- Meeting Notes
document created on Jun 11 2024 by John Nduli, last updated on Jan 10 2025 by Munyoki Kilyungi
...editting on the AI paper
* IN PROGRESS: @shelby RAG engine only works with OpenAI, figure out Claude Sonnet integration
* IN PROGRESS: @jnduli get up to speed on gn-auth
* @jgart enabling acme service...
- RQTL Implementation for GeneNetwork Design Proposal
document created on Oct 15 2024 by Alexander_Kabui, last updated on Nov 12 2024 by Alexander_Kabui
...the STARTED stage, the stdout should notify the user that execution has begun.
- In the IN PROGRESS stage, we need to fetch logs from the script being executed at each computation step. Please refer...
- Tux01 hard disk crash
issue opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...One spinning disk crashed on Sept. 26th. It was used for Arthur's HOME and backups.
# Tags
* assigned: pjotrp
* priority: medium
* status: in progress
* keywords: system, tux01, hard disk crash
# Info...
- Tux02 Production
issue opened on Oct 07 2021 by Pjotr Prins, last updated on Jun 13 2025 by Pjotr Prins; 17 of 22 tasks done
...in progress
* priority: medium
* type: system administration
* keywords: systems, tux02, production
## Tasks
* [X] update guix guix-1.3.0-9.f743f20
* [X] set up nginx (Debian)
* [X] test ipmi console...
- Designing an issue tracker on gemini
✓ issue opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
...kanban: Brain storm
Keywords are fairly flexible, but common ones are
* request
* bug
* critical bug
* enhancement
* in progress
* testing
* later
* documentation
* help wanted
* closed
the keyword...
- 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
...in progress
* keywords: rdf, critical, metadata
Read the design-doc here:
=> /topics/add-metadata-to-trait-page
This task is related to:
=> /issues/capture-data-on-BXDs-in-RDF
# Tasks
## Exploration...
- Zoomed mapping result are empty for certain traits
issue opened on Apr 11 2022 by Zachary Sloan, last updated on Apr 13 2022 by Zachary Sloan
...in progress
* priority: high
This issue appears to be caused by marker namees being duplicated. If a marker name appears in an earlier chromosome, it ends up displayed first in the GEMMA results...
- Hoot Genome Browser
document created on Sep 23 2025 by Pjotr Prins, last updated on Sep 24 2025 by Johannes Medagbe
...in progress
* keywords: mapping
# Tasks
* [ ] Embed hoot browser in GN2 as a pilot
* + [ ] Guix package for JS and minimal JBrowse2?
* + [ ] Embedding code in GN2
* [ ] Create two tracks for QTL...
- Redirect Users to the Correct URL on Login for GN2
✓ issue opened on Sep 17 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
...in progress
* keywords: gn-auth, auth, redirect, login, completed, closed, done
* type: feature-request
## Description
The goal is to redirect users to the login page for services that require...
- Capture state of phenotypes in a HASH
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi
Capture state of phenotypes in a HASH
## Tags
* assigned: pjotrp, zsloan
* type: enhancement, feature-request
* status: in progress
* priority: medium
* keywords: phenotypes, REST, UI
## Description...
- Set Up gn-guile in tux02
issue opened on Aug 29 2024 by Munyoki Kilyungi, last updated on Oct 22 2024 by Munyoki Kilyungi; 3 of 3 tasks done
...in-progress
* deadline: 2024-10-23 Wed
## Tasks
* [-] Create gn-guile container.
* [X] Merge gn2 UI PR.
=> https://github.com/genenetwork/genenetwork2/pull/854 Feature/gn editor UI
* [-] Test out...
- Report invalid search queries passed to the search API
issue opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
...in progress
genenetwork2 offloads search to the genenetwork3 search API. When there is an error in the genenetwork3 API call, genenetwork2 has no idea what went wrong and cannot produce a good...
- issues/custom_data_for_scatterplot.gmi
issue opened on Mar 09 2023 by Zachary Sloan
...in-progress
* keywords: scatterplot, correlation
## Description
Currently the correlation scatterplot just takes the two trait/dataset names as input (so the page can be linked to others). The...
- Sheepdog
issue opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
...status: in progress, halted
* priority: medium
* keywords: system, sheepdog
## Tasks
* [X] add locking functionality for tags - added borg with-lock (test)
* [X] chgrp functionality in sheepdog_borg...
