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706 All
210 open issues
274 closed issues
222 documents
0 commits
Benchmark DuckDB against LMDB for storing genotypes
duckdb
lmdb
genotypes
benchmarking
parquet
qtl
open
waiting
feature-request
medium
issue
opened 5 hours ago by Alexander_Kabui
Writing a guix package with Claude code
document
created 2 weeks ago by Pjotr Prins, last updated 6 hours ago by Pjotr Prins
Singularity on Octopus
document
created 2 weeks ago by Pjotr Prins, last updated 6 hours ago by Pjotr Prins
Guix system containers and how we use them
document
created on Mar 31 2023 by Arun Isaac, last updated 6 hours ago by Pjotr Prins
Implementation of storing genotypes in LMDB
lmdb
genotypes
versioning
open
in progress
feature-request
high
issue
opened 2 weeks ago by Alexander_Kabui, last updated 8 hours ago by Alexander_Kabui; 8 of 12 tasks done
gn-ai search UI/UX enhancements (web-native)
in-progress
issue
opened 11 days ago by Munyoki Kilyungi, last updated 9 days ago by Munyoki Kilyungi
Prompt As UI
in-progress
issue
opened on Feb 18 2026 by Munyoki Kilyungi, last updated 14 days ago by Munyoki Kilyungi; 40 of 43 tasks done
Reverse Genotyping Approach for BXD
genotyping
smoothing
qtl hotspots
biological signals
noise
markers (snps)
reverse genotyping
ongoing
high
project
issue
opened 2 weeks ago by Lisso_; 4 of 9 tasks done
Installation with Guix
document
created on Jun 18 2023 by Pjotr Prins, last updated 2 weeks ago by Pjotr Prins
Octopus pages/links
document
created 2 weeks ago by Pjotr Prins
Cosigt (on Octopus)
document
created 2 weeks ago by Pjotr Prins
PubMed local
document
created 2 weeks ago by Pjotr Prins
Apps
system
sheepdog
shepherd
medium
in progress
enhancement
issue
opened on Nov 19 2024 by Pjotr Prins, last updated 2 weeks ago by Pjotr Prins; 34 of 74 tasks done
Slurm User Guide on Octopus HPC
document
created on Feb 11 2024 by Pjotr Prins, last updated 2 weeks ago by Pjotr Prins
LMDB-Based Correlation Computation Report
in-progress
issue
opened 6 weeks ago by Alexander_Kabui, last updated 3 weeks ago by Alexander_Kabui; 4 of 4 tasks done
Dumping Probesets from MariaDB to LMDB
lmdb
probeset
documentation
script
datasets
in progress
issue
opened 3 weeks ago by Alexander_Kabui
Trait page breaks when gn-guile is down
medium
cd
traits
gn-guile
in-progress
issue
opened 4 weeks ago by Alexander_Kabui, last updated 4 weeks ago by Alexander_Kabui; 0 of 1 tasks done
Trouble shoot rqlt2 in GN2 (improve comptutations), dump genotypes (HS, Kilifish) to LMDB, reverse genotyping progress
active
issue
opened 5 weeks ago by Lisso_; 0 of 3 tasks done
Trouble shoot rqlt2 in GN2 (improve comptutations), dump genotypes (HS, Kilifish) to LMDB, reverse genotyping progress
active
issue
opened 5 weeks ago by Lisso_; 0 of 3 tasks done
Attaining Build Sanity
document
created 7 weeks ago by Munyoki Kilyungi, last updated 6 weeks ago by Munyoki Kilyungi
Implement File-Based, and CLI-Based Configuration for "gn-guile"
gn-guile
config
configs
configuration
open (awaiting patch(es) review)
high
feature
issue
opened 6 weeks ago by Frederick Muriuki Muriithi, last updated 6 weeks ago by Frederick Muriuki Muriithi
QTLReaper script fails but job is marked as successfully completed.
bug
completed
gn-uploader
uploader
data
datasets
medium
✓ issue
opened 6 weeks ago by Frederick Muriuki Muriithi, last updated 6 weeks ago by Frederick Muriuki Muriithi
Restrict access to "Make Public" Feature of Resources
bug
completed
gn-auth
auth
gn2
genenetwork2
data
datasets
medium
✓ issue
opened 6 weeks ago by Frederick Muriuki Muriithi, last updated 6 weeks ago by Frederick Muriuki Muriithi
Add Privileges for gn-docs Editing
feature-request
completed
gn-auth
auth
gn2
genenetwork2
wiki
medium
✓ issue
opened 6 weeks ago by Frederick Muriuki Muriithi, last updated 6 weeks ago by Frederick Muriuki Muriithi
Implement Upload of Genotypes
feature request
feature-request
open
gn-uploader
uploader
data
datasets
genotypes
medium
issue
opened 6 weeks ago by Frederick Muriuki Muriithi
"Delete All" Phenotypes Path Fails on Production.
bug
open
gn-uploader
uploader
data
datasets
medium
issue
opened 6 weeks ago by Frederick Muriuki Muriithi
RDF Refinement
in-progress
issue
opened on Feb 18 2026 by Munyoki Kilyungi, last updated 6 weeks ago by Johannes Medagbe; 73 of 80 tasks done
Delete Phenotypes
uploader
gn-uploader
delete phenotypes
phenotypes
feature-request
feature request
high
completed
✓ issue
opened on Feb 18 2026 by Frederick Muriuki Muriithi, last updated 6 weeks ago by Johannes Medagbe
Synchronise gn-docs Changes
gn-guile
gn-docs
feature-request
feature request
high
open
issue
opened on Feb 18 2026 by Frederick Muriuki Muriithi, last updated 6 weeks ago by Johannes Medagbe
Investigate and fix "qtl2::calc_genoprob()" run due to failing with negative length vectors
in progress
bug
issue
opened 8 weeks ago by Lisso_, last updated 6 weeks ago by Johannes Medagbe
Machines
document
created 8 weeks ago by Pjotr Prins, last updated 6 weeks ago by Johannes Medagbe
Install and use Claude Code using Guix
document
created 8 weeks ago by Pjotr Prins, last updated 6 weeks ago by Johannes Medagbe
Local Search Not Working
issue
opened on Feb 02 2026 by Munyoki Kilyungi, last updated on Feb 18 2026 by Munyoki Kilyungi
Expose LMBD in RDF
in-progress
issue
opened on Feb 10 2026 by Munyoki Kilyungi, last updated on Feb 18 2026 by Munyoki Kilyungi; 9 of 18 tasks done
Virtuoso Crash Inside Container
✓ issue
opened on Feb 12 2026 by Munyoki Kilyungi, last updated on Feb 16 2026 by Munyoki Kilyungi
Running snakemake workflows on octopus
document
created on Feb 12 2026 by Arun Isaac
New Server
hardware
servers
deploy
feature-request
feature reques
medium
completed
✓ issue
opened on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe; 6 of 6 tasks done
Samples: ...
completed
high
gn-uploader
uploader
background jobs
bug
improvement
✓ issue
opened on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe
Jobs: Track Who Jobs Belong To
gn-libs
genenetwork
async jobs
asynchronous jobs
background jobs
enhancement
medium
completed
✓ issue
opened on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe
Pass on Unknown GET Parameters
gn-auth
authorisation
feature-request
enhancement
medium
completed
✓ issue
opened on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe
Improve Authorization Checks
open
high
gn-auth
auth
authorisation
authorization
improvement
refactor
issue
opened on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe; 2 of 11 tasks done
mechanical-rob: Add Partial Correlations Tests
enhancement
genenetwork2
gn2
mechanical-rob
partial correlations
tests
regression
completed
medium
✓ issue
opened on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe; 5 of 5 tasks done
Error Adding Trait(s) to Collection(s) While Logged Out
gn2
genenetwork2
genenetwork 2
collections
high
open
bug
issue
opened on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe
Setting Up or Migrating Production Across Machines
document
created on Feb 10 2026 by Frederick Muriuki Muriithi, last updated on Feb 11 2026 by Johannes Medagbe
Octopussy needs love
document
created on Dec 21 2025 by Pjotr Prins, last updated on Feb 10 2026 by Pjotr Prins
Moosefs
document
created on Jan 01 2026 by Pjotr Prins, last updated on Feb 10 2026 by Pjotr Prins
Build an AI system for GN
llm
rag
ai
agent
in-progress
medium
feature
issue
opened on Feb 04 2026 by Johannes Medagbe; 4 of 6 tasks done
Global Search Performance/Optimisation
✓ issue
opened on Jan 19 2026 by Munyoki Kilyungi, last updated on Feb 03 2026 by Munyoki Kilyungi; 3 of 3 tasks done
Profiling GN
✓ issue
opened on Jul 23 2025 by Munyoki Kilyungi, last updated on Feb 03 2026 by Munyoki Kilyungi
Migrate Genenetwork Production from tux03 to tux04, Jan2026-Feb2026
genenetwork
production
migration
high
open
issue
opened on Jan 21 2026 by Frederick Muriuki Muriithi, last updated on Feb 03 2026 by Frederick Muriuki Muriithi; 8 of 8 tasks done
RDF Content Negotiation
✓ issue
opened on Jan 23 2026 by Munyoki Kilyungi, last updated on Jan 26 2026 by Munyoki Kilyungi
Guix installation and versions
document
created on Jan 24 2026 by Pjotr Prins, last updated on Jan 24 2026 by Pjotr Prins
Updating Guix profiles (for production and development)
document
created on Jun 14 2022 by Arun Isaac, last updated on Jan 24 2026 by Pjotr Prins
Expose Versioned "rdf.genenetwork.org" Namespaces
✓ issue
opened on Jan 06 2026 by Munyoki Kilyungi, last updated on Jan 23 2026 by Munyoki Kilyungi; 4 of 4 tasks done
Restore backup
document
created on Feb 07 2023 by Pjotr Prins, last updated on Jan 22 2026 by Frederick Muriuki Muriithi
Power
document
created on Jan 20 2026 by Frederick Muriuki Muriithi, last updated on Jan 20 2026 by Frederick Muriuki Muriithi
Testing performance
document
created on Mar 08 2023 by Pjotr Prins, last updated on Jan 17 2026 by Pjotr Prins
Octopus Maintenance
document
created on Feb 13 2023 by Pjotr Prins, last updated on Jan 17 2026 by Pjotr Prins
Test pangenome derived genotypes
document
created on Nov 04 2025 by Pjotr Prins, last updated on Jan 17 2026 by Pjotr Prins
Virtuoso Fails to Start Due to Incorrect Log File Ownership
✓ issue
opened on Jan 15 2026 by Munyoki Kilyungi
Unable to View Dataset Metadata
to-do
high
✓ issue
opened on Jan 06 2026 by Munyoki Kilyungi, last updated on Jan 13 2026 by Munyoki Kilyungi
Lizard maintenance
document
created on Jul 18 2021 by Pjotr Prins, last updated on Jan 11 2026 by Pjotr Prins
Update gn-libs in CD container
to-do
high
✓ issue
opened on Jan 06 2026 by Munyoki Kilyungi, last updated on Jan 07 2026 by Munyoki Kilyungi
XAPIAN Search General Issues
✓ issue
opened on Jun 21 2024 by Munyoki Kilyungi, last updated on Jan 06 2026 by Munyoki Kilyungi
Update RDF Generation and Ingress to Virtuoso
done
high
✓ issue
opened on Oct 15 2024 by Munyoki Kilyungi, last updated on Jan 06 2026 by Munyoki Kilyungi
Prevent Weak Passwords
feature-request
feature request
security
password
gn-auth
medium
open
issue
opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
Mapping Error
gn2
genenetwork2
genenetwork 2
mapping
medium
bug
✓ issue
opened on Jul 03 2024 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
guix-bioinformatics: Remove `guix-rust-past-crates` channel
guix-bioinformatics
guix-rust-past-crates
guix
rust
crates
bug
open
normal
issue
opened on Oct 27 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
ProbeSet not Applicable to All Data
gn-uploader
uploader
probeset
high
bug
✓ issue
opened on Jun 20 2024 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
Replace Redis with SQL
gn-uploader
uploader
redis
sqlite
sqlite3
feature
feature-request
feature request
low
open
issue
opened on Mar 12 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
Query Bug: DatabaseError
gnqna
bug
open
high
issue
opened on Oct 27 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi
Pin Channel Commits; Decouple from Guix
guix-bioinformatics
guix
enhancement
medium
✓ issue
opened on Nov 03 2025 by Frederick Muriuki Muriithi, last updated on Dec 31 2025 by Frederick Muriuki Muriithi; 4 of 5 tasks done
Octopus/Tux maintenance
document
created on Apr 06 2025 by AndreaGuarracino, last updated on Dec 22 2025 by Pjotr Prins
Guix packages
document
created on Dec 23 2022 by Pjotr Prins, last updated on Dec 21 2025 by Pjotr Prins
Fixating Guix for GN
document
created on Dec 21 2025 by Pjotr Prins
Epochs
document
created on Nov 04 2025 by Pjotr Prins, last updated on Dec 20 2025 by Pjotr Prins
Precompute PublishData
document
created on Oct 29 2025 by Pjotr Prins, last updated on Dec 19 2025 by Pjotr Prins
PanGEMMA Genotype Format
document
created on Dec 17 2025 by Pjotr Prins, last updated on Dec 19 2025 by Pjotr Prins
Publications on Genenetwork
document
created on Dec 19 2025 by Frederick Muriuki Muriithi
Octopus sysmaintenance
systems
octopus
system administration
open
high
issue
opened on Oct 12 2021 by Pjotr Prins, last updated on Dec 12 2025 by Pjotr Prins; 1 of 8 tasks done
Speeding up GEMMA
high
feature
issue
opened on Nov 11 2025 by Pjotr Prins, last updated on Dec 12 2025 by Pjotr Prins; 5 of 15 tasks done
Planned Guix Updates
guix-bioinformatics
guix
enhancement
medium
open
issue
opened on Nov 14 2025 by Munyoki Kilyungi
Improving Alerting/Logging in GN2
document
created on Aug 23 2022 by Munyoki Kilyungi, last updated on Nov 14 2025 by Munyoki Kilyungi
Failing Services' Startup
deployment
ci
cd
high
completed
bug
✓ issue
opened on Aug 20 2025 by Frederick Muriuki Muriithi, last updated on Nov 11 2025 by Munyoki Kilyungi
Guix CI failure: guix-past build breaks due to missing (libchop)
high
bug
infrastructure
✓ issue
opened on Nov 11 2025 by Munyoki Kilyungi, last updated on Nov 11 2025 by Munyoki Kilyungi
Jobs: Allow Job Cascades
gn-libs
genenetwork
async jobs
asynchronous jobs
