OpenWorm GitHub Organization — Repository Inventory¶
- Last Updated: 2026-02-19
- Total Repositories: 109
- Source: github.com/orgs/openworm
Purpose¶
This inventory identifies which of OpenWorm's 109 GitHub repositories are:
- Active and maintained (useful for current DD work)
- Referenced in Design Documents (DD001-DD021)
- Dormant but potentially reusable (could be revived)
- Deprecated (archived, do not use)
Core Simulation Stack (5 repos)¶
These repos implement DD001–DD003, DD013–DD014, DD020 — the foundation of the simulation.
| Repository | Last Push | Stars | Status | Design Documents |
|---|---|---|---|---|
| OpenWorm | 2026-02-09 | 2,943 | Active — Meta-repo | DD013 |
| c302 | 2026-02-18 | 135 | Active | DD001, DD002, DD005–DD009, DD018–DD019 |
| sibernetic | 2026-02-13 | 384 | Active | DD002 (coupling), DD003, DD004, DD007, DD019 |
| ConnectomeToolbox | 2026-02-19 | 4 | Active (Neural Circuit L4 Maintainer) | DD020 |
| Worm3DViewer | 2025-12-01 | 0 | Active (visualization prototype) | DD014, DD014.2 |
All 5 are essential. Changes to these repos affect multiple DDs.
Data Access Layer (5 repos)¶
| Repository | Last Push | Stars | Status | Design Documents |
|---|---|---|---|---|
| owmeta | 2024-07-29 | 153 | Deferred (Phase 3+) | DD008 — see OWMeta Ecosystem |
| owmeta-core | 2025-03-18 | 3 | Deferred (Phase 3+) | DD008 — see OWMeta Ecosystem |
| tracker-commons | 2025-04-23 | 14 | Maintained | DD021 (WCON 1.0 spec) |
| open-worm-analysis-toolbox | 2020-01-16 | 48 | Archived — Revival needed | DD010 (Tier 3), DD021 (revival plan) |
| movement_validation | 2017-06-21 | 16 | ARCHIVED — Do not use | DD021 (historical — superseded by analysis toolbox) |
Status:
cect(ConnectomeToolbox) is the working data layer for Phase 1-2 (DD020)owmetais deferred to Phase 3+ (DD008 acknowledges this)- Analysis toolbox blocks Tier 3 validation (DD021 8-task revival plan, 33 hours)
NeuroML / Modeling (4 repos)¶
| Repository | Last Push | Stars | Status | Design Documents |
|---|---|---|---|---|
| CElegansNeuroML | 2023-03-30 | 140 | Archived (authoritative NeuroML files) | DD001 (NeuroML cell definitions) |
| Blender2NeuroML | 2026-02-17 | 17 | Active | DD014.2 (Virtual Worm meshes source) |
| muscle_model | 2025-05-15 | 48 | Maintained | DD002 (Boyle & Cohen implementation) |
| hodgkin_huxley_tutorial | 2025-10-30 | 49 | Active | DD011 (orientation badge "HH Tutorial Graduate") |
Note
CElegansNeuroML is dormant but its NeuroML files are still authoritative. DD001 references this repo for cell template locations.
Visualization / Browsers (6 repos)¶
| Repository | Last Push | Stars | Status | Design Documents |
|---|---|---|---|---|
| Worm3DViewer | 2025-12-01 | 0 | Active (Neural Circuit L4 Maintainer) | DD014 Phase 1 (Trame viewer evolution) |
| wormbrowser | 2026-02-13 | 49 | Active | DD014 (historical 3D browser, still maintained) |
| openwormbrowser-ios | 2026-01-20 | 20 | Active | Mobile version of worm browser |
| WCONViewer | 2025-12-17 | 0 | Maintained | DD021 (WCON visualization tool) |
| Worm2D | 2025-07-24 | 0 | Maintained | 2D worm simulation — Boyle-Cohen body model with c302 integration (see DD001, DD003) |
| WormWorx | 2025-09-05 | 7 | Maintained | Alternative C. elegans simulator |
Geppetto Platform (5 repos) — Deferred¶
| Repository | Last Push | Stars | Status | Notes |
|---|---|---|---|---|
| org.geppetto.frontend | 2025-04-03 | 29 | Deferred | DD014 mentions Geppetto (not using for Phase 1-2) |
| geppetto-client | 2025-04-18 | 6 | Deferred | |
| org.geppetto.core | 2025-03-28 | 22 | Deferred | |
| org.geppetto.datasources | 2025-03-28 | 2 | Deferred | |
| org.geppetto.docs | 2020-08-04 | 3 | Archived |
DD014 Decision: Not using Geppetto for Phase 1-2 (too heavy, Java-based). Using Trame (PyVista) instead. Geppetto could be revisited in Phase 3 if needed.