- Search results presentation
issue opened on Apr 04 2023 by Alexander_Kabui
...in progress
* keywords: UI,search
## Notes
The idea is to research and find good design for search results in global search
Currently the results are displayed in tabular form and too many columns...
- Search results for SNP looks weird
issue opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
...medium
* status: in progress
* keywords: UI, SNP, from github
## Description
=> https://github.com/genenetwork/genenetwork2/issues/395
### Description
After an update using the latest datatables...
- Enable all DataTables to call the same code
issue opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
...open, in progress
* keywords: tables, javascript
# Description
Currently most DataTables are drawn independently, so each separate page has its own DataTables initialization code. This results...
- Marker covariates implemented wrong in rqtl_wrapper.R
issue opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...waiting on Danny to get back to me with the fix (which I'll then add to rqtl_wrapper.R)
## Tags
* type: bug
* assigned: zsloan, danny
* status: in progress, halted
* keywords: marker covariates...
- Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
issue opened on Jul 21 2022 by Zachary Sloan
...open, in progress
* keywords: data, meta-data
# Description
Currently you can't do an analysis beween traits from the "main" BXD group and traits from any of the BXD individuals groups, but it should...
- Using guix-bioinformatics in a channels.scm file
issue opened on Aug 15 2021 by Efraim Flashner, last updated on Oct 09 2022 by Pjotr Prins
I think we should move to ssh keys and cgit. The latter has to run in a container, ideally.
## Tags
* assigned: efraimf, pjotrp
* type: bug
* keywords: guix-bioinformatics
* status: in progress...
- Add an 'Edit Issue' Link to Tissue
✓ issue opened on Mar 24 2022 by Frederick Muriuki Muriithi, last updated on Apr 15 2022 by Arun Isaac
...open, in progress
* keywords: tissue, edit issue
## Description
Add an `Edit Issue` link on each issue that drops the user in the forge's (currently GitHub) editting mode for the selected file.
- Troubleshoot response inconsistencies for GN-llm
issue opened on Jan 10 2024 by Alexander_Kabui
...In Progress
# Description
There are discrepancies when asking questions on Qnqa using Fahamu. Sometimes, responses take too long, and related queries with differing sentence structures may result...
- List of proposed changes for PCA traits/figures in Correlation Matrix page
issue opened on Jan 09 2023 by Zachary Sloan
...in-progress
* keywords: pca, correlations
## Description
Rob proposed the following changes to the PCA traits/figures:
1. Add the percentage of variance accounted for by each trait to the table...
- Parsing genotyfiles
issue opened on Jul 11 2023 by Alexander_Kabui
...alexm
* type: debug
* priority: high
* status: in progress
## Once you identify the genofile identify
the file in the GENOTYPE_FILES and extract sample_listx
for entire parsing code refer to...
- Global Search Performance/Optimisation
issue opened 30 hours ago by Munyoki Kilyungi; 0 of 3 tasks done
...in-progress
## Description
Global search is slow. Search latency sits at ~30 seconds. Historically, identical queries completed within 1–4 seconds. Root cause unclear, maybe hardware problems.
- Add the option to save traits uploaded with the Submit Trait option
issue opened on Jul 19 2022 by Zachary Sloan
...-request
* status: open, in progress
* keywords: data, meta-data
# Description
Current the Submit Trait feature only allows for trait data (submitted as just a string of values) to be saved as a "temp"...
- Deploy GeneNetwork
document created on Jan 18 2023 by Arun Isaac, last updated on Aug 27 2024 by Frederick Muriuki Muriithi
...docs, documentation
* keywords: deploy, deployment, deploying, guix, guix container, guix system container
* status: in progress
# Description
This page attempts to document the deployment process...
- 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
...in progress
* keywords: mapping
I currently have it displaying regions in mouse with text and a UCSC genome browser link to the corresponding human region as a track for the mapping figure.
# TODO
[X]...
- Annotation
issue opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
...a matching reference genome. In the future we'll build this out with pangenome support.
# Tags
* assigned: pjotrp,zsloan,arthurc,robw
* priority: medium
* type: enhancement
* status: open, in progress...