background jobs
enhancement
medium
open
issue
opened on Nov 05 2025 by Frederick Muriuki Muriithi
Guix Rust Bootstrap
document
created on Oct 22 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
IMPG AGC bindings
document
created on Oct 22 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
Pangenotypes
document
created on Oct 11 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
Aider
document
created on Oct 29 2025 by Pjotr Prins, last updated on Nov 05 2025 by Johannes Medagbe
Export Uploaded Data to LMDB and RDF Stores
api
data upload
gn-uploader
open
feature-request
medium
issue
opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Oct 20 2025 by Frederick Muriuki Muriithi; 0 of 6 tasks done
R/qtl2 LMDB Adapter
document
created on Sep 04 2025 by Alexander_Kabui, last updated on Oct 20 2025 by Frederick Muriuki Muriithi
uACME Error: "urn:ietf:params:acme:error:unauthorized"
uacme
certificates
"urn:ietf:params:acme:error:unauthorized"
bug
high
completed
✓ issue
opened on Oct 19 2025 by Frederick Muriuki Muriithi, last updated on Oct 20 2025 by Frederick Muriuki Muriithi
Genenetwork3 Configurations
bug
configuration
config
gn2
genenetwork
genenetwork2
completed
normal
✓ issue
opened on Jun 15 2023 by Frederick Muriuki Muriithi, last updated on Oct 15 2025 by Frederick Muriuki Muriithi
Markdown Editing Service: Not Deployed
production
container
tux04
critical
completed
fixed
bug
✓ issue
opened on Oct 26 2024 by Frederick Muriuki Muriithi, last updated on Oct 15 2025 by Frederick Muriuki Muriithi
gn-guile: Activations on Production not Running as Expected
gn-guile
deployment
activation-service-type
bug
high
completed
fixed
✓ issue
opened on Aug 15 2025 by Frederick Muriuki Muriithi, last updated on Oct 15 2025 by Frederick Muriuki Muriithi
AuthorisationError in gn uploader
error
critical
obsoleted
✓ issue
opened on May 14 2025 by Lisso_, last updated on Oct 15 2025 by Frederick Muriuki Muriithi
Handling Tissue in Uploader
gn-uploader
tissues
archived
feature-request
high
wontfix
✓ issue
opened on Mar 28 2024 by Frederick Muriuki Muriithi, last updated on Oct 15 2025 by Frederick Muriuki Muriithi; 2 of 2 tasks done
Genenetwork2 Configurations
bug
configuration
config
gn2
genenetwork
genenetwork2
obsoleted
normal
✓ issue
opened on Jun 14 2023 by Frederick Muriuki Muriithi, last updated on Oct 15 2025 by Frederick Muriuki Muriithi
Refresh Token Failure
gn2
genenetwork2
bug
high
obsoleted
✓ issue
opened on Jan 08 2025 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Can't Masquarade as another user as a system admin
completed
critical
✓ issue
opened on May 15 2024 by Munyoki Kilyungi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Fix Refresh Token
gn-auth
token
refresh token
jwt
feature-request
bug
high
obsolete
✓ issue
opened on Dec 05 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Remove `bin/genenetwork2` Script
gn2
bin/genenetwork2
startup script
medium
completed
improvement
✓ issue
opened on Sep 04 2025 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi; 6 of 6 tasks done
Explanation of how Sample Lists are handled in GN2 (and may be handled moving forward)
document
created on Sep 19 2024 by Zachary Sloan, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
A Listing of Features and/or Bugs without Dedicated Issues
bug
feature
high
completed
listing
✓ issue
opened on Feb 16 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Provide Link to Register User on Sign-In Page
register user
gn-auth
genenetwork
medium
bug
✓ issue
opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Provide Page/Link for/to Uploaded Data
gn-uploader
uploader
data dashboard
feature
feature request
feature-request
medium
completed
✓ issue
opened on Jul 10 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Link Authentication/Authorisation
gn-uploader
gn-auth
authorisation
authentication
uploader
upload
feature request
feature-request
critical
completed
✓ issue
opened on Jun 24 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Rework "View-Resource" Page
gn-auth
resource
resources
view resource
enhancement
medium
completed
✓ issue
opened on Jul 31 2025 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
R/qtl2 Maps Error
r/qtl2
r/qtl2 maps
gn3
genetwork3
genenetwork 3
high
completed
bug
✓ issue
opened on May 15 2025 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Handle OAuth Errors Better
gn2
genenetwork2
ui
user interface
oauth
oauth errors
high
completed
bug
✓ issue
opened on Oct 25 2024 by Frederick Muriuki Muriithi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Spam Entries in Auth (Production)
auth
completed
✓ issue
opened on Mar 07 2024 by Munyoki Kilyungi, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Correlations timing out for "UMUTAffy Hippocampus Exon (Feb09) RMA" correlations (and probably some others)
correlations
completed
high
bug
✓ issue
opened on Oct 17 2022 by Zachary Sloan, last updated on Oct 14 2025 by Frederick Muriuki Muriithi
Installing GPU on Balg01 server
document
created on Oct 04 2025 by Pjotr Prins, last updated on Oct 07 2025 by Pjotr Prins
Stand-up Notes
document
created on Oct 04 2025 by Munyoki Kilyungi
Backup Drops
document
created on Sep 22 2025 by Pjotr Prins, last updated on Sep 24 2025 by Johannes Medagbe
Hoot Genome Browser
document
created on Sep 23 2025 by Pjotr Prins, last updated on Sep 24 2025 by Johannes Medagbe
Tux04/Tux05 disk issues
medium
unclear
hardware
systems
issue
opened on May 03 2024 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins; 12 of 12 tasks done
Update production checklist
document
created on May 10 2025 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins
Borg backups
document
created on Feb 09 2025 by Pjotr Prins, last updated on Sep 13 2025 by Pjotr Prins
Security
document
created on Sep 09 2025 by Pjotr Prins
GPU Graphics Driver Set-Up
document
created on Sep 01 2025 by Munyoki Kilyungi, last updated on Sep 04 2025 by Munyoki Kilyungi
rewrite sampledata fetching with genofiles using scheme
stalled
closed.
high
improvement
issue
opened on Jul 19 2023 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 2 of 6 tasks done
Implement No-Login Requirement for GNQA
gnqa
user experience
authentication
llm
medium
completed
feature
✓ issue
opened on Jun 04 2025 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 4 of 4 tasks done
Merge GNQA to Production
completed
production
gnqa
integration
✓ issue
opened on Feb 12 2024 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 2 of 2 tasks done
Xapian to Text Transformer
completed
feature
llm
genenetwork2
xapian
transform
✓ issue
opened on Sep 09 2024 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui
Gn Markdown Editor implementation
markdown
editor
done
completed.
enhancement
issue
opened on Aug 07 2023 by Alexander_Kabui, last updated on Sep 01 2025 by Alexander_Kabui; 5 of 5 tasks done
Virtuoso
document
created on Aug 27 2021 by Pjotr Prins, last updated on Aug 20 2025 by Pjotr Prins
Debugging and developing code
document
created on Mar 19 2024 by Pjotr Prins, last updated on Aug 20 2025 by Pjotr Prins
Our virtuoso instances
document
created on Mar 31 2023 by Arun Isaac, last updated on Aug 20 2025 by Pjotr Prins
Broken Aliases
aliases
aliases server
high
open
bug
issue
opened on Oct 21 2024 by Frederick Muriuki Muriithi, last updated on Aug 15 2025 by Frederick Muriuki Muriithi; 3 of 4 tasks done
issues/systems/t02-crash.gmi
issue
opened on Aug 12 2025 by Pjotr Prins
Precompute mapping input data
document
created on Apr 23 2025 by Pjotr Prins, last updated on Jul 29 2025 by Pjotr Prins
CD is slow
deployment
server
high
in progress
bug
issue
opened on Jul 20 2025 by Pjotr Prins, last updated on Jul 24 2025 by Pjotr Prins; 2 of 8 tasks done
Troubleshooting inside the GN dev container
troubleshooting
logs
webhooks
systems
debugging
container
issue
opened on Jul 22 2025 by Munyoki Kilyungi, last updated on Jul 22 2025 by Munyoki Kilyungi
CI/CD for genetwork projects
document
created on Oct 12 2022 by Munyoki Kilyungi, last updated on Jul 22 2025 by Pjotr Prins
Deploying GeneNetwork CD
issue
opened on Jul 18 2025 by Munyoki Kilyungi, last updated on Jul 18 2025 by Munyoki Kilyungi
UTHSC E-mail
document
created on Jul 18 2025 by Pjotr Prins
Precompute steps
document
created on May 07 2024 by Pjotr Prins, last updated on Jul 10 2025 by Pjotr Prins
UTHSC VPN with free software
document
created on Aug 22 2022 by Arun Isaac, last updated on Jul 05 2025 by Pjotr Prins
guix build gn-uploader: error
guix
gn-uploader
bug
critical
✓ issue
opened on Mar 13 2024 by Frederick Muriuki Muriithi, last updated on Jun 19 2025 by Pjotr Prins
E-Mail Verification
gn-auth
oauth2
email
enhancement
medium
completed
✓ issue
opened on Jun 04 2024 by Zachary Sloan, last updated on Jun 19 2025 by Pjotr Prins
Tux02 Production
systems
tux02
production
system administration
medium
in progress
issue
opened on Oct 07 2021 by Pjotr Prins, last updated on Jun 13 2025 by Pjotr Prins; 17 of 22 tasks done
Starting GN1
document
created on Dec 08 2022 by Pjotr Prins, last updated on Jun 13 2025 by Pjotr Prins
Next steps
document
created on Jun 06 2025 by Pjotr Prins
Use a recent Rust on Octopus
document
created on Jun 04 2025 by Pjotr Prins
Production on tux04
issue
opened on May 10 2025 by Pjotr Prins, last updated on May 14 2025 by Frederick Muriuki Muriithi; 10 of 12 tasks done
MariaDB
document
created on May 10 2025 by Pjotr Prins, last updated on May 14 2025 by Frederick Muriuki Muriithi
Using autossh to Keep SSH Tunnels Alive
document
created on Apr 23 2025 by Alexander_Kabui, last updated on May 14 2025 by Frederick Muriuki Muriithi
Deploying genecup
document
created on Apr 22 2025 by Pjotr Prins, last updated on May 14 2025 by Frederick Muriuki Muriithi
Generate Heatmaps Failing
genenetwork3
gn3
gn3
heatmaps
medium
open
bug
issue
opened on Oct 15 2024 by Frederick Muriuki Muriithi, last updated on Apr 08 2025 by Frederick Muriuki Muriithi
Broken Collections Features
gn2
genenetwork2
genenetwork 2
collections
high
open
bug
issue
opened on Apr 07 2025 by Frederick Muriuki Muriithi, last updated on Apr 08 2025 by Frederick Muriuki Muriithi
CTL Maps Error
ctl
ctl maps
gn3
genetwork3
genenetwork 3
high
open
bug
issue
opened on Apr 08 2025 by Frederick Muriuki Muriithi, last updated on Apr 08 2025 by Frederick Muriuki Muriithi
Fix Display for the Time Consumed for Correlations
gn2
genenetwork2
genenetwork 2
gn3
genenetwork3 genenetwork 3
correlations
time display
low
completed
bug
✓ issue
opened on Mar 31 2025 by Frederick Muriuki Muriithi, last updated on Mar 31 2025 by Frederick Muriuki Muriithi
Synchronising the Different Environments
document
created on Mar 12 2025 by Frederick Muriuki Muriithi
Production Container: `mechanical-rob` Failure
genenetwork
production
mechanical-rob
bug
high
completed
fixed
✓ issue
opened on Feb 19 2025 by Frederick Muriuki Muriithi, last updated on Mar 10 2025 by Frederick Muriuki Muriithi
OctoRAID
issue
opened on Feb 28 2025 by Pjotr Prins
Penguin2 RAID 5
in progress
issue
opened on Feb 28 2025 by Pjotr Prins
MariaDB Database Architecture
document
created on Jun 29 2024 by Pjotr Prins, last updated on Feb 24 2025 by Pjotr Prins
OntoGPT
document
created on Feb 24 2025 by Pjotr Prins
Rework Hard Dependence on Github
gn-guile
github
bug
medium
open
issue
opened on Feb 14 2025 by Frederick Muriuki Muriithi, last updated on Feb 14 2025 by Frederick Muriuki Muriithi
Rendering Images Linked in Markdown Documents
gn-guile
images
markdown
bug
high
open
issue
opened on Feb 11 2025 by Frederick Muriuki Muriithi
GeneNetwork Releases
document
created on Feb 10 2025 by Frederick Muriuki Muriithi
Fix Pairscan Mapping
pairscan
debug
fix
mapping
bug
medium
issue
opened on Jan 13 2025 by Alexander_Kabui
Meeting Notes
document
created on Jun 11 2024 by John Nduli, last updated on Jan 10 2025 by Munyoki Kilyungi
Meeting Notes
document
created on Jan 10 2025 by Munyoki Kilyungi
Genenetwork Streaming Functionality
document
created on Jan 10 2025 by Alexander_Kabui
Investigate and Fix `rm` Command in `rqtl` Logs
external
qtl
rqtl
bug
logs
in progress
bug
issue
opened on Jan 08 2025 by Alexander_Kabui, last updated on Jan 09 2025 by Munyoki Kilyungi; 4 of 6 tasks done
Fix Broken Global Search UI
ui
bug
in progress
high
issue
opened on Jan 07 2025 by Alexander_Kabui, last updated on Jan 07 2025 by Alexander_Kabui; 0 of 2 tasks done
DNS changes
document
created on Sep 03 2022 by Pjotr Prins, last updated on Nov 22 2024 by Pjotr Prins
Add (2nd) boot and other partitions
document
created on Nov 19 2024 by Pjotr Prins, last updated on Nov 19 2024 by Pjotr Prins
gn-guile Configurations
gn-guile
markdown editing
open
high
bug
issue
opened on Nov 18 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
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
