2025 by Pjotr Prins; 33 of 74 tasks done
...it works on reboot (systemd)
* [-] singlecell (siamak)
* [-] rn6app (hao - remove)
* [-] genome-browser (defunct)
To fix them we need to validate the sheepdog monitor and make sure they are working...
- Annotate traits page with metadata from RDF
✓ issue opened on Sep 30 2022 by Munyoki Kilyungi, last updated on Dec 15 2022 by Munyoki Kilyungi; 16 of 16 tasks done
...query for the trait:
```
PREFIX gn: <http://genenetwork.org/>
SELECT ?name ?dataset ?dataset_group ?title ?summary ?aboutTissue ?aboutPlatform ?aboutProcessing
WHERE {
?dataset gn:accessionId "GN112"...