- AI UI Enhancements
issue opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
AI UI Enhancements
## Tags
* Assigned: alexm, shelbys
* Keywords: UI, GNQA
* Type: critical
* Status: In Progress
## Description
This issue addresses user feedback received during the testing phase...
- Penguin2 RAID 5
issue opened on Feb 28 2025 by Pjotr Prins
...@pjotrp
* status: in progress
# Description
The current RAID contains 3 disks:
```
root@penguin2:~# cat /proc/mdstat
md0 : active raid5 sdb1[1] sda1[0] sdg1[4]
/dev/md0 33T 27T 4.2T 87%...
- GN1 Production
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done
...in progress
* kanban: pjotrp
* assigned: pjotrp, zachs, robw
## List of outstanding issues
(see also E-mail Rob 14 Sep 2021)
* [ ] Fix annotating metadata - or do we have GN2 alternative?
=> gn1-...
- Scree Plot appears to be incorrect
issue opened on May 19 2022 by Zachary Sloan, last updated on Jun 15 2022 by BonfaceKilz
.../sens/195214c1833d435b3406fa55abf2b6f4 Jupyter notebook
for a demo on what it should look like using the GN API.
## Tags
* assigned: zsloan, alexm
* type: bug
* priority: medium
* status: in-progress...
- 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
...in progress
* Keyword : search, UI, bug, Refactor
* Type: UI, bug
## Description
The Global search UI layout is broken on certain browser versions.
This issue was reported to occur for **Firefox...
- Create Custom RIF XAPIAN Index
issue opened on Oct 16 2024 by Munyoki Kilyungi, last updated on Oct 22 2024 by Munyoki Kilyungi
...in-progress
* deadline: 2024-10-23 Wed
## Description
Given the GN Wiki search page:
=> https://cd.genenetwork.org/genewiki GeneWiki Entries Search
We only search by symbol. Add custom XAPIAN index...
- Return canned text if notebook description returns none
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Return canned text if notebook description returns none
## Tags
* type: bug
* assigned: jgart
* priority: high
* status: in progress
* keywords: binderlite, notebooks
## Description
Notebooks that do...
- Integrate styling of app with GN2
issue opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...in progress
* assigned: jgart
* type: bug
* priority: medium
* keywords: binderlite, notebooks, styling, UI
## Description
Currently using antiweb for styling with modifications.
=> https://git.sr.ht/~...
- Error Handling: External Errors
✓ issue opened on Jan 29 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
.../830
We can then maybe incorporate the use of UUIDs in the errors, to help with tracking the errors in the logs where necessary.
----
Some work has been done on this, but it is still a work in progress.
- BNW interface for GN2
document created on Oct 18 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...in progress
* keywords: BNW
## Todo
The current output reads:
```
<title>Opening BNW</title>
<form method="post" action="http://bnw.genenetwork.org/BNW/sourcecodes/bn_genenet.php" name="bnwform" id...
- Fix Opaque Errors
✓ issue opened on Feb 12 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
...help them fix issues on their own where possible.
As an example, see "Standard-Error Files Upload - Opaque Error Message" below.
Fixed issues are marked with [x], in progress, or partially fixed issue...
- Wrong CSV in ITP_10001 longevity dataset
✓ issue opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
...bug, in progress, metadata, phenotypes
## Description
[From Suheeta]:
"I downloaded the sample csv file for ITP_10001 to add a couple of attributes to it. What I see is that the csv file is somewhat...
- Each shepherd service needs its own guix profile.
issue opened on Nov 03 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
...a guix shell/environment:
* bnw
* cronjob-gitea
* cronjob-pubmed (genecup)
* genecup
* gitea
* ipfs
* power
* rn6app
* singlecell
## Tags
* assigned: efraim, pjotrp
* type: bug
* status: in progress...
- Implementation of QTL Analysis Using r-qtl2 in GeneNetwork
document created on Nov 12 2024 by Alexander_Kabui, last updated on Nov 12 2024 by Alexander_Kabui
...In Progress
## Description
This document outlines the implementation of a QTL analysis tool in GeneNetwork using r-qtl2 (see docs: https://kbroman.org/qtl2/) and explains what the script does.