RQTL Implementation for GeneNetwork Design Proposal
document
created on Oct 15 2024 by Alexander_Kabui, last updated on Nov 12 2024 by Alexander_Kabui
Cannot Connect to MariaDB
issue
opened on Nov 05 2024 by Frederick Muriuki Muriithi, last updated on Nov 08 2024 by Frederick Muriuki Muriithi
Python Requests Error in Container
production
container
tux04
python
requests
completed
fixed
critical
bug
✓ issue
opened on Nov 01 2024 by Frederick Muriuki Muriithi, last updated on Nov 07 2024 by Frederick Muriuki Muriithi
Handle Temporary Directories in the Container
production
container
tux04
completed
critical
feature
✓ issue
opened on Nov 01 2024 by Frederick Muriuki Muriithi, last updated on Nov 05 2024 by Frederick Muriuki Muriithi
Containerising Production: Issues
production
container
tux04
completed
critical
bug
✓ issue
opened on Oct 26 2024 by Frederick Muriuki Muriithi, last updated on Nov 05 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
GeneNetwork Services
document
created on Oct 26 2024 by Frederick Muriuki Muriithi, last updated on Nov 01 2024 by Frederick Muriuki Muriithi
Virtuoso: Shutdown Clears Data
production
container
tux04
virtuoso
completed
critical
bug
✓ issue
opened on Oct 28 2024 by Frederick Muriuki Muriithi, last updated on Oct 30 2024 by Frederick Muriuki Muriithi
Set-up Virtuoso+Xapian on Production
virtuoso
ops
high
✓ issue
opened on Nov 22 2023 by Munyoki Kilyungi, last updated on Oct 28 2024 by Frederick Muriuki Muriithi; 1 of 1 tasks done
Setup Mailing on Tux04
production
container
tux04
critical
bug
✓ issue
opened on Oct 28 2024 by Frederick Muriuki Muriithi, last updated on Oct 28 2024 by Frederick Muriuki Muriithi
MGAMMA design philosophy
issue
opened on Apr 17 2024 by Pjotr Prins, last updated on Oct 27 2024 by Pjotr Prins
UM-HET3 Timing: Slow
production
container
tux04
um-het3
critical
open
bug
issue
opened on Oct 26 2024 by Frederick Muriuki Muriithi, last updated on Oct 26 2024 by Frederick Muriuki Muriithi
Replace Neo4J with Virtuoso
issue
opened on Oct 22 2024 by Munyoki Kilyungi
Set Up gn-guile in tux02
in-progress
high
issue
opened on Aug 29 2024 by Munyoki Kilyungi, last updated on Oct 22 2024 by Munyoki Kilyungi; 3 of 3 tasks done
Create Custom RIF XAPIAN Index
in-progress
medium
issue
opened on Oct 16 2024 by Munyoki Kilyungi, last updated on Oct 22 2024 by Munyoki Kilyungi
How to upgrade slurm on octopus
document
created on Aug 29 2024 by Arun Isaac, last updated on Oct 18 2024 by Arun Isaac
Check for Mandatory Settings
gn3
gn3
genenetwork3
settings
config
configs
configurations
bug
improvement
high
open
issue
opened on Oct 18 2024 by Frederick Muriuki Muriithi; 0 of 3 tasks done
Deploying Your Flask Application Under a URL Prefix With GUnicorn
document
created on Oct 17 2024 by Frederick Muriuki Muriithi
Error when loading GN2 with old pre-update session
gn-auth
gn2
bug
medium
✓ issue
opened on Jun 03 2024 by Zachary Sloan, last updated on Oct 17 2024 by Zachary Sloan
Fix Xapian search bug
xapian
gn2
gn3
high
✓ issue
opened on Jun 07 2024 by Zachary Sloan, last updated on Oct 17 2024 by Zachary Sloan
The * Search for Genotypes Not Working
medium
bug
✓ issue
opened on Sep 17 2024 by Zachary Sloan, last updated on Oct 17 2024 by Zachary Sloan
Set up Guix for new users
document
created on Oct 17 2024 by Arun Isaac, last updated on Oct 17 2024 by Arun Isaac
Redirect Users to the Correct URL on Login for GN2
feature-request
gn-auth
auth
redirect
completed
done
in progress
medium
✓ issue
opened on Sep 17 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
GNQA Integration to Global Search Design Proposal
complete
done
feature
llm
genenetwork2
✓ issue
opened on Sep 02 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 9 of 9 tasks done
Cleanup GN2 Base HTML File
completed
done
refactoring
base
html
javascript
cleanup
✓ issue
opened on Sep 23 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 3 of 3 tasks done
Redesign Global Search Design
completed
done
enhancement
global search
design
html
✓ issue
opened on Sep 26 2024 by Alexander_Kabui, last updated on Oct 16 2024 by Alexander_Kabui; 2 of 2 tasks done
Edit RIF Metadata in GN2
high
✓ issue
opened on Jul 29 2024 by Munyoki Kilyungi, last updated on Oct 15 2024 by Munyoki Kilyungi; 15 of 15 tasks done
R/qtl2
document
created on Oct 07 2024 by Pjotr Prins
topics/lmms/bulklmm/readme.gmi
document
created on Oct 07 2024 by Pjotr Prins
BioHackRxiv
document
created on Oct 07 2024 by Pjotr Prins
Permutations
document
created on Aug 18 2024 by Pjotr Prins, last updated on Oct 07 2024 by Pjotr Prins
Resources: Duplicates in Resources List
gn-auth
auth
authorisation
resources
medium
bug
✓ issue
opened on Oct 03 2024 by Frederick Muriuki Muriithi, last updated on Oct 03 2024 by Frederick Muriuki Muriithi
Example Python script for setting privileges for user/group
issue
opened on Oct 03 2024 by Zachary Sloan
[gn3/ADR-002] Move RDF Test Cases to Build Container
document
created on Sep 30 2024 by Munyoki Kilyungi, last updated on Oct 02 2024 by Munyoki Kilyungi
[gn3/ADR-001] Remove Stack Traces in GN3
document
created on Sep 10 2024 by Munyoki Kilyungi, last updated on Sep 30 2024 by Munyoki Kilyungi
Using Architecture Decision Records at GeneNetwork
document
created on Sep 25 2024 by Munyoki Kilyungi, last updated on Sep 25 2024 by Munyoki Kilyungi
Genotypes, Assemblies, Markers and GeneNetwork
document
created on Sep 23 2024 by Frederick Muriuki Muriithi
Working with Virtuoso for Local Development
document
created on Sep 20 2024 by Munyoki Kilyungi, last updated on Sep 20 2024 by Munyoki Kilyungi
Xapian indexing
document
created on Oct 30 2022 by Arun Isaac, last updated on Sep 20 2024 by Munyoki Kilyungi
[gn-transform-databases/ADR-002] Remodel GeneRIF_BASIC (NCBI RIFs) Metadata To Be More Compact
document
created on Sep 20 2024 by Munyoki Kilyungi
[gn-transform-databases/ADR-001] Remodel GeneRIF_BASIC (NCBI RIFs) Metadata Using predicateObject Lists
document
created on Sep 07 2024 by Munyoki Kilyungi, last updated on Sep 20 2024 by Munyoki Kilyungi
[gn-transform-databases/ADR-000] Remodel GeneRIF Metadata Using predicateObject Lists
document
created on Sep 07 2024 by Munyoki Kilyungi, last updated on Sep 20 2024 by Munyoki Kilyungi
GEMMA output differs from R/qtl2
database
gemma
reaper
rqtl2
bug
enhancement
high
✓ issue
opened on Aug 01 2024 by Pjotr Prins, last updated on Sep 20 2024 by Pjotr Prins
[gn3/ADR-000] Add RDF Test Cases
document
created on Sep 10 2024 by Munyoki Kilyungi, last updated on Sep 19 2024 by Munyoki Kilyungi
[gn-guile/ADR-000] Extend Markdown Editor to push to Git Bare Repo
document
created on Sep 04 2024 by Munyoki Kilyungi, last updated on Sep 19 2024 by Munyoki Kilyungi
Uploading Samples
gn-uploader
uploader
samples
strains
feature-request
high
open
issue
opened on Sep 18 2024 by Frederick Muriuki Muriithi, last updated on Sep 19 2024 by Frederick Muriuki Muriithi
New Privileges: Samples Ordering
gn-auth
auth
privileges
samples
ordering
feature-request
feature request
medium
open
issue
opened on Sep 19 2024 by Frederick Muriuki Muriithi
Various UI issues raised by Rob (8/19/2024)
medium
user-interface
issue
opened on Aug 19 2024 by Zachary Sloan, last updated on Sep 18 2024 by Zachary Sloan; 12 of 13 tasks done
Feature Request: Create Test Accounts
gn-auth
auth
test accounts
medium
feature request
feature-request
open
issue
opened on Sep 16 2024 by Frederick Muriuki Muriithi, last updated on Sep 17 2024 by Frederick Muriuki Muriithi
Quality Control of Data in Uploaded R/qtl2 Bundles
quality control
qc
r/qtl2 bundle
medium
feature request
completed
✓ 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
gn-uploader container: Running wrong genenetwork2
guix
gn-uploader
bug
high
completed
✓ issue
opened on Mar 18 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Send out Confimation Emails on Registration
gn-auth
email
user registration
email confirmation
feature request
feature-request
medium
completed
✓ issue
opened on Feb 27 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Global Search: Unhandled Error
global search
gn2
genenetwork2
bug
high
✓ issue
opened on Mar 04 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
GeneNetwork2: Account Registration Error
genenetwork2
account management
user
registration
completed
critical
bug
✓ issue
opened on Mar 19 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Error Handling: External Errors
error handling
high
bug
✓ issue
opened on Jan 29 2024 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Reset/Forgot Password Feature for GN2
feature-request
gn-auth
auth
reset password
critical
✓ issue
opened on May 15 2024 by Munyoki Kilyungi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Configurations
bug
ci
cd
configuration
config
completed
normal
✓ issue
opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Sep 16 2024 by Frederick Muriuki Muriithi
Paths in Flask Application
document
created on Sep 11 2024 by Frederick Muriuki Muriithi
Haley-Knott Regression Mapping Error
gn2
genenetwork2
genenetwork 2
mapping
haley-knott
high
completed
bug
✓ issue
opened on Sep 11 2024 by Frederick Muriuki Muriithi
Refactoring gn-llm code and adding test modules
completed
enchancements
refactoring
llm
tests
✓ issue
opened on Jan 17 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui
Integrating gn-auth with gn-llm
done
completed
high
feature
llm
auth
✓ issue
opened on Jan 10 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui
Fetch Pubmed data to GNQA
completed
enhancements
llm
pubmed
api
references
✓ issue
opened on Feb 12 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 6 of 6 tasks done
Editing Case-Attributes
document
created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Sep 09 2024 by Munyoki Kilyungi
GN-LLM Integration
completed
done
closed.
high
feature
issue
opened on Dec 12 2023 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 3 of 3 tasks done
Implement Reference Rating for gn-llm
completed
enhancements
llm
reference
rating
✓ issue
opened on Jan 11 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 2 of 2 tasks done
GN2 Integration with LLM search using cached results
open
enhancement
llm
genenetwork2
issue
opened on Aug 26 2024 by John Nduli, last updated on Sep 09 2024 by Alexander_Kabui; 2 of 6 tasks done
Implementing Efficient Database Caching for Query Responses in GN-LLM system
done
completed
enhancements
llm
caching
database
query
response
✓ issue
opened on Jan 17 2024 by Alexander_Kabui, last updated on Sep 09 2024 by Alexander_Kabui; 3 of 3 tasks done
Add Case Attributes to RDF
open
high
issue
opened on Sep 03 2024 by Munyoki Kilyungi
Deploy GeneNetwork
document
created on Jan 18 2023 by Arun Isaac, last updated on Aug 27 2024 by Frederick Muriuki Muriithi
Configuring Nginx on the Host System
document
created on Aug 27 2024 by Frederick Muriuki Muriithi
GN Markdown Editor Integration
markdown
integration
guile
high
in progress
issue
opened on Jun 07 2024 by Alexander_Kabui, last updated on Aug 22 2024 by Alexander_Kabui; 9 of 10 tasks done
Permission Hooks System Design
document
created on Aug 20 2024 by John Nduli
GN-AUTH FAQ
document
created on Aug 19 2024 by John Nduli, last updated on Aug 19 2024 by John Nduli
MGAMMA LMM
high
feature
issue
opened on Aug 19 2024 by Artyom Bologov; 3 of 5 tasks done
R/qtl2 and GEMMA Format Notes
document
created on Dec 27 2023 by Frederick Muriuki Muriithi, last updated on Aug 18 2024 by Pjotr Prins
Mechanical Rob
document
created on Aug 23 2022 by Arun Isaac, last updated on Aug 16 2024 by Munyoki Kilyungi
Search Improvements: capital insensitive search for RIF+WIKI; Examples
virtuoso
ops
high
issue
opened on Mar 14 2023 by Arun Isaac, last updated on Aug 16 2024 by Munyoki Kilyungi
Setting Up a Basic Pre-Commit Hook for Linting Scheme Files
document
created on Aug 07 2024 by Munyoki Kilyungi, last updated on Aug 07 2024 by Munyoki Kilyungi
Setting up Local Development Database
document
created on Aug 19 2022 by Frederick Muriuki Muriithi, last updated on Aug 01 2024 by Arun Isaac
Inspect Discrepancies Between Xapian and SQL Search.
issue
opened on Aug 01 2024 by Pjotr Prins
Set password when virtuoso containers are rebuilt
stalled
issue
opened on Jul 07 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Remove References to Old gn-auth code
stalled
auth
issue
opened on Feb 21 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Remove overrides to bootstrap classes in bootstrap-custom.css
stalled
issue
opened on Mar 27 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Move Search to Xapian
open
xapian
high
✓ issue
opened on Sep 08 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Move GN Racket Rest API to GNU Guile
stalled
api
metadata
medium
issue
opened on Jan 08 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Inspect Discrepancies Between Xapian and SQL Search.