AI / LLM Integration (1 repo)¶
| Repository | Last Push | Stars | Status | Purpose |
|---|---|---|---|---|
| openworm.ai | 2026-02-19 | 3 | VERY ACTIVE | LLM/AI scripts — may inform DD015 (AI Contributors) |
Note
This repo is brand new or recently revived. Should be reviewed for DD015 AI contributor infrastructure.
Educational / Outreach (3 repos)¶
| Repository | Last Push | Stars | Status | Purpose |
|---|---|---|---|---|
| hodgkin_huxley_tutorial | 2025-10-30 | 49 | Active | DD011 badge "Neuron Modeling Foundations" |
| openworm.github.io | 2026-02-01 | 29 | Active | Website (static HTML) |
| openworm_docs | 2024-07-02 | 44 | Inactive (being replaced by this site) | ReadTheDocs documentation |
Research Models & Data (17 repos)¶
External research code and datasets forked into the OpenWorm org. Not under active OpenWorm development, but code is recent and directly reusable for DDs.
| Repository | Last Push | Stars | DD Reuse |
|---|---|---|---|
| CE_locomotion | 2026-02-18 | 2 | VERY ACTIVE — DD001–DD003 (neuromechanical locomotion, Boyle-Cohen 2D body model used by boyle_berri_cohen_trajectory.py), DD023 (proprioceptive model, 30-50 hr savings) |
| NicolettiEtAl2024_MN_IN | 2025-11-04 | 0 | DD001, DD005 (motor/interneuron HH models), DD007 (pharyngeal neuron init), DD023 (B-class templates) |
| wormneuroatlas | 2025-10-22 | 2 | DD005 (CeNGEN), DD010 (Tier 2 — Randi 2023 data), DD020 (complementary connectome data) |
| CelegansNeuromechanicalGaitModulation | 2025-08-01 | 1 | DD003 (gait physics, Boyle-Cohen 2D body model used by boyle_berri_cohen_trajectory.py), DD017 (surrogate training data), DD023 (proprioceptive/curvature logic) |
| tierpsy-tracker | 2025-06-29 | 2 | DD010 (Tier 3 validation tool), DD021 (may replace 33-hr toolbox revival) |
| JohnsonMailler_MuscleModel | 2025-05-15 | 2 | DD002 (alternative muscle model), DD007 (Ca²⁺ coupling for pharyngeal muscle) |
| NeuroPAL | 2025-04-29 | 5 | DD005 (cell ID validation), DD010 (Tier 1 neuron ID), DD024 (validation data) |
| NicolettiEtAl2019_NeuronModels | 2025-04-28 | 1 | DD001/DD005 (AWCon, RMD HH fits), DD010 (Tier 1 calibration expansion) |
| wormpose | 2025-02-21 | 0 | DD017 (Component 4 training data), DD021 (skeleton format bridge) |
| PlateauNoiseModel | 2025-01-30 | 0 | DD007 (pharyngeal plateau potentials — already cited) |
| sibernetic_v3 | 2024-09-27 | 1 | DD003 (next-gen SPH), DD013 (simulation stack), DD017 (bulk training data gen) |
| NemaNode | 2024-05-30 | 1 | DD020 (cross-validation connectome data), DD014 (interactive visualization reference) |
| worm-functional-connectivity | 2023-07-07 | 0 | DD010 (Tier 2 alt. functional connectivity), DD017 (loss function target) |
| multi-dev-sibernetic | 2023-01-20 | 1 | DD003 (multi-device SPH), DD017 (bulk sim data gen), DD023 (coupling patterns) |
| wormvae | 2022-04-26 | 0 | DD017 (connectome-constrained VAE — Components 2/4) |
| WormsenseLab_ASH | 2021-09-28 | 3 | DD005 (ASH calibration — already cited), DD010 (Tier 1 electrophysiology) |
| owmeta-sciunit | 2021-04-23 | 2 | DD010 (Tier 1 SciUnit framework), DD013 (CI integration) |
High-priority evaluations:
- tierpsy-tracker: If the OpenWorm fork reads WCON, it may replace the entire 33-hour analysis toolbox revival (DD021)
- CE_locomotion: Already implements