- Branding and front-end-services
issue opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
...specific datasets
* + [ ] Show specific publications
* + [ ] Show specific twitter feed
# Tags
* assigned: pjotrp
* type: feature
* priority: high
* status: in progress
* keywords: website, branding
- Quality Control of Data in Uploaded R/qtl2 Bundles
✓ issue opened on Feb 02 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi; 10 of 15 tasks done
...following "key" details the meanings of certain notations in this file:
* [ ]: not started
* [-]: partially done or in progress
* [x]: completed
### [x] Control File
* [x] MUST exist in bundle
* [x]...
- Some correlations running very slowly
issue opened on Mar 06 2023 by Zachary Sloan, last updated on Mar 07 2023 by Pjotr Prins
...in-progress
* keywords: correlations, database
## Description
Some correlations (it specifically seems to be ones done against ProbeSet databases) are running extremely slowly.
After looking into...
- GN1 github problem
issue opened on Dec 17 2022 by Pjotr Prins
...error: failed to push some refs to 'git@github.com:genenetwork/genenetwork1.git'
```
This is because of a resync of lily. I should not do that again.
# Tags
* assigned: pjotrp
* status: in progress...
- Expose Versioned "rdf.genenetwork.org" Namespaces
✓ issue opened 2 weeks ago by Munyoki Kilyungi, last updated 5 days ago by Munyoki Kilyungi; 4 of 4 tasks done
...in-progress
## Description
We have switched all RDF namespaces from "genenetwork.org" to the versioned base "rdf.genenetwork.org/v1." These endpoints don't resolve yet.
## What changed
Replaced...
- GN2 Time Machines
issue opened on Aug 19 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 4 of 10 tasks done
...of interacting services and a larger dependency graph.
Here I track what it takes today to install a fallback instance of GN2 that is 'frozen' in time.
## Tags
* assigned: pjotrp
* status: in progress...
- Fix GN1 Network Graph
issue opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
...Graph
* status: in progress
* kanban: pjotrp
* assigned: pjotrp, zachs
## Tracking
To reproduce this bug: select a 'shopping basket' and click on network graph. No image is shown.
We needed to revert...
- GN Services
document created on Sep 15 2021 by Pjotr Prins, last updated on Dec 23 2022 by Pjotr Prins
...in progress
* keywords: gn services, documentation
# Description
First make sure to have a stable guix checkout. E.g.
```
gn3@tux01:~/production/gn-proxy$ /home/wrk/opt/guix-pull/bin/guix pull -p...
- Linking genotype files to datasets
issue opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
...in progress
## Notes
A dataset can have multiple groups. In order to fetch all possible sample data fetch all possible groups in a dataset then use that to fetch all linked genofiles
As an example...
- Fallbacks and backups
issue opened on Aug 31 2021 by Pjotr Prins, last updated on Jun 28 2024 by Pjotr Prins; 3 of 25 tasks done
...in progress
* priority: critical
## Tasks
* [X] fix redis queue and sheepdog server
* [X] check backups on tux01
* [ ] drop tux02 backups off-site
* [ ] backup ratspub, r/shiny, bnw, covid19, hegp...
- Investigate and Fix `rm` Command in `rqtl` Logs
issue opened on Jan 08 2025 by Alexander_Kabui, last updated on Jan 09 2025 by Munyoki Kilyungi; 4 of 6 tasks done
...in progress
* keywords: external, qtl, rqtl, bug, logs
## Description
For QTL analysis, we invoke the `rqtl` script as an external process through Python's `subprocess` module.
For reference, see...
- Phenotype Naming Conventions
document created on Nov 23 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
...motor Learning
* M_CONSTRICT
* F_LD_TRANSITIONS
* LOC OFLD 20-25
* Cnt_AdrWts
* Hbidm
Since we have a second-generation curation tool in progress, it would be great to apply some formal reasoning...
- GN Markdown Editor Integration
issue opened on Jun 07 2024 by Alexander_Kabui, last updated on Aug 22 2024 by Alexander_Kabui; 9 of 10 tasks done
...Markdown Editor Integration
## Tags
* assigned: alexm
* status: in progress
* priority: high
* tags: markdown, integration, guile
## Notes
This is a to-do list to integrate the GN Markdown editor into...
- Data Uploads: Inserting Data
document created on Jan 27 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
...in progress
* keywords: data uploads
### Introduction
The current uploader work documented in `editing-data.gmi` only caters
for the following operations by people with the right access:
- Editing...