✓ issue
opened on Jul 10 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
genenetwork2 CD sometimes fails to restart
✓ issue
opened on Mar 17 2023 by Arun Isaac, last updated on Jul 29 2024 by Munyoki Kilyungi
Edit Dataset Metadata
metadata editing
stalled
editing
high
issue
opened on Jan 10 2024 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi; 4 of 6 tasks done
Add genotype file paths to RDF
stalled
bug
issue
opened on Jun 19 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
Add Documentation For Set Up and Data Retrieval For AI Repo
phenotypes
ui
high
✓ issue
opened on Dec 01 2023 by Munyoki Kilyungi, last updated on Jul 29 2024 by Munyoki Kilyungi
GeneNetwork Authentication/Authorisation Architecture
document
created on Dec 04 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2024 by Frederick Muriuki Muriithi
Rating System: No Indication for Login Requirement
gnqna
user experience
ux
medium
open
bug
issue
opened on Jul 24 2024 by Solomon Shelby
Get GNQA Ready for evaluation
completed
immediate
ui
gnqa
evaluation
issue
opened on Mar 21 2024 by Solomon Shelby, last updated on Jul 24 2024 by Solomon Shelby; 2 of 2 tasks done
Guides Vs References
document
created on Jul 16 2024 by John Nduli, last updated on Jul 17 2024 by John Nduli
Hash RDF Graph
✓ issue
opened on Jun 10 2024 by Munyoki Kilyungi, last updated on Jul 10 2024 by Munyoki Kilyungi
Types of Data in GeneNetwork
document
created on Jul 02 2024 by Frederick Muriuki Muriithi, last updated on Jul 10 2024 by Frederick Muriuki Muriithi
Improving RIF+WIKI Search
document
created on Jul 04 2024 by Munyoki Kilyungi, last updated on Jul 05 2024 by Munyoki Kilyungi
Login issues with gn-auth
gn-auth
auth
authorisation
authentication
registration
completed
fixed
critical
bug
✓ issue
opened on Mar 01 2024 by Pjotr Prins, last updated on Jul 03 2024 by Frederick Muriuki Muriithi
Problem With Roles: Privilege Escalation
gn-auth
authorisation
authorization
roles
privileges
completed
fixed
critical
bug
✓ issue
opened on Jun 06 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 8 of 8 tasks done
Fix Flash Messages
flask
flash
completed
fixed
bug
low
✓ issue
opened on Jan 05 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi
Move Uploader to tux02
gn-uploader
guix
container
deploy
completed
fixed
high
migration
✓ issue
opened on Mar 12 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 3 of 3 tasks done
gn-uploader: Resume Upload
gn-uploader
uploader
upload
resume upload
feature request
feature-request
medium
completed
fixed
✓ issue
opened on Jun 24 2024 by Frederick Muriuki Muriithi, last updated on Jul 03 2024 by Frederick Muriuki Muriithi; 4 of 4 tasks done
Check Genotypes in the Database for R/qtl2 Uploads
gn-uploader
uploader
upload
genotypes
geno
completed
fixed
high
bug
✓ issue
opened on Jun 26 2024 by Frederick Muriuki Muriithi, last updated on Jul 01 2024 by Frederick Muriuki Muriithi
Genome Details
document
created on Jul 01 2024 by Frederick Muriuki Muriithi
Fallbacks and backups
critical
in progress
systems
fallback
backup
deploy
enhancement
issue
opened on Aug 31 2021 by Pjotr Prins, last updated on Jun 28 2024 by Pjotr Prins; 3 of 25 tasks done
Instrumenting RAM usage
document
created on Jun 27 2024 by Munyoki Kilyungi
Implement "Refresh Token" Feature for JWTs
gn-auth
token
refresh token
jwt
feature-request
bug
high
completed
fixed
✓ issue
opened on Apr 26 2024 by Frederick Muriuki Muriithi, last updated on Jun 26 2024 by Frederick Muriuki Muriithi
test1-auth.genenetwork.org Can't Find Templates
gn-auth
deployment
test1
bug
completed
fixed
critical
✓ issue
opened on Mar 02 2024 by Frederick Muriuki Muriithi, last updated on Jun 26 2024 by Frederick Muriuki Muriithi
Speed Up QC on R/qtl2 Bundles
issue
opened on Jun 24 2024 by Frederick Muriuki Muriithi
Each shepherd service needs its own guix profile.
shepherd
system administration
high
in progress
bug
issue
opened on Nov 03 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
genecup is currently running as root on penguin2.
high
genecup
penguin2
failure
✓ issue
opened on Aug 15 2021 by Efraim Flashner, last updated on Jun 21 2024 by Pjotr Prins
Indicating Heterozygosity
document
created on Jun 20 2024 by Frederick Muriuki Muriithi, last updated on Jun 20 2024 by Frederick Muriuki Muriithi
Logging Handler Improvements for GN3
enhancement
low
issue
opened on Jun 11 2024 by John Nduli
Sort by Attributes
genenetwork2
sorting
attributes
high
feature-request
feature request
✓ issue
opened on May 31 2024 by Frederick Muriuki Muriithi, last updated on May 31 2024 by Zachary Sloan
Bug: Incorrect code for GN2 generic error handler
errors
exceptions
gn2
bug
medium
bug
✓ issue
opened on May 28 2024 by Alexander_Kabui, last updated on May 29 2024 by Alexander_Kabui
issues/sorting-correlation-nan-vals.gmi
correlations
sorting
nan
done
completed
medium
bug
✓ issue
opened on Nov 28 2022 by AlexanderKabui, last updated on May 29 2024 by Alexander_Kabui
GNQA UI Enhancements
completed
enhancement
ui
gnqa
✓ issue
opened on Feb 12 2024 by Alexander_Kabui, last updated on May 29 2024 by Alexander_Kabui; 1 of 1 tasks done
GN3 Error Handling
document
created on May 28 2024 by Alexander_Kabui
Bug when using HTMX Ajax Post request
htmx
error
javascript
api
complete
high
bug
✓ issue
opened on May 14 2024 by Alexander_Kabui, last updated on May 28 2024 by Alexander_Kabui
MGAMMA CLI
high
feature
issue
opened on Apr 17 2024 by Pjotr Prins, last updated on May 18 2024 by Artyom Bologov; 4 of 6 tasks done
MGAMMA Convert
high
feature
issue
opened on Apr 17 2024 by Pjotr Prins, last updated on May 18 2024 by Artyom Bologov; 7 of 11 tasks done
Fire up system container for GN-QA System
document
created on May 13 2024 by Munyoki Kilyungi, last updated on May 13 2024 by Munyoki Kilyungi
StrainId wrong
unknown
bug
issue
opened on May 07 2024 by Pjotr Prins
LMM precomputed scores
database
gemma
reaper
ongoing
bug
enhancement
high
issue
opened on Mar 16 2023 by Pjotr Prins, last updated on May 07 2024 by Pjotr Prins; 0 of 1 tasks done
tux01 running out of RAM
medium
database
systems
✓ issue
opened on Sep 03 2022 by Pjotr Prins, last updated on May 03 2024 by Pjotr Prins; 1 of 6 tasks done
Edit OAuth2 Clients
gn-auth
issue
oauth2
enhancement
high
completed
✓ issue
opened on Apr 24 2024 by Frederick Muriuki Muriithi, last updated on May 02 2024 by Frederick Muriuki Muriithi
Data Upload Process
document
created on Apr 30 2024 by Munyoki Kilyungi, last updated on Apr 30 2024 by Munyoki Kilyungi
Re-use JWTs in gn3
critical
✓ issue
opened on Apr 30 2024 by Munyoki Kilyungi
Move GN Dataset to Git
metadata
high
✓ issue
opened on Feb 08 2024 by Munyoki Kilyungi, last updated on Apr 30 2024 by Munyoki Kilyungi; 4 of 4 tasks done
Genotype database
document
created on Jun 03 2022 by Arun Isaac, last updated on Apr 27 2024 by Pjotr Prins
MGAMMA
issue
opened on Apr 17 2024 by Pjotr Prins, last updated on Apr 27 2024 by Artyom Bologov
Handle Invalid Login Errors Correctly
gn-auth
issue
high
completed
bug
✓ issue
opened on Apr 24 2024 by Frederick Muriuki Muriithi, last updated on Apr 26 2024 by Frederick Muriuki Muriithi
Tasks
high
feature
issue
opened on Jun 27 2023 by GregFa, last updated on Apr 26 2024 by Pjotr Prins; 0 of 2 tasks done
MariaDB: Move to InnoDB Engine
mariadb
innodb
medium
unclear
enhancement
documentation
correlations
database
in-progress
high
issue
opened on Dec 28 2021 by Pjotr Prins, last updated on Apr 24 2024 by Pjotr Prins; 0 of 8 tasks done
Adding Species
document
created on Apr 24 2024 by Frederick Muriuki Muriithi, last updated on Apr 24 2024 by Frederick Muriuki Muriithi
Adding Platforms
document
created on Apr 04 2024 by Frederick Muriuki Muriithi, last updated on Apr 24 2024 by Frederick Muriuki Muriithi
Generating Key-Pairs
document
created on Apr 18 2024 by Frederick Muriuki Muriithi, last updated on Apr 22 2024 by Frederick Muriuki Muriithi
Data Integrity for Table Identifiers
data integrity
mariadb
gn-uploader
completed
critical
bug
✓ issue
opened on Apr 16 2024 by Frederick Muriuki Muriithi, last updated on Apr 17 2024 by Frederick Muriuki Muriithi
Logging with Flask and Gunicorn
document
created on Apr 15 2024 by Frederick Muriuki Muriithi
Moving /gnu
document
created on Apr 13 2024 by Pjotr Prins, last updated on Apr 13 2024 by Pjotr Prins
Fallbacks
document
created on Feb 18 2024 by Pjotr Prins, last updated on Apr 09 2024 by Pjotr Prins
Fallback issues
critical
in progress
systems
fallback
deploy
bug
issue
opened on Mar 22 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins; 3 of 6 tasks done
Fire up system container for GN
document
created on Mar 02 2024 by Pjotr Prins, last updated on Apr 05 2024 by Pjotr Prins
Unresponsive Virtuoso in CD
critical
✓ issue
opened on Apr 02 2024 by Munyoki Kilyungi
Julia Deployment
document
created on Apr 01 2024 by Pjotr Prins
Invoking SQLite3: CLI
document
created on Mar 30 2024 by Frederick Muriuki Muriithi
Database: `ProbeSetSE` Schema Bug
database
mariadb
schema
open
critical
bug
issue
opened on Mar 22 2024 by Frederick Muriuki Muriithi, last updated on Mar 22 2024 by Frederick Muriuki Muriithi
Deploying gn-auth
document
created on Mar 04 2024 by Frederick Muriuki Muriithi, last updated on Mar 12 2024 by Frederick Muriuki Muriithi
Dump sample data to LMDB
lmdb
rdf
stalled
high
issue
opened on Dec 15 2022 by Munyoki Kilyungi, last updated on Mar 06 2024 by Munyoki Kilyungi; 0 of 5 tasks done
UI Frontend for RDF
issue
✓ issue
opened on Oct 11 2023 by Munyoki Kilyungi, last updated on Mar 06 2024 by Munyoki Kilyungi
Add Sample Size to RDF
rdf
metadata
stalled
high
issue
opened on Dec 15 2022 by Munyoki Kilyungi, last updated on Mar 06 2024 by Munyoki Kilyungi
AI UI Enhancements
in progress
critical
ui
gnqa
issue
opened on Mar 01 2024 by Pjotr Prins; 0 of 3 tasks done
Remove externally loaded JS
guix
medium
completed
ui
enhancement
✓ issue
opened on Apr 18 2022 by BonfaceKilz, last updated on Feb 28 2024 by Alexander_Kabui; 3 of 3 tasks done
Read Samples/Cases/Individuals From Database
completed
qc
quality control
samples
strains
cases
gn-uploader
critical
bug
✓ issue
opened on Jan 20 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
QC: Fix Integration Tests
bug
quality control
qc
tests
gn-uploader
completed
medium
✓ issue
opened on Jan 09 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
Fix Opaque Errors
opaque errors
errors
ux
user experience
gn-uploader
high
bug
completed
✓ issue
opened on Feb 12 2024 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
Upload Strains
qc
quality control
strains
gn-uploader
feature-request
high
completed
✓ issue
opened on Dec 06 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi; 5 of 5 tasks done
Rework Test: Remove redis as Test Dependency
improvement
gn-uploader
tests
medium
completed
✓ issue
opened on Oct 27 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
Temp traits don't seem to be handled by the authorization system
bug
authentication
authorisation
oauth2
temp-traits
gn-auth
completed
high
✓ issue
opened on Jul 28 2023 by Zachary Sloan, last updated on Feb 27 2024 by Frederick Muriuki Muriithi
Rework Resources
auth
authorisation
resources
gn-auth
refactor
feature request
design change
medium
completed
✓ issue
opened on Sep 06 2023 by Frederick Muriuki Muriithi, last updated on Feb 27 2024 by Frederick Muriuki Muriithi; 2 of 3 tasks done
Handle "too-many-password-attempts"
security
password
medium
open
bug
issue
opened on Feb 27 2024 by Frederick Muriuki Muriithi
GeneNetwork Uploader Requirements
document
created on Feb 22 2024 by Frederick Muriuki Muriithi, last updated on Feb 22 2024 by Frederick Muriuki Muriithi
Improve Logging in GN3 RDF endpoints
rdf
gn3
api
high
✓ issue
opened on Feb 10 2024 by Munyoki Kilyungi, last updated on Feb 14 2024 by Munyoki Kilyungi
document
created on Feb 10 2024 by Pjotr Prins, last updated on Feb 12 2024 by Pjotr Prins
GN3 Setup on tux01 - Non-Deterministic Behavior
gn3
ops
guix
high
✓ issue
opened on Jan 15 2024 by Munyoki Kilyungi, last updated on Feb 10 2024 by Munyoki Kilyungi
Octopus HPC
document
created on Feb 10 2024 by Pjotr Prins
GN3 NGINX Timeout
bug
medium
cd
gn3
✓ issue
opened on Jan 15 2024 by Alexander_Kabui, last updated on Jan 25 2024 by Alexander_Kabui
Fix Failing GN2 tests
ci
medium
✓ issue
opened on Jan 12 2024 by Munyoki Kilyungi, last updated on Jan 15 2024 by Munyoki Kilyungi
Large Language Models (LLMs) & Metadata
document
created on Jun 23 2023 by Solomon Shelby, last updated on Jan 12 2024 by Solomon Shelby
Troubleshoot response inconsistencies for GN-llm
in progress
llm
high
issue
opened on Jan 10 2024 by Alexander_Kabui
Add HTML Page for Genotypes
virtuoso
ui
high
✓ issue
opened on Jan 09 2024 by Munyoki Kilyungi, last updated on Jan 10 2024 by Munyoki Kilyungi
Add HTML Page for ProbeSet Page
virtuoso
ui
high
✓ issue
opened on Dec 14 2023 by Munyoki Kilyungi, last updated on Jan 09 2024 by Munyoki Kilyungi