StretchReceptor.cpp— 30-50 hours of proprioception work saved (DD023) - NicolettiEtAl models: Published HH parameter fits expand the ~20-neuron calibration set for DD005
Repo-to-DD Cross-Reference¶
| DD | Primary Repos | Secondary Repos (research/reuse) |
|---|---|---|
| DD001 (Neural) | c302, CElegansNeuroML | hodgkin_huxley_tutorial (education), NicolettiEtAl2024_MN_IN, NicolettiEtAl2019_NeuronModels (HH fits) |
| DD002 (Muscle) | c302, sibernetic (coupling) | muscle_model, JohnsonMailler_MuscleModel (alternatives) |
| DD003 (Body Physics) | sibernetic | sibernetic_v3 (next-gen), multi-dev-sibernetic (multi-device), CelegansNeuromechanicalGaitModulation (gait) |
| DD004 (Cell Identity) | sibernetic | — |
| DD005 (Cell-Type Specialization) | c302, wormneuroatlas | NeuroPAL (cell ID), NicolettiEtAl models (calibration), WormsenseLab_ASH (electrophysiology) |
| DD006 (Neuropeptides) | c302 | — |
| DD007 (Pharynx) | c302 | PlateauNoiseModel (plateau potentials), JohnsonMailler_MuscleModel (Ca²⁺ coupling), NicolettiEtAl models (pharyngeal neurons) |
| DD008 (Data Integration) | owmeta, owmeta-core | ConnectomeToolbox (Phase 1-2 bridge), owmeta ecosystem (9 repos — see below) |
| DD009 (Intestine) | c302 | — |
| DD010 (Validation) | open-worm-analysis-toolbox, tracker-commons | wormneuroatlas (Tier 2), tierpsy-tracker (Tier 3), owmeta-sciunit (Tier 1), worm-functional-connectivity (Tier 2 alt.), NicolettiEtAl models (Tier 1 calibration) |
| DD013 (Integration) | OpenWorm (meta-repo) | owmeta-sciunit (CI validation) |
| DD014 (Visualization) | Worm3DViewer, OpenWorm (Docker) | wormbrowser, WCONViewer, Worm2D, NemaNode (interactive reference) |
| DD014.2 (Mesh Deformation) | Blender2NeuroML (Virtual Worm meshes) | — |
| DD017 (Hybrid ML) | openworm-ml (TBD) | CE_locomotion, wormvae (VAE), wormpose (pose data), CelegansNeuromechanicalGaitModulation (training data), multi-dev-sibernetic (bulk sims) |
| DD018 (Egg-Laying) | c302 | — |
| DD019 (Touch) | c302, sibernetic (bidirectional coupling) | — |
| DD020 (Connectome) | ConnectomeToolbox | wormneuroatlas (complementary), NemaNode (cross-validation), VarshneyEtAl2011 (historical) |
| DD021 (Movement Toolbox) | open-worm-analysis-toolbox, tracker-commons | tierpsy-tracker (may replace toolbox), wormpose (skeleton bridge) |
| DD023 (Proprioception) | c302, sibernetic | CE_locomotion (StretchReceptor.cpp), CelegansNeuromechanicalGaitModulation (gait logic), NicolettiEtAl2024_MN_IN (B-class templates) |
| DD024 (Validation Data) | — | NeuroPAL, wormneuroatlas (validation datasets) |
For DD Authors: How to Reference Repos¶
In Integration Contract — Repository & Packaging section:
| Item | Value |
|------|-------|
| **Repository** | `openworm/c302` |
| **Docker stage** | `neural` in multi-stage Dockerfile (DD013) |
| **`versions.lock` key** | `c302` |
| **Build dependencies** | NEURON 8.2.6 (pip), ConnectomeToolbox/`cect` (pip), pyNeuroML (pip) |
Always link to repos:
- Use full URL in first mention:
openworm/c302 - Subsequent mentions:
c302(no link needed)
OWMeta Ecosystem (9 repos) — Deferred to Phase 3+¶
DD008 defers OWMeta integration to Phase 3+. These repos are working code but not needed until the semantic data layer is activated. cect (ConnectomeToolbox) serves as the Phase 1-2 data bridge.