- GeneNetwork Hacking Documentation
document created on Mar 11 2022 by Frederick Muriuki Muriithi, last updated on Jul 18 2022 by Frederick Muriuki Muriithi
...in progress
* priority: medium
* keywords: traits, datasets, hacking
## Unifying Principles
Like GNU Guix has the concepts of Packages, Monads, G-Expressions and the like as some of the unifying...
- Precompute steps
document created on May 07 2024 by Pjotr Prins, last updated on Jul 10 2025 by Pjotr Prins
...work on CWL. Rather than trying to write a workflow in bash, we'll use ccwl and accompanying tools to scale up the effort.
# Tags
* assigned: pjotrp
* type: precompute, gemma
* status: in progress...
- Build an AI system for GN
document created on Sep 24 2025 by Johannes Medagbe, last updated on Nov 19 2025 by johannesm
...in progress
* keywords: llm, rag, ai, agent
## Description
The aim is to build an AI system/agent/RAG able to digest mapping results and metadata in GN for analysis scaling. This is not quite...
- CI/CD for genetwork projects
document created on Oct 12 2022 by Munyoki Kilyungi, last updated on Jul 22 2025 by Pjotr Prins
...staggered across the entire deployment cycle to help with quick iteration of the code.
## Tags
* assigned: bonfacem, fredm, efraimf, aruni
* keywords: deployment, CI, CD, testing
* status: in progress...
- Apps
issue opened on Nov 19 2024 by Pjotr Prins, last updated 5 weeks ago by Pjotr Prins; 33 of 74 tasks done
...in progress
* priority: medium
* keywords: system, sheepdog, shepherd
# Tasks
* [ ] Get services running
* [ ] Move guix shell into containers
* [ ] Make sure the container starts up on reboot and/or...
- 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
...it is translating utf8mb3 for every comparison. Changing the table and indices to utf8mb4 or latin1 (on production) fixed it.
# Tags
* assigned: pjotrp, aruni
* priority: medium
* status: in progress...
- Fetch trait data using genofiles
issue opened on Jul 11 2023 by Alexander_Kabui, last updated on Jul 13 2023 by Alexander_Kabui; 2 of 3 tasks done
...in progress
## Notes
since Genenetwork database does not have all genotype files when fetching sample data use genotypes to fetch trat data given a dataset and the trait
Having fetched the sample...
- Configuring Nginx on the Host System
document created on Aug 27 2024 by Frederick Muriuki Muriithi
...in progress
## Introduction
We deploy the GeneNetwork system within GNU Guix system containers. All the configurations and HTTPS certificates are handled from within the container, thus all the host...
- Setting Up or Migrating Production Across Machines
document created on Apr 17 2025 by Frederick Muriuki Muriithi, last updated on Oct 07 2025 by Frederick Muriuki Muriithi
...in-progress
* assigned: fredm
* priority: undefined
* keywords: migration, production, genenetwork
* interested-parties: pjotrp, zachs
## Introduction
Recent events (Late 2024 and early 2025) have...
- 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
...in progress
* priority: critical
# Tasks
* [X] 502 timeout errors
* [X] Rqtl2 not working
* [X] 413 error
* [ ] BNW error
* [ ] Monitor service - both systemd and sheepdog
* [ ] Files in /tmp
## 502...
- CD is slow
issue opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
...DNS server was not responding. Using Google's DNS made things go fast again. We will probably introduce dnsmasq in the container to make things even faster.
# Tags
* type: bug
* status: in progress...
- Precompute mapping input data
document created on Apr 23 2025 by Pjotr Prins, last updated on Jul 29 2025 by Pjotr Prins
...doing anything we use Locus_old to identify updates by setting it to NULL. See the header of list-traits-to-compute.scm.
# Tags
* assigned: pjotrp
* type: precompute, gemma
* status: in progress...
- MariaDB: Move to InnoDB Engine
issue opened on Dec 28 2021 by Pjotr Prins, last updated on Apr 24 2024 by Pjotr Prins; 0 of 8 tasks done
...because they are small.
Actually ProbeData and ProbeSE (containing the Affy data) are not referenced in GN2. I need to check that.
## Tasks
* assigned: pjotrp
* priority: high
* status: in-progress...