GN3 API Configurations on CD
completed
high
bug
configurations
cd
api
genenetwork3
✓ issue
opened on Jan 08 2024 by Alexander_Kabui, last updated on Jan 08 2024 by Alexander_Kabui
LMM Notes
document
created on Aug 13 2021 by Pjotr Prins, last updated on Jan 08 2024 by Solomon Shelby
Troubleshoot https://luna.genenetwork.org/ai/ asking questions
llm
high
✓ issue
opened on Jan 04 2024 by Munyoki Kilyungi, last updated on Jan 04 2024 by Munyoki Kilyungi
issues/data_upload_gn/hurdles_updating_names_to_GN.gmi
issue
opened on Dec 21 2023 by Lisso_, last updated on Jan 04 2024 by Lisso_
My Software Development Journey so far,
document
created on Dec 04 2023 by fetche-lab, last updated on Jan 04 2024 by Lisso_
CI rethink
gnsoc
issue
opened on Jun 23 2023 by Arun Isaac, last updated on Jan 03 2024 by Arun Isaac; 7 of 8 tasks done
Add GeneList to Metadata
virtuoso
rdf
high
✓ issue
opened on Dec 13 2023 by Munyoki Kilyungi, last updated on Dec 20 2023 by Munyoki Kilyungi
Make xapian index rebuild conditional on database checksums
✓ issue
opened on Jun 01 2023 by Arun Isaac, last updated on Dec 19 2023 by Arun Isaac; 3 of 3 tasks done
Trait Page Errors on CD
trait page
completed
critical
high
bug
✓ issue
opened on Nov 22 2022 by Frederick Muriuki Muriithi, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
Make Existing Data Public View by Default
migration
authentication
authorisation
oauth2
data migration
completed
medium
✓ issue
opened on May 24 2023 by Frederick Muriuki Muriithi, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
Import Collections Pop-up Bug
collections
completed
bug
urgent
✓ issue
opened on Dec 12 2023 by Zachary Sloan, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
Collections Count Bug
collections
completed
bug
medium
✓ issue
opened on Dec 18 2023 by Frederick Muriuki Muriithi, last updated on Dec 18 2023 by Frederick Muriuki Muriithi
Handling Resource Links in ProbeSet Page
virtuoso
rdf
high
✓ issue
opened on Nov 22 2023 by Munyoki Kilyungi, last updated on Dec 14 2023 by Munyoki Kilyungi
Add/Share Datasets HTMX Page
✓ issue
opened on Dec 04 2023 by Munyoki Kilyungi, last updated on Dec 08 2023 by Munyoki Kilyungi
Clean up Authorisation
feature request
completed
obsoleted
medium
authorisation
reference
✓ issue
opened on Nov 19 2021 by BonfaceKilz, last updated on Dec 04 2023 by Frederick Muriuki Muriithi; 4 of 4 tasks done
Put user info in the a/c name in the menu
document
created on Mar 14 2022 by Frederick Muriuki Muriithi, last updated on Dec 04 2023 by Frederick Muriuki Muriithi
Replace Hard coded authentication with gn-proxy
document
created on Mar 14 2022 by Frederick Muriuki Muriithi, last updated on Dec 04 2023 by Frederick Muriuki Muriithi
Authentication/authorisation design
document
created on Oct 17 2022 by Pjotr Prins, last updated on Dec 04 2023 by Frederick Muriuki Muriithi
Automated Testing
document
created on Oct 12 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
Add Metadata To The Trait Page (RDF)
document
created on Sep 28 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
Utility Scripts
document
created on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Dec 03 2023 by Pjotr Prins
Use exceptions to indicate errors
document
created on Aug 25 2022 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
Maybe monad
document
created on Sep 25 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
Coding guidelines
document
created on Aug 25 2022 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
Coding Anti-Patterns
document
created on Sep 29 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
Building a ~guix pack~ for Environment Sharing
document
created on Sep 13 2022 by Frederick Muriuki Muriithi, last updated on Dec 03 2023 by Pjotr Prins
How to Submit a Temp trait (for testing purposes or otherwise)
document
created on Aug 02 2023 by Zachary Sloan, last updated on Dec 03 2023 by Pjotr Prins
How to Start GN2 and GN3
document
created on Dec 08 2022 by Zachary Sloan, last updated on Dec 03 2023 by Pjotr Prins
Phenotype Naming Conventions
document
created on Nov 23 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
Developing against GeneNetwork
document
created on Jun 18 2023 by Pjotr Prins, last updated on Dec 03 2023 by Pjotr Prins
Useful Shell Scripts
document
created on Oct 06 2022 by Munyoki Kilyungi, last updated on Dec 03 2023 by Pjotr Prins
CI Rethink slides
document
created on Jul 13 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
Continuous Deployment logs
document
created on Feb 15 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
Using pudb
document
created on Dec 21 2021 by jgart, last updated on Dec 03 2023 by Pjotr Prins
Using PDB to Troubleshoot Python Code
document
created on Dec 03 2023 by Pjotr Prins
Running pudb From an External Environment
document
created on Dec 03 2023 by Pjotr Prins
Using pudb with pytest
document
created on Dec 21 2021 by jgart, last updated on Dec 03 2023 by Pjotr Prins
Profiling Python code
document
created on Dec 03 2023 by Pjotr Prins
Adding Quantitative Tracks Using BigWig Files
document
created on Nov 14 2023 by cel7t, last updated on Dec 03 2023 by Pjotr Prins
Queries and Prepared Statements in Python
document
created on Sep 27 2022 by Frederick Muriuki Muriithi, last updated on Dec 03 2023 by Pjotr Prins
Xapian search
document
created on May 02 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
Xapian search queries
document
created on Feb 13 2023 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
Xapian scalability
document
created on Oct 10 2022 by Arun Isaac, last updated on Dec 03 2023 by Pjotr Prins
topics/xapian/xapian-indexing-on-tux01.gmi
document
created on Jul 27 2023 by Zachary Sloan, last updated on Dec 03 2023 by Pjotr Prins
Shepherd
document
created on Aug 27 2021 by Pjotr Prins, last updated on Dec 02 2023 by Pjotr Prins
Minor Phenotype Page UI updates
phenotypes
ui
high
✓ issue
opened on Nov 30 2023 by Munyoki Kilyungi, last updated on Dec 01 2023 by Munyoki Kilyungi; 6 of 6 tasks done
Genotype correlations only returning results from first chromosome
correlations
high
bug
✓ issue
opened on Oct 21 2022 by Zachary Sloan, last updated on Nov 29 2023 by Zachary Sloan
Buggy Use of `urllib.parse.urljoin`
url
completed
low
bug
✓ issue
opened on Jul 25 2022 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Big File Upload Fails
qc
quality control
completed
bug
high
✓ issue
opened on Jan 17 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Add to Collection Error
collections
completed
bug
urgent
✓ issue
opened on Oct 09 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Rewrite qc and qc-uploads in Python3
quality control
completed
high
rewrite
✓ issue
opened on Apr 11 2022 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Conflating `dataset_id` with `inbred_set_id`
critical
editing
bug
✓ issue
opened on Jul 18 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Remove bcrypt as a Dependency
improvement
gn-auth
dependencies
low
completed
✓ issue
opened on Oct 27 2023 by Frederick Muriuki Muriithi, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Phenotype Correlation Error
completed
correlations
correlation
high
bug
✓ issue
opened on Sep 28 2022 by Zachary Sloan, last updated on Nov 28 2023 by Frederick Muriuki Muriithi
Move Data Endpoints from GN2 to GN3
api
feature-request
medium
✓ issue
opened on Nov 03 2023 by Frederick Muriuki Muriithi, last updated on Nov 03 2023 by Frederick Muriuki Muriithi
Gn Markdown Editor implementation
high
feature
issue
opened on Nov 03 2023 by Alexander_Kabui; 4 of 5 tasks done
Bug with linking data
bug
authentication
authorisation
oauth2
xapian
open
high
issue
opened on Jul 26 2023 by Zachary Sloan, last updated on Oct 19 2023 by Frederick Muriuki Muriithi
GeneNetwork/AI workshop
document
created on Oct 08 2023 by Pjotr Prins, last updated on Oct 12 2023 by Pjotr Prins
Fix Failing MR Failing Tests
high
✓ issue
opened on Sep 13 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Fix possible python 3.10 linting errors after bump from 3.9
✓ issue
opened on Jun 06 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Migrate to Python3.10
python3.10
high
✓ issue
opened on Jul 12 2023 by Frederick Muriuki Muriithi, last updated on Oct 11 2023 by Munyoki Kilyungi; 0 of 1 tasks done
Rework Fetching Settings
refactor
low
✓ issue
opened on Sep 25 2022 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Model Menu In RDF
rdf
high
modelling
✓ issue
opened on Apr 18 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Integrate Feed Analyser
feed analyser
medium
feature-request
✓ issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 11 2023 by Munyoki Kilyungi
Incorrect PubMed IDs in the Publication Table
rdf
sql
high
✓ issue
opened on May 09 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Improve sparql results
rdf
sparql
high
improvement
✓ issue
opened on Jul 07 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Autogenerate documentation: trees, and labels
rdf
gnsoc2023
high
feature
nextgendatabases
✓ issue
opened on Jun 23 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Try out Auth Code Locally
review
✓ issue
opened on Apr 21 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi; 2 of 2 tasks done
Order entries in CSV dump
csv
data
improvement
✓ issue
opened on Mar 20 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Modelling Phenotype Data
critical
✓ issue
opened on Aug 08 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Genotype Metadata
medium
feature
✓ issue
opened on Nov 29 2022 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Need Guix packages
guix
packages
environments
medium
unclear
bug
✓ issue
opened on Mar 12 2022 by Pjotr Prins, last updated on Oct 11 2023 by Munyoki Kilyungi
Create a new UI language for gn2
low
unclear
ui
✓ issue
opened on Apr 18 2022 by BonfaceKilz, last updated on Oct 11 2023 by Munyoki Kilyungi
Broken Indexing
xapian
high
cd
✓ issue
opened on May 03 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Ontologies
document
created on Jul 31 2023 by Munyoki Kilyungi, last updated on Oct 11 2023 by Munyoki Kilyungi
Decommission machines
unclear
system administration
systems
high
issue
opened on Oct 06 2021 by Pjotr Prins, last updated on Sep 22 2023 by Pjotr Prins; 11 of 22 tasks done
Understanding GN's Classification Scheme
document
created on Aug 29 2023 by Munyoki Kilyungi, last updated on Aug 31 2023 by Munyoki Kilyungi
Invalid Token Error
authentication
completed
resolved
high
bug
✓ issue
opened on Aug 25 2023 by Zachary Sloan, last updated on Aug 31 2023 by Frederick Muriuki Muriithi
Fix Broken UTF-8 characters in our Database
high
database
✓ issue
opened on Nov 29 2022 by Munyoki Kilyungi, last updated on Aug 29 2023 by Munyoki Kilyungi
GNSoC 2023
document
created on Jun 21 2023 by Pjotr Prins, last updated on Aug 24 2023 by Pjotr Prins
This document has some useful SQL tricks
document
created on Aug 08 2023 by Munyoki Kilyungi, last updated on Aug 11 2023 by Munyoki Kilyungi
Improving Metadata Audit
document
created on Jul 25 2023 by Frederick Muriuki Muriithi, last updated on Aug 11 2023 by Frederick Muriuki Muriithi
Temporary Traits Access Concerns
temp traits
temporary traits
access control
open
medium
feature request
issue
opened on Aug 03 2023 by Frederick Muriuki Muriithi
Brittle Fix for Editing Metadata
open
metadata
editing
high
bug
issue
opened on Aug 02 2023 by Frederick Muriuki Muriithi
Snellius
document
created on Mar 20 2023 by Pjotr Prins, last updated on Aug 01 2023 by Pjotr Prins
Paginate Resources Page
feature request
resources
data linking
auth
open
medium
issue
opened on Jul 27 2023 by Frederick Muriuki Muriithi
UI issues/improvements
feature-request
authentication
authorisation
oauth2
resources
ui
open
medium
issue
opened on Jul 26 2023 by Zachary Sloan
Reasons There is HTML and CSS in GN3
document
created on Jul 26 2023 by Frederick Muriuki Muriithi
Search is case sensitive
issue
opened on Jul 26 2023 by Arun Isaac
Guixify LLM container
gnsoc
✓ issue
opened on Jul 20 2023 by Munyoki Kilyungi, last updated on Jul 25 2023 by Munyoki Kilyungi
Delete Rejected Diffs from Database
high
editing
metadata audit
feature request
✓ issue
opened on Jul 25 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
Editing Trait Metadata and Sample Data
document
created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
Editing Data
document
created on Nov 23 2021 by BonfaceKilz, last updated on Jul 25 2023 by Frederick Muriuki Muriithi
Show "Edit" Button for All Users
editing
high
feature request
✓ issue
opened on Jul 24 2023 by Frederick Muriuki Muriithi, last updated on Jul 24 2023 by Frederick Muriuki Muriithi
Show Last Edited
open
editing
medium
feature request
issue
opened on Jul 24 2023 by Frederick Muriuki Muriithi
Queries for fetching/editing metadata
document
created on Jul 22 2023 by Munyoki Kilyungi
