Owner

ssi-dk

17 indexed repositories · View on GitHub

SCDB
R package for maintaining data bases with slowly-changing-dimensions

R · 8 stars
diseasy

R · 5 stars
diseasystore
R package that provides a feature store tailored towards disease modelling

R · 4 stars
MMASeq
Package for the species specific analysis WP6 MicrobeSeq

Python · 2 stars
sofi_core

Python · 2 stars
aedseo
Automated and Early Detection of Seasonal Epidemic Onset and Burden Levels

R · 1 star
uQCme
Microbial Quality Control Web Application

Python · 1 star
landingzones
A script for helping manage entry and exit points across machines for with cron.

Python · 1 star
AEF-DDF

R · 1 star
bifrostlib
Python API for bifrost

Python · 0 stars
bifrost_run_launcher

Python · 0 stars
bifrost_impl_sofi

Python · 0 stars
bifrost_ssi_stamper
Bifrost Component: SSI Stamper - Runs SSI's QC check on samples using metrics generated from Assemblatron, Min Read Check and Whats my sp...

Python · 0 stars
bifrost_bridge

Python · 0 stars
bifrost_assemblatron
Bifrost Component: Assemblatron - De-novo assembly of paired reads for QC and downstream Analysis purposes

Python · 0 stars
bifrost_cge_mlst
Bifrost Component: CGE MLST - Runs kma on a mlst DB using paired reads

Python · 0 stars
synthetic-sequencer

Python · 0 stars

Beginner friendly Everything

Open All

Consider invoking nested Snakemake in-process, not through the shell Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ssi-dk/MMASeq#231 · Opened Sep 18, 2026
Implement NextSeq FASTQ saved-run replay CLI and Docker image Open

Difficulty 5/5 Over a week Newbie friendliness 30/100

ssi-dk/synthetic-sequencer#1 · Opened Sep 11, 2026
MMAdeploy should support HTTP download of read files Open

Enhancement

Difficulty 3/5 1-2 days Newbie friendliness 45/100

ssi-dk/MMASeq#227 · Opened Sep 4, 2026
Ensuring long table generation by exporting the functionality outto the launcher. Open

Implementation

Difficulty 4/5 3-5 days Newbie friendliness 52/100

ssi-dk/MMASeq#226 · 1 comment · Opened Sep 4, 2026
FEATURE: Remove logging Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 52/100

ssi-dk/diseasy#292 · Opened Aug 27, 2026
Enhance the `k` time window in `seasonal_onset()` to fracmented time series Open

enhancement

ssi-dk/aedseo#107 · 1 assignee · Opened Aug 26, 2026
Spades container issue Open

External

Difficulty 3/5 1-2 days Newbie friendliness 58/100

ssi-dk/MMASeq#223 · 5 comments · Opened Aug 20, 2026
Review type issues with this package Open

Difficulty 3/5 1-2 days Newbie friendliness 48/100

ssi-dk/bifrost_bridge#15 · Opened Aug 19, 2026
Add error catcher for wrongly formatted species configs Open

Implementation

Difficulty 2/5 1-3 hours Newbie friendliness 70/100

ssi-dk/MMASeq#198 · Opened Aug 4, 2026
Automatically publish standalone bundle for version releases Open

needs-triage

Difficulty 3/5 1-2 days Newbie friendliness 70/100

ssi-dk/landingzones#38 · 1 comment · Opened Jul 31, 2026
Plasmidfinder v2 does not work with Python v3.12 Open

External

Difficulty 4/5 3-5 days Newbie friendliness 55/100

ssi-dk/MMASeq#193 · 1 comment · Opened Jul 3, 2026
FEATURE: Per-variant outcomes from `DiseasyImmunity` in `DiseasyModelOdeSeir` Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ssi-dk/diseasy#266 · 1 comment · Opened Jul 3, 2026
MMAdeploy --test all modules Open

Bug External Implementation

Difficulty 4/5 3-5 days Newbie friendliness 38/100

ssi-dk/MMASeq#183 · Opened Jun 29, 2026
SQL identifiers are manually pasted/quoted in several places Open

bug ChatGPT triage

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ssi-dk/SCDB#240 · Opened Jun 19, 2026
Checksum serialisation can collide Open

bug ChatGPT triage

Difficulty 4/5 3-5 days Newbie friendliness 42/100

ssi-dk/SCDB#239 · Opened Jun 19, 2026
Incorrectly specified dependencies Open

bug ChatGPT triage

Difficulty 2/5 1-3 hours Newbie friendliness 64/100

ssi-dk/SCDB#238 · Opened Jun 19, 2026
`is.historical()` edge-cases Open

bug ChatGPT triage

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

ssi-dk/SCDB#236 · Opened Jun 19, 2026
Lock design is weak for shared DBs Open

bug triage

Difficulty 5/5 Over a week Newbie friendliness 25/100

ssi-dk/SCDB#235 · Opened Jun 19, 2026
Lock failures are swallowed. Open

bug ChatGPT triage

Difficulty 3/5 1-2 days Newbie friendliness 62/100

ssi-dk/SCDB#234 · Opened Jun 19, 2026
Locks are not exception safe Open

bug ChatGPT triage

Difficulty 3/5 1-2 days Newbie friendliness 55/100

ssi-dk/SCDB#233 · Opened Jun 19, 2026
Suggestion: Single download of all files/databases Open

Enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

ssi-dk/MMASeq#156 · 5 comments · Opened Jun 11, 2026
FEATURE: Regions in seir_example_data Open

enhancement

ssi-dk/diseasy#255 · 1 assignee · Opened Jun 8, 2026
FEATURE: Sub-group immunity differences Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

ssi-dk/diseasy#254 · 1 comment · Opened Jun 6, 2026
FEATURE: Variants in seir_example_data Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 58/100

ssi-dk/diseasy#252 · Opened Jun 6, 2026
Timezone of timestamp can vary, allow setting it Open

Difficulty 3/5 1-2 days Newbie friendliness 55/100

ssi-dk/landingzones#28 · Opened Jun 2, 2026
Download failure in `deploy_dataset` should probably exit program Open

Bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

ssi-dk/MMASeq#135 · 3 comments · Opened May 26, 2026
What should relative config paths be resolved relative to? Open

Difficulty 5/5 Over a week Newbie friendliness 35/100

ssi-dk/uQCme#18 · Opened May 7, 2026
Usage of old assembly_qc (mapping_qc entries) or outdated (dev) assemblatron entries. Open

ssi-dk/bifrost_ssi_stamper#11 · 1 assignee · Opened Feb 18, 2026
GridOut attribute error during development and testing Open

ssi-dk/bifrost_assemblatron#12 · 2 assignees · Opened Feb 16, 2026
Renaming funcitons for future 1.0.0 release Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

ssi-dk/SCDB#218 · 2 comments · Opened Jan 21, 2026
Provide warnings for unknown Modules and potentially unused keywords Open

Implementation

Difficulty 4/5 3-5 days Newbie friendliness 42/100

ssi-dk/MMASeq#108 · Opened Jan 14, 2026
MLST db-dl script no longer supported Open

External Implementation

Difficulty 2/5 1-3 hours Newbie friendliness 35/100

ssi-dk/MMASeq#104 · 2 comments · Opened Dec 9, 2025
FEATURE: Add `$describe()` to `DiseasyModelOdeSeir` Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ssi-dk/diseasy#203 · Opened Dec 8, 2025
add bar chart values to fields, allow them to show variation from the mean Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

ssi-dk/uQCme#4 · Opened Nov 28, 2025
FEATURE: `DiseasyModel` methods updating the set of parameters Open

enhancement

ssi-dk/diseasy#197 · 1 assignee · Opened Nov 18, 2025
FEATURE: `DiseasyParameters` - a module to define sampling / optimisation strategies for parameters Open

enhancement

ssi-dk/diseasy#196 · 1 assignee · Opened Nov 18, 2025
FEATURE: Interface `DiseasyActivity` with `DiseasyRegion` Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

ssi-dk/diseasy#191 · 1 comment · Opened Nov 11, 2025
FEATURE: `DiseasyRegions` Open

enhancement

ssi-dk/diseasy#188 · 3 comments · 1 assignee · Opened Nov 11, 2025
Add support MLST for E.coli and A.Baumanii (RAR) Open

Enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

ssi-dk/MMASeq#86 · 1 comment · Opened Oct 20, 2025
Handle Module failure Open

Bug

ssi-dk/MMASeq#54 · 1 comment · 1 assignee · Opened Sep 15, 2025
Rerun with new sequence entries not handled correctly Open

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ssi-dk/bifrost_run_launcher#31 · Opened Aug 28, 2025
Development guide Open

Documentation

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ssi-dk/MMASeq#25 · Opened May 6, 2025
FEATURE: Add Oracle Database to the benchmarks Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ssi-dk/SCDB#185 · Opened Feb 26, 2025
FEATURE: Implement Oracle DB specific translations Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

ssi-dk/SCDB#182 · Opened Feb 25, 2025
FEATURE: Add Oracle Database to the CI tests Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ssi-dk/SCDB#181 · 3 comments · Opened Feb 25, 2025
FEATURE: Support for Oracle Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

ssi-dk/SCDB#179 · 1 comment · Opened Feb 24, 2025
FEATURE: Invisibly return `db_table` from `defer_db_cleanup()` Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 65/100

ssi-dk/SCDB#171 · Opened Feb 6, 2025
FEATURE: Allow model templates to specify allowed functional modules Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 28/100

ssi-dk/diseasy#165 · Opened Feb 4, 2025
FEATURE: "Eigenvecter method" of initialisation for `DiseasyModelOdeSeir` Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

ssi-dk/diseasy#163 · Opened Feb 3, 2025
Misspecified `observable_regex` in `DiseasystoreEcdcRespiratoryViruses` Open

bug

Difficulty 1/5 Under an hour Newbie friendliness 55/100

ssi-dk/diseasystore#205 · Opened Jan 30, 2025

ssi-dk

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