Fetch trait data using genofiles
in progress
high
improvement
issue
opened on Jul 11 2023 by Alexander_Kabui, last updated on Jul 13 2023 by Alexander_Kabui; 2 of 3 tasks done
Sample Data not Appearing in Phenotype-Editing Page
editing
phenotype
phenotype editing
bug
urgent
✓ issue
opened on Jul 12 2023 by Frederick Muriuki Muriithi, last updated on Jul 12 2023 by Frederick Muriuki Muriithi
Editing Phenotypes
document
created on Jul 07 2023 by Frederick Muriuki Muriithi, last updated on Jul 12 2023 by Frederick Muriuki Muriithi
Implementing parallel correlation with rust
correlation
rust
parralel
completed
medium
upgrade
✓ issue
opened on Apr 25 2022 by Alexander Kabui, last updated on Jul 11 2023 by Alexander_Kabui; 12 of 15 tasks done
Parsing genotyfiles
in progress
high
debug
issue
opened on Jul 11 2023 by Alexander_Kabui
Linking genotype files to datasets
in progress
high
debug
issue
opened on Jul 07 2023 by Alexander_Kabui, last updated on Jul 11 2023 by Alexander_Kabui
Info-Files Editing
document
created on Jul 07 2023 by Frederick Muriuki Muriithi
Sparql Examples
document
created on Apr 04 2023 by Munyoki Kilyungi, last updated on Jul 07 2023 by Pjotr Prins
Scheme Macros
document
created on Jul 05 2023 by Munyoki Kilyungi
Letsencrypt
open
critical
bug
issue
opened on Oct 13 2021 by Pjotr Prins, last updated on Jul 04 2023 by Pjotr Prins; 2 of 5 tasks done
Modifying dump macros
document
created on Jul 01 2023 by Munyoki Kilyungi
LMDB Phenotype/Genotype Store
document
created on Jun 22 2023 by Munyoki Kilyungi, last updated on Jun 30 2023 by Alexander_Kabui
issues/fix-genotype-filename-HSNIH-Palmer.gmi
high
bug fix
issue
opened on Jun 27 2023 by GregFa
issues/add-pluto-notebooks.gmi
high
feature
issue
opened on Jun 27 2023 by GregFa
Upload probeset metadata
bug
✓ issue
opened on Jun 19 2023 by Munyoki Kilyungi, last updated on Jun 26 2023 by Munyoki Kilyungi
Create Traits Endpoints in RDF
feature
✓ issue
opened on May 18 2023 by Munyoki Kilyungi, last updated on Jun 19 2023 by Munyoki Kilyungi; 3 of 3 tasks done
Branding and front-end-services
website
branding
in progress
high
feature
issue
opened on Jun 14 2023 by Pjotr Prins; 0 of 1 tasks done
Genenetwork3 Effective UID
bug
ci
cd
effective uid
genenetwork3
gn3
completed
critical
✓ issue
opened on Jun 05 2023 by Frederick Muriuki Muriithi, last updated on Jun 09 2023 by Frederick Muriuki Muriithi
OAuth2
document
created on May 29 2023 by Frederick Muriuki Muriithi, last updated on Jun 07 2023 by Frederick Muriuki Muriithi
NGINX Configuration Notes
document
created on Jun 01 2023 by Zachary Sloan
CLI Utility Scripts
document
created on May 29 2023 by Frederick Muriuki Muriithi, last updated on May 30 2023 by Frederick Muriuki Muriithi
Build Registration Page for OAuth2 Clients
feature request
authentication
authorisation
oauth2
completed
high
✓ issue
opened on Dec 22 2022 by Frederick Muriuki Muriithi, last updated on May 30 2023 by Frederick Muriuki Muriithi
Slow query
slow query
in progress
medium
issue
opened on May 27 2023 by Pjotr Prins, last updated on May 29 2023 by Pjotr Prins; 0 of 2 tasks done
OpenSMTPD
document
created on May 27 2023 by Pjotr Prins
Enable User Masquerade
feature request
authentication
authorisation
oauth2
completed
medium
✓ issue
opened on May 22 2023 by Frederick Muriuki Muriithi, last updated on May 23 2023 by Frederick Muriuki Muriithi
Use "Authorisation Code Flow" for Authentication
feature request
improvement
authentication
authorisation
oauth2
authorisation code flow
completed
critical
✓ issue
opened on May 08 2023 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
Migrate User Collections
bug
authentication
authorisation
oauth2
user collections
completed
critical
✓ issue
opened on May 08 2023 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
Migrate User Accounts from Redis to new Auth DB
feature request
authentication
authorisation
oauth2
wontfix
high
✓ issue
opened on Dec 22 2022 by Frederick Muriuki Muriithi, last updated on May 22 2023 by Frederick Muriuki Muriithi
Amazon Web Services
document
created on May 15 2023 by AndreaGuarracino, last updated on May 18 2023 by Munyoki Kilyungi
Give Examples of Fetching GeneRIF Metadata in Sparql
generif
metadata
rdf
documentation
✓ issue
opened on Apr 04 2023 by Munyoki Kilyungi, last updated on May 18 2023 by Munyoki Kilyungi
Document xapian search code architecture
✓ issue
opened on Mar 20 2023 by Arun Isaac, last updated on May 05 2023 by Arun Isaac
Troubleshoot CD Menu Failure
stalled
modelling
✓ issue
opened on Apr 21 2023 by Munyoki Kilyungi, last updated on Apr 26 2023 by Munyoki Kilyungi
Upload GeneWiki RDF metadata to CD
generif
metadata
rdf
✓ issue
opened on Apr 17 2023 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Add GeneRIF page
generif
metadata
rdf
feature
✓ issue
opened on Apr 14 2023 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Add mouse data-set
stalled
medium
issue
opened on Jun 30 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 0 of 4 tasks done
Unable to open new tab for mapping/ correlations with Chrome
mapping
correlation
google chrome
ui
from github
medium
unclear
bug
✓ issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 18 2023 by Munyoki Kilyungi
Document redis data
documentation
data
redis
unclear
stalled
low
bug
✓ issue
opened on Nov 27 2021 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi
Proxy has hard coded URLs
proxy
configuration
settings
unclear
medium
bug
✓ issue
opened on Oct 22 2021 by Pjotr Prins, last updated on Apr 18 2023 by Munyoki Kilyungi
Error when fetching SNPs in a search page
high
critical
✓ issue
opened on Sep 28 2022 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Fix Case Attribute Work (Consecutive CRUD applications)
medium
case attributes
data editing
bug
stalled
✓ issue
opened on Apr 06 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 0 of 2 tasks done
Uninformative error when batch submitting unknown strains
medium
metatadata
✓ issue
opened on May 05 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi
Editing traits for BXDs is failing for "%" substitution
high
bug
✓ issue
opened on Nov 09 2022 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Editing Metadata [Improvements to Make]
metadata
phenotypes
high
ui
✓ issue
opened on Mar 31 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 7 of 11 tasks done
Editing Case Attribute
case attributes
data editing
bug
✓ issue
opened on Mar 16 2023 by Munyoki Kilyungi, last updated on Apr 18 2023 by Munyoki Kilyungi
Cannot Edit Metadata of BXD Traits Effectively
high
metadata
✓ issue
opened on Apr 28 2022 by BonfaceKilz, last updated on Apr 18 2023 by Munyoki Kilyungi; 10 of 12 tasks done
Dump GeneWiki data
high
✓ issue
opened on Mar 30 2023 by Munyoki Kilyungi, last updated on Apr 17 2023 by Munyoki Kilyungi
Coupling current_app and db_utils
configurations
completed
fixed
bug
high
✓ issue
opened on Apr 04 2023 by Frederick Muriuki Muriithi, last updated on Apr 15 2023 by Frederick Muriuki Muriithi
Add Cis-Trans plot
database
gemma
unclear
enhancement
medium
issue
opened on Apr 07 2023 by Pjotr Prins
Fix load-rdf.scm script
✓ issue
opened on Apr 05 2023 by Munyoki Kilyungi, last updated on Apr 05 2023 by Munyoki Kilyungi
GeneNetwork SQL Database to RDF
document
created on Mar 24 2023 by Pjotr Prins, last updated on Apr 04 2023 by Arun Isaac
Dump GeneWiki Metadata
metadata
rdf
feature
✓ issue
opened on Mar 16 2023 by Munyoki Kilyungi, last updated on Apr 04 2023 by Munyoki Kilyungi
Search results presentation
ui
in progress
issue
opened on Apr 04 2023 by Alexander_Kabui
Report invalid search queries passed to the search API
in progress
enhancement
issue
opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
Improve presentation of search results
xapian
ui
stalled
✓ issue
opened on Feb 13 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
Add search syntax hints to web UI
xapian
ui
completed
✓ issue
opened on Feb 15 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
Enter key in global search field
ui
completed
✓ issue
opened on Feb 13 2023 by Arun Isaac, last updated on Apr 04 2023 by Alexander_Kabui
Document all virtuoso instances
✓ issue
opened on Mar 20 2023 by Arun Isaac, last updated on Mar 31 2023 by Arun Isaac
Use genodb in genenetwork
issue
opened on Jul 19 2022 by Arun Isaac, last updated on Mar 31 2023 by Arun Isaac
Xapian Search Results not Quite as Expected
xapian
medium
bug
✓ issue
opened on Mar 25 2023 by Frederick Muriuki Muriithi, last updated on Mar 31 2023 by Arun Isaac
Search queries with quoted author names don't work
issue
opened on Mar 28 2023 by Arun Isaac
Case Attribute Editing Problems
high
bug
metadata
case-attributes
✓ issue
opened on May 02 2022 by Zachary Sloan, last updated on Mar 20 2023 by Munyoki Kilyungi
Databases Getting Out of Wack
database
gemma
reaper
unclear
bug
enhancement
high
issue
opened on Mar 03 2022 by jgart, last updated on Mar 16 2023 by Pjotr Prins
ProbeData
database
mariadb
innodb
probedata
enhancement
medium
unclear
issue
opened on Dec 30 2021 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac
Annotation
mapping
architecture
open
in progress
enhancement
medium
issue
opened on Sep 14 2022 by Pjotr Prins, last updated on Mar 14 2023 by Arun Isaac; 0 of 5 tasks done
issues/search-hyphen-issue.gmi
issue
opened on Feb 24 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
sample data caching bug
correlation
caching
open
bug
medium
issue
opened on Feb 11 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
issues/adding-traits-from-mapping.gmi
issue
opened on Feb 24 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
issues/add-collection-import.gmi
collections
medium
bug
✓ issue
opened on Apr 29 2022 by Zachary Sloan, last updated on Mar 14 2023 by Arun Isaac
Global search doesn't seem to return phenotype traits
global search
phenotypes
bug
high
✓ issue
opened on Nov 11 2022 by Zachary Sloan, last updated on Mar 14 2023 by Zachary Sloan
ProbeSetData
database
mariadb
innodb
enhancement
medium
unclear
issue
opened on Dec 31 2021 by Pjotr Prins, last updated on Mar 13 2023 by Pjotr Prins; 15 of 17 tasks done
slow text search query
issue
opened on Mar 12 2023 by Pjotr Prins
Hanging database
high
unclear
database
bug
issue
opened on Dec 21 2021 by Pjotr Prins, last updated on Mar 11 2023 by Pjotr Prins
issues/custom_data_for_scatterplot.gmi
scatterplot
correlation
in-progress
high
feature
issue
opened on Mar 09 2023 by Zachary Sloan
Some correlations running very slowly
correlations
database
in-progress
high
bug
issue
opened on Mar 06 2023 by Zachary Sloan, last updated on Mar 07 2023 by Pjotr Prins
Lisp links
document
created on Feb 28 2023 by Pjotr Prins
BigBlueButton
document
created on Mar 05 2022 by jgart, last updated on Feb 28 2023 by Pjotr Prins
Support searching using SNP names
enhancement
issue
opened on Feb 15 2023 by Arun Isaac
Default search query in search field
issue
opened on Feb 13 2023 by Arun Isaac
Full text search
✓ issue
opened on Jun 30 2022 by Arun Isaac, last updated on Feb 13 2023 by Arun Isaac; 1 of 1 tasks done
Bug when a user quickly clicks "Compute" for mapping on the trait page
mapping
trait-page
completed
high
bug
issue
opened on Feb 06 2023 by Zachary Sloan, last updated on Feb 13 2023 by Zachary Sloan
AI Community Symposium at iHub
document
created on Jan 26 2023 by Brian Muhia, last updated on Jan 30 2023 by Pjotr Prins
Pkgconfig
document
created on Jan 25 2023 by Pjotr Prins
CLI Script to Generate Text Files
inprogress
correlations
materialised views
optimisation
script
high
feature
improvement
issue
opened on Dec 19 2022 by Frederick Muriuki Muriithi, last updated on Jan 23 2023 by Alexander_Kabui
Add option to directly link to mapping results
medium
mapping
issue
opened on Jan 19 2023 by Zachary Sloan
Running postgres in a Guix container
document
created on Jan 17 2023 by Pjotr Prins
List of proposed changes for PCA traits/figures in Correlation Matrix page
pca
correlations
in-progress
medium
feature
chore
issue
opened on Jan 09 2023 by Zachary Sloan
R/qtl JSONDecodeError
✓ issue
opened on Dec 23 2022 by Pjotr Prins, last updated on Dec 24 2022 by Pjotr Prins; 3 of 3 tasks done
metadata caching bug
medium
completed
bug
correlation
caching
metadata
✓ issue
opened on Mar 18 2022 by Alexander Kabui, last updated on Dec 23 2022 by Pjotr Prins; 2 of 2 tasks done
Using curl
document
created on Dec 23 2022 by Pjotr Prins
GN1 annotation page broken
gn1
genenetwork1
annotation
from github
bug
overdue
high
issue
opened on Dec 23 2022 by Pjotr Prins
GN Services
document
created on Sep 15 2021 by Pjotr Prins, last updated on Dec 23 2022 by Pjotr Prins
Correlation results wrong for certain traits/datasets
correlations
ongoing
high
issue
opened on Dec 12 2022 by Zachary Sloan, last updated on Dec 22 2022 by Zachary Sloan
Do not conflict with 'random' module
completed
✓ issue
opened on Dec 20 2022 by Arun Isaac, last updated on Dec 21 2022 by Frederick Muriuki Muriithi
Materialised Views for Correlations
completed
correlations
materialised views
optimisation
high
feature
improvement
✓ issue
opened on Oct 19 2022 by Frederick Muriuki Muriithi, last updated on Dec 19 2022 by Frederick Muriuki Muriithi
GN1 Pairscan
missing dependency
binary blob
gn1
critical
bug
✓ issue
opened on Sep 15 2021 by Pjotr Prins, last updated on Dec 17 2022 by Pjotr Prins
Marker mapping
marker
gn1
high
bug
✓ issue
opened on Sep 15 2021 by Pjotr Prins, last updated on Dec 17 2022 by Pjotr Prins
GN1 github problem
systems
tux02
production
gn1
system administration
medium
in progress
issue
opened on Dec 17 2022 by Pjotr Prins
GN1 annotation page broken
gn1
genenetwork1
annotation
from github
bug
testing
high
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Dec 17 2022 by Pjotr Prins; 0 of 2 tasks done
Annotate traits page with metadata from RDF
rdf
critical
metadata
in progress
high
✓ issue
opened on Sep 30 2022 by Munyoki Kilyungi, last updated on Dec 15 2022 by Munyoki Kilyungi; 16 of 16 tasks done
Add LICENSE page to GN2
gn2
license
enhancement
medium
issue
opened on Dec 12 2022 by Pjotr Prins
GN1 metadata
gn1
genenetwork1
annotation
bug
overdue
high
issue
opened on Dec 09 2022 by Pjotr Prins; 0 of 3 tasks done
Update production
document
created on Dec 07 2022 by Pjotr Prins, last updated on Dec 09 2022 by Pjotr Prins
Correlations: Returning Fewer Results
correlations
fewer results
ongoing
high
issue
opened on Nov 07 2022 by AlexanderKabui, last updated on Nov 25 2022 by Zachary Sloan
Decouple Tasks in Correlations Results Display
ongoing
correlations
medium
bug
issue
opened on Oct 24 2022 by Frederick Muriuki Muriithi, last updated on Nov 25 2022 by Frederick Muriuki Muriithi
Fix some display issue with the Correlation Results table (plus add column resizing)
correlation
datatables
javascript
bug
feature-enhancement
medium
✓ issue
opened on May 11 2022 by Zachary Sloan, last updated on Nov 22 2022 by Zachary Sloan
Correlations: Fewer Results than Expected
correlations
open
critical
bug
issue
opened on Nov 22 2022 by Frederick Muriuki Muriithi
Correlations are not including f1 parents
correlation
f1
ongoing
high
bug
issue
opened on Nov 07 2022 by AlexanderKabui, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
Remove Extra Partial Correlations Options
high
bug
completed
partial correlations
✓ issue
opened on May 16 2022 by Frederick Muriuki Muriithi, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
Correlations time out
critical
completed
bug
correlations
time out
✓ issue
opened on Aug 06 2021 by Pjotr Prins, last updated on Nov 22 2022 by Frederick Muriuki Muriithi; 2 of 3 tasks done
Correlations are wrongly always using all samples
correlations
completed
high
bug
✓ issue
opened on Oct 21 2022 by Zachary Sloan, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
Correlations fail for at least some ProbeSet datasets (as the target dataset)
correlations
completed
high
bug
✓ issue
opened on Oct 17 2022 by Zachary Sloan, last updated on Nov 22 2022 by Frederick Muriuki Muriithi
Dataset Queried Twice
complete
performance enhancement
optimisation
medium
bug
✓ issue
opened on Oct 20 2022 by Frederick Muriuki Muriithi, last updated on Nov 21 2022 by AlexanderKabui
Data Uploads: Zero Representation
data uploads
high
bug
✓ issue
opened on Feb 08 2022 by BonfaceKilz, last updated on Nov 11 2022 by Munyoki Kilyungi
Notify a user after a minor change
medium
ui
refactor
enhancement
✓ issue
opened on Nov 09 2022 by Munyoki Kilyungi, last updated on Nov 11 2022 by Munyoki Kilyungi
Long samplenames overflow in Haplotype Analyst
global search
phenotypes
ongoing
ui
medium
issue
opened on Nov 11 2022 by Zachary Sloan
User Registration
document
created on Nov 02 2022 by Frederick Muriuki Muriithi
Password Reset
document
created on Nov 02 2022 by Frederick Muriuki Muriithi
Run Correlations in External Process
bug
completed
correlations
asynchronous jobs
external process
high
feature
✓ issue
opened on Oct 19 2022 by Frederick Muriuki Muriithi, last updated on Oct 31 2022 by Frederick Muriuki Muriithi
Errors, defects and missing data in the database
issue
opened on Oct 27 2022 by Arun Isaac, last updated on Oct 30 2022 by Arun Isaac
Orchestration and fallbacks
document
created on Sep 02 2022 by Pjotr Prins, last updated on Oct 25 2022 by Pjotr Prins
Pre-Cache Datasets
cache
optimisation
open
enhancement
medium
issue
opened on Oct 24 2022 by Frederick Muriuki Muriithi
Do Bulk Query for Correlation Results' Display
enhancement
correlations
bulk queries
optimisation
high
✓ issue
opened on Oct 21 2022 by Frederick Muriuki Muriithi, last updated on Oct 24 2022 by Frederick Muriuki Muriithi
Replace IPFS
document
created on Oct 06 2022 by Pjotr Prins, last updated on Oct 23 2022 by Pjotr Prins
Debug RISC-V assembly with QEMU and GDB
document
created on Oct 19 2022 by Arun Isaac
Database Migrations
pending
database migrations
high
feature
issue
opened on Oct 19 2022 by Frederick Muriuki Muriithi
Developer links for
document
created on May 06 2022 by Arun Isaac, last updated on Oct 16 2022 by Pjotr Prins
Interesting links for coders
document
created on Oct 16 2022 by Pjotr Prins
Global search does not close connections properly (and is slow)
global search
db connections
medium priority
from github
stalled
medium
bug
✓ issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 14 2022 by Arun Isaac
Global search problems
global search
brca2
bug
low
later
✓ issue
opened on Aug 26 2022 by Pjotr Prins, last updated on Oct 14 2022 by Arun Isaac; 1 of 2 tasks done
Automatically find broken links on GN2
gn1
gn2
broken links
from github
completed
medium
bug
✓ issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 2 of 2 tasks done
Search results for SNP looks weird
ui
snp
from github
in progress
medium
bug
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
Capture Data on the BXDs in RDF
rdf
bxd
rest
from github
high priority
feature-request
enhancement
unclear
high
✓ issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi
Better Logging
low
deployment
404
enhancement
✓ issue
opened on Aug 23 2022 by Munyoki Kilyungi, last updated on Oct 12 2022 by Munyoki Kilyungi
Handle Configuration Files
gn2
configuration
deploy
stalled
medium
bug
issue
opened on Dec 03 2021 by BonfaceKilz, last updated on Oct 12 2022 by Munyoki Kilyungi
Fix Case Attribute Work (Same Columns)
case attributes
data editing
bug
✓ issue
opened on Apr 06 2022 by BonfaceKilz, last updated on Oct 12 2022 by Munyoki Kilyungi; 9 of 9 tasks done
Automated Testing
testing
ci
cd
enhancement
medium
✓ issue
opened on Feb 10 2022 by Frederick Muriuki Muriithi, last updated on Oct 12 2022 by Munyoki Kilyungi; 0 of 10 tasks done
Using guix-bioinformatics in a channels.scm file
medium
in progress
guix-bioinformatics
bug
issue
opened on Aug 15 2021 by Efraim Flashner, last updated on Oct 09 2022 by Pjotr Prins
Terminal output to the browser
binderlite
notebooks
ansi2html
medium
feature-request
issue
opened on Oct 28 2021 by jgart, last updated on Oct 07 2022 by Arun Isaac
Rebooting the GN production machine(s)
systems
tux01
tux02
production
system administration
medium
unclear
issue
opened on Jan 01 2022 by Pjotr Prins, last updated on Oct 06 2022 by Pjotr Prins; 4 of 4 tasks done
'TempDataSet' object has no attribute 'query_for_group' (error)
tempdataset
from github
bug
high
✓ issue
opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Sep 28 2022 by Alexander_Kabui
Mapping: Haley-Knott Regression: Zooming Bug
bug
medium
mapping
haley-knott regression
✓ issue
opened on Sep 22 2022 by Zachary Sloan, last updated on Sep 28 2022 by Alexander_Kabui
Failing Tests
genenetwork2
tests failure
completed
done
critical
bug
✓ issue
opened on Aug 03 2022 by Frederick Muriuki Muriithi, last updated on Sep 20 2022 by Alexander_Kabui
Fix Missing Genotype Files for GEMMA
gemma
technical debt
pending
bug
medium
issue
opened on Sep 13 2022 by Frederick Muriuki Muriithi, last updated on Sep 20 2022 by Frederick Muriuki Muriithi; 1 of 3 tasks done
GEMMA should report name of missing genotype file
✓ issue
opened on Aug 20 2022 by Arun Isaac, last updated on Sep 19 2022 by Arun Isaac
Missing Python Module(s) for GeneNetwork3
python-modules
open
high
bug
issue
opened on Sep 19 2022 by Frederick Muriuki Muriithi
Add track for showing which regions in mouse/rat correspond to human regions to the mapping figure
mapping
open
in progress
feature-request
medium
issue
opened on Jul 21 2022 by Zachary Sloan, last updated on Sep 14 2022 by Pjotr Prins
Simplify `dataset.py` in GeneNetwork2
technical debt
pending
bug
medium
issue
opened on Sep 13 2022 by Frederick Muriuki Muriithi
Markdown docs
gn1
documentation
unclear
medium
enhancement
issue
opened on Sep 10 2022 by Pjotr Prins
Replace sqlalchemy with MySQLdb
medium
refactor
✓ issue
opened on Aug 29 2022 by Munyoki Kilyungi, last updated on Sep 08 2022 by Munyoki Kilyungi
Tests for the genodb genotype database
✓ issue
opened on Aug 30 2022 by Arun Isaac, last updated on Sep 05 2022 by Alexander_Kabui
Second production on tux02
issue
opened on Aug 23 2022 by Arun Isaac, last updated on Sep 05 2022 by Alexander_Kabui
GN2 Time Machines
systems
production
system administration
medium
in progress
issue
opened on Aug 19 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 4 of 10 tasks done
MySQLdb._exceptions.OperationalError: (1040, 'Too many connections')
mysql
database
bug
✓ issue
opened on Aug 29 2022 by Munyoki Kilyungi, last updated on Sep 05 2022 by Alexander_Kabui; 2 of 2 tasks done
Genewiki conversion
gn1
documentation
unclear
medium
enhancement
issue
opened on Aug 26 2022 by Pjotr Prins, last updated on Sep 05 2022 by Alexander_Kabui; 0 of 3 tasks done
Timeout in CD
cd
✓ issue
opened on Jul 22 2022 by Arun Isaac, last updated on Aug 17 2022 by Arun Isaac
Miscellaneous UI issues
low
user-interface
ui
✓ issue
opened on Apr 08 2022 by Zachary Sloan, last updated on Aug 08 2022 by Munyoki Kilyungi
Enable all DataTables to call the same code
tables
javascript
open
in progress
refactor
medium
issue
opened on Jul 26 2022 by Zachary Sloan, last updated on Jul 27 2022 by Zachary Sloan
Allow analyses to be done between traits from "individuals" groups and their corresponding "main" group
data
meta-data
open
in progress
feature-request
medium
issue
opened on Jul 21 2022 by Zachary Sloan
UI Design
ui
quality control
medium
feature-request
✓ issue
opened on Dec 01 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Quality Control Project
quality control
feature-request
high
✓ issue
opened on Nov 19 2021 by Arthur Centeno, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Quality Control Checks
quality control
high
feature-request
✓ issue
opened on Nov 17 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Gene Symbol Mappings
✓ issue
opened on Nov 22 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Enumerating all QC checks
quality control
high
feature-request
✓ issue
opened on Nov 19 2021 by jgart, last updated on Jul 20 2022 by Frederick Muriuki Muriithi
Add the option to save traits uploaded with the Submit Trait option
data
meta-data
open
in progress
feature-request
medium
issue
opened on Jul 19 2022 by Zachary Sloan
GeneNetwork Hacking Documentation
document
created on Mar 11 2022 by Frederick Muriuki Muriithi, last updated on Jul 18 2022 by Frederick Muriuki Muriithi
Broken continuous deployment
completed
critical
✓ issue
opened on Jul 06 2022 by Arun Isaac, last updated on Jul 11 2022 by Frederick Muriuki Muriithi
Add convenience templates
tissue
gnbug
low
feature-request
✓ issue
opened on Oct 28 2021 by jgart, last updated on Jul 11 2022 by Arun Isaac
Add a transient interface for tissue
low
linter
tissue
feature-request
✓ issue
opened on Mar 28 2022 by BonfaceKilz, last updated on Jul 08 2022 by Arun Isaac
Slow Correlations and UI crashes
correlations
ui
crash
critical
bug
✓ issue
opened on Oct 18 2021 by BonfaceKilz, last updated on Jul 08 2022 by Alexander_Kabui
Gn3 network dependency
medium
stalled
bug
network_connections
ctl
wgcna
issue
opened on Mar 18 2022 by Alexander Kabui, last updated on Jul 08 2022 by Alexander_Kabui; 0 of 2 tasks done
A linter for gnbug
under discussion
low
gnbug
linter
tissue
feature-request
✓ issue
opened on Oct 28 2021 by jgart, last updated on Jul 06 2022 by Arun Isaac
Render images in tissue web output
tissue
feature request
✓ issue
opened on Apr 20 2022 by Arun Isaac, last updated on Jul 06 2022 by Arun Isaac
Some Historical Context
document
created on Jul 05 2022 by BonfaceKilz
Clean Up
database
mariadb
database administration
unclear
issue
opened on Jan 02 2022 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
ProbeSetXRef
medium
unclear
enhancement
documentation
probesetxref
database
mariadb
innodb
issue
opened on Dec 29 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
ProbeSE
database
mariadb
innodb
probese
enhancement
medium
unclear
issue
opened on Dec 30 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
Sheepdog
system
sheepdog
medium
in progress
halted
enhancement
issue
opened on Nov 08 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac; 3 of 17 tasks done
GN1 Time machines
systems
system administration
unclear
high
issue
opened on Oct 07 2021 by Pjotr Prins, last updated on Jul 01 2022 by Arun Isaac
Public inbox
issue
opened on Jun 29 2022 by Arun Isaac
Redirect HTTP to HTTPS
medium
completed
http
https
✓ issue
opened on Jul 31 2021 by Arun Isaac, last updated on Jun 24 2022 by Frederick Muriuki Muriithi
Improve Menu Generation and Move it to GN3
menu generation
gn2
gn3
completed
medium
bug
✓ issue
opened on May 16 2022 by Frederick Muriuki Muriithi, last updated on Jun 23 2022 by Frederick Muriuki Muriithi; 2 of 3 tasks done
Scree Plot appears to be incorrect
correlations
pca
scree-plot
in-progress
medium
bug
issue
opened on May 19 2022 by Zachary Sloan, last updated on Jun 15 2022 by BonfaceKilz
Add "Target" (Y) Column in Partial Correlations Selection Table
partial correlations
datatables
completed
migration
feature-request
medium
✓ issue
opened on Apr 22 2022 by Frederick Muriuki Muriithi, last updated on May 26 2022 by Frederick Muriuki Muriithi
GN3: Technical Debt
gn3
enhancement
medium
✓ issue
opened on Feb 08 2022 by BonfaceKilz, last updated on May 25 2022 by BonfaceKilz
issues/fetch-sample-data.gmi
medium
sample data
gn2
gn3
✓ issue
opened on Aug 09 2021 by BonfaceKilz, last updated on May 25 2022 by BonfaceKilz
Missing CI/CD Definitions for "Service" Daemons
bug
medium
ci-cd
service daemons
gn3
✓ issue
opened on May 16 2022 by Frederick Muriuki Muriithi, last updated on May 16 2022 by Frederick Muriuki Muriithi; 1 of 1 tasks done
Partial Correlation
document
created on Oct 15 2021 by Frederick Muriuki Muriithi, last updated on May 16 2022 by Frederick Muriuki Muriithi
Effect size for GEMMA is a MUST
issue
opened on Apr 18 2022 by Rob Williams, last updated on Apr 29 2022 by Arun Isaac
Make Partial Correlations Table Searchable
partial correlations
datatables
pending
migration
feature-request
medium
issue
opened on Apr 22 2022 by Frederick Muriuki Muriithi
Fix Collection Export
collections
high
bug
✓ issue
opened on Apr 20 2022 by Zachary Sloan, last updated on Apr 21 2022 by Zachary Sloan
Mapping figure can't be horizontally scrolled
mapping
medium
✓ issue
opened on Apr 20 2022 by Zachary Sloan, last updated on Apr 21 2022 by Zachary Sloan
DOL group mapping issues
mapping
medium
bug
✓ issue
opened on Apr 07 2022 by Zachary Sloan, last updated on Apr 20 2022 by Zachary Sloan
Add an 'Edit Issue' Link to Tissue
tissue
edit issue
open
in progress
feature-request
enhancement
medium
✓ issue
opened on Mar 24 2022 by Frederick Muriuki Muriithi, last updated on Apr 15 2022 by Arun Isaac
Cool Interfaces We Should Emulate
low
stalled
ui
issue
opened on Apr 13 2022 by BonfaceKilz, last updated on Apr 14 2022 by BonfaceKilz
Zoomed mapping result are empty for certain traits
high
in progress
bug
mapping user interface display failure
issue
opened on Apr 11 2022 by Zachary Sloan, last updated on Apr 13 2022 by Zachary Sloan
correlation error: 'NoneType' object is not iterable
correlations
from github
high priority
completed
high
bug
✓ issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 13 2022 by Alexander Kabui
Wrong CSV in ITP_10001 longevity dataset
critical bug
in progress
metadata
phenotypes
critical
bug
✓ issue
opened on Apr 11 2022 by BonfaceKilz, last updated on Apr 12 2022 by BonfaceKilz
Building Guix packages for RISC-V
document
created on Apr 08 2022 by Arun Isaac
BXD102xBXD077F1 Error
correlations
from github
unclear
critical
bug
✓ issue
opened on Mar 22 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Zachary Sloan
Adding principal component to collection returns an error
collections
from github
bug
high
unclear
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi, last updated on Apr 07 2022 by Alexander Kabui
Remove everything elastic search
elasticsearch
purge
done
low
enhancement
✓ issue
opened on Oct 22 2021 by Pjotr Prins, last updated on Apr 01 2022 by BonfaceKilz
topics/data-uploads/inserting-traits.gmi
document
created on Mar 30 2022 by Zachary Sloan, last updated on Mar 30 2022 by Zachary Sloan
Top 10 Things to Test
document
created on Mar 28 2022 by BonfaceKilz
Error when attempt to zoom to a chromosome after mapping a PCA trait
pca
from github
high priority
unclear
high
bug
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi
Multi-trait heat map failed
heatmap
from github
stalled
medium
bug
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi
Slow query
slow query
from github
stalled
high
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi
Add search, select and export to datatables table
datatables
ui
low priority
unclear
feature-request
low
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi
Capture state of phenotypes in a HASH
phenotypes
rest
ui
medium
in progress
enhancement
feature-request
issue
opened on Mar 23 2022 by Frederick Muriuki Muriithi
Fetch trait names for phenotypes
phenotype
from github
feature-request
enhancement
unclear
pending
issue
opened on Mar 22 2022 by Frederick Muriuki Muriithi
Variant Browser seems to be using mm9
variant browser
mm9
from github
stalled
bug
unclear
issue
opened on Mar 22 2022 by Frederick Muriuki Muriithi
csv export meta data are not commented out
csv
from github
meta data
unclear
bug
high
issue
opened on Mar 22 2022 by Frederick Muriuki Muriithi
Hide stale issues in gnbug
tissue
gnbug
low
unclear
enhancement
feature-request
✓ issue
opened on Jan 31 2022 by Arun Isaac, last updated on Mar 22 2022 by Arun Isaac
Sort gnbug issues most recent first
tissue
gnbug
stalled
medium
enhancement
feature-request
✓ issue
opened on Jan 31 2022 by Arun Isaac, last updated on Mar 22 2022 by Arun Isaac
Migrate GN1 Clustering
document
created on Jul 18 2021 by Pjotr Prins, last updated on Mar 22 2022 by Frederick Muriuki Muriithi
Remove Elastic Search
bug
done
completed
chore
elasticsearch
✓ issue
opened on Oct 28 2021 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
GN1 symbols
gn1
symbols
unclear
medium
bug
issue
opened on Nov 23 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi; 0 of 2 tasks done
Arthur mentioned last meet that GeneNetwork2 does not redirect http urls to https.
gn2
http
https
unclear
medium
bug
issue
opened on Dec 05 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Document API endpoints for GeneNetwork3
gn3
documentation
issue
opened on Mar 04 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Large datasets crash gemma
gemma
crash
high
bug
unclear
issue
opened on Mar 12 2022 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi; 0 of 7 tasks done
Guix: Using guix shell with root file
guix
guix shell
root file
low
unclear
issue
opened on Jan 27 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Return canned text if notebook description returns none
binderlite
notebooks
in progress
high
bug
issue
opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
R Kernel Dying
unclear
high
bug
issue
opened on Jan 17 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Integrate styling of app with GN2
binderlite
notebooks
styling
ui
medium
bug
ongoing
in progress
issue
opened on Oct 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
When binderlite finds an unkown package in a guix manifest
high
binderlite
notebooks
unclear
bug
issue
opened on Oct 01 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Add Regular Expression to Prevent Invalid Input
high
binderlite
notebooks
unclear
bug
issue
opened on Oct 01 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Add configuration to set server name
binderlite
notebooks
configuration
high
unclear
feature-request
issue
opened on Nov 10 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Shapiro Wilk Test
document
created on Nov 24 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Defining a scheme sexp comment with a reader macro
document
created on Feb 02 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Lisp For Schemers
document
created on Dec 29 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Common Lisp Condition Handling
document
created on Dec 28 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Debugging Lisp
document
created on Dec 22 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Common LISP: sly
document
created on Jan 29 2022 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Common LISP: Notes
document
created on Feb 09 2022 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Non-Clustered and Flippable Heatmaps
document
created on Oct 01 2021 by Frederick Muriuki Muriithi, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Ideas and References
document
created on Nov 22 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
gemtext cheatsheet
document
created on Dec 21 2021 by jgart, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
GeneNetwork documentation
document
created on Nov 16 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Data Uploads: Reversing a Diff
document
created on Feb 03 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Data Uploads: Inserting Data
document
created on Jan 27 2022 by BonfaceKilz, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Weechat
document
created on Nov 04 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
COVID-19
document
created on Nov 14 2021 by Pjotr Prins, last updated on Mar 16 2022 by Frederick Muriuki Muriithi
Tux01 hard disk crash
system
tux01
hard disk crash
in progress
medium
issue
opened on Sep 29 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
GN1 Slowness
gn1
high
bug
issue
opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
GN1 Production
in progress
gn1
critical
bug
issue
opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi; 3 of 8 tasks done
Fix GN1 Network Graph
in progress
gn1
network graph
high
bug
issue
opened on Sep 15 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Marker covariates implemented wrong in rqtl_wrapper.R
medium
marker covariates
in progress
halted
bug
issue
opened on Sep 22 2021 by Zachary Sloan, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Multivariate GEMMA hangs (issue 243)
high
unclear
gemma
failure
issue
opened on Aug 16 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Make build green
build
complete
failure
✓ issue
opened on Dec 21 2021 by BonfaceKilz, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Medaka Inbred Kiyosu-Karlsruhe (MIKK) Panel
medaka
mikk
unclear
data
issue
opened on Sep 22 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Show Template for when Git URL is not Found
binderlite
template
medium
bug
issue
opened on Sep 28 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
GeneNetwork CLI
document
created on Sep 20 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Adding Terminal Output
document
created on Aug 07 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Add button to delete an entire dataset in gn2
document
created on Sep 08 2021 by BonfaceKilz, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Jupyter notebooks
document
created on Sep 01 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
Binding notebooks
document
created on Aug 22 2021 by jgart, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
BNW interface for GN2
document
created on Oct 18 2021 by Pjotr Prins, last updated on Mar 14 2022 by Frederick Muriuki Muriithi
gemma-wrapper has incomplete files
✓ issue
opened on Nov 14 2021 by Pjotr Prins, last updated on Feb 17 2022 by Pjotr Prins; 2 of 2 tasks done
GEMMA GSL ERROR: function value is not finite in brent.c
✓ issue
opened on Aug 14 2021 by Pjotr Prins, last updated on Feb 17 2022 by Pjotr Prins
file upload size limit
✓ issue
opened on Feb 16 2022 by jgart, last updated on Feb 16 2022 by jgart
Designing an issue tracker on gemini
help wanted
documentation
later
testing
enhancement
bug
request
critical bug
in progress
✓ issue
opened on Jul 25 2021 by Pjotr Prins, last updated on Feb 02 2022 by Pjotr Prins
Open notebook directly if full path to notebook file is given
feature-request
✓ issue
opened on Nov 04 2021 by jgart, last updated on Dec 22 2021 by Frederick Muriuki Muriithi
Nginx forwarding error regarding static assets
✓ issue
opened on Nov 10 2021 by jgart, last updated on Dec 22 2021 by Frederick Muriuki Muriithi
issues/binderlite/add-spinner-for-submit-form.gmi
feature-request
✓ issue
opened on Nov 10 2021 by jgart, last updated on Dec 22 2021 by Frederick Muriuki Muriithi
Binderlite Notebook Gallery
✓ issue
opened on Oct 04 2021 by jgart, last updated on Oct 21 2021 by jgart
gnbug cat
feature-request
✓ issue
opened on Sep 22 2021 by jgart, last updated on Sep 28 2021 by jgart
Maybe `gnbug` should be an alias for `gnbug list`
bug
✓ issue
opened on Sep 22 2021 by jgart, last updated on Sep 22 2021 by Arun Isaac