| Repository | Last Push | Stars | Role |
|---|---|---|---|
| owmeta | 2024-07-29 | 153 | Primary data integration — semantic RDF graph |
| owmeta-core | 2025-03-18 | 3 | Core library for OWMeta |
| owmeta-bundles | 2023-05-19 | 2 | Data bundles for owmeta |
| owmeta-pytest-plugin | 2023-02-04 | 2 | Pytest plugin for testing with owmeta-core |
| owmeta-core-data | 2023-01-20 | 1 | Schema data for owmeta-core |
| owmeta-movement | 2021-12-24 | 2 | Movement data utilities (DD021 related) |
| owmeta-modeldb | 2021-05-10 | 2 | ModelDB integration |
| rdflib-zodb | 2022-05-30 | 2 | RDFLib Store backed by ZODB |
| YAROM | 2020-01-25 | 3 | Yet Another RDF-Object Mapper (predecessor to owmeta-core) |
Inactive Repos (14 repos)¶
Post-2020 activity but no current DD priority. Not broken, just not in the critical path.
| Repository | Last Push | Stars | Description |
|---|---|---|---|
| MetaWorm | 2024-06-30 | 2 | Related project — see Full History |
| simulate | 2025-03-07 | 0 | Links to online simulations of the worm |
| VarshneyEtAl2011 | 2024-02-09 | 0 | Historical connectome data (DD020 uses Cook2019 instead) |
| bt-gsoc-2019 | 2024-01-29 | 1 | BitTorrent Client, Access Control and Data Integrity (GSoC) |
| OpenWormData | 2023-06-02 | 3 | Data bundle — superseded by cect/owmeta |
| movement_cloud | 2022-11-15 | 6 | Cloud movement analysis — superseded by DD021 revival plan |
| Newsletter | 2022-09-10 | 1 | Community newsletter |
| sibernetic_view | 2022-07-30 | 0 | Sibernetic model viewer |
| hydramuscle | 2022-06-16 | 1 | Biophysical model of the muscle of Hydra (not C. elegans) |
| robots | 2021-11-10 | 24 | C. elegans robots |
| worm-math-book | 2021-06-12 | 2 | Online book: mathematical concepts and models |
| openworm-scholar | 2021-05-09 | 2 | Enhanced notifications of published research |
| jenkins | 2021-01-05 | 1 | Old CI infrastructure |
| simple-C-elegans | 2020-06-08 | 6 | Minimalist Python C. elegans model — DD011 onboarding resource |
Archived / Pre-2020 Repository List (21 repos)¶
Last pushed before Jan 2020. Historical or experimental. May contain useful code or data but likely requires modernization.
| Repository | Last Push | Stars | Description | Potential DD Reuse |
|---|---|---|---|---|
| OpenData | 2019-08-25 | 4 | GSoC 2019 Open Data project | — |
| ChannelWorm2 | 2018-09-16 | 11 | Ion channel models (v2) | DD005 (ion channel curation) |
| ChannelWorm | 2018-08-27 | 12 | Ion channel models (v1) | DD005 (ion channel database, HH fitter) |
| model_completion_dashboard | 2018-07-08 | 2 | Model Completion Dashboard | — |
| tests | 2018-06-03 | 3 | Cross-repo tests | DD013 (historical CI patterns) |
| recurrent | 2018-02-12 | 2 | Natural language date parsing | — |
| org.wormsim.frontend | 2017-08-12 | 3 | WormSim frontend | — |
| movement_validation_cloud | 2017-05-13 | 1 | Cloud movement validation | — |
| owcs | 2017-04-16 | 2 | — | — |
| neuronal-analysis | 2017-03-05 | 4 | Neuronal dataset tools | DD010 (Tier 1 comparison scripts) |
| behavioral_syntax | 2017-01-30 | 5 | Behavioral syntax (Andre Brown) | DD010 (Tier 3 behavioral features) |
| pharyngeal_muscle_model | 2017-01-19 | 3 | pm3 pharyngeal muscle NEURON model | DD007 (Ca²⁺ oscillations — already cited, 20-30 hr savings) |
| CyberElegans | 2016-12-19 | 36 | Neuromechanical model | DD001–DD003, DD017 (benchmark) |
| sibernetic_NEURON | 2016-12-19 | 5 | Sibernetic-NEURON interface | DD013 (coupling patterns) |
| skeletonExtraction | 2016-12-19 | 8 | Sibernetic → COLLADA animation | DD014, DD021 (skeleton extraction logic) |
| sibernetic_config_gen | 2016-12-19 | 4 | Sibernetic scene config generator | DD013 (scene generation) |
| BlueBrainProjectShowcase | 2016-10-18 | 2 | BBP models in NeuroML | DD001 (NeuroML reference models) |
| SegWorm | 2016-05-27 | 5 | Schafer lab MATLAB code (Yemini) | DD021 (historical ground truth) |
| HeuristicWorm | 2015-05-11 | 3 | Heuristic worm model | — |
| org.wormsim.bower | 2015-04-29 | 2 | WormSim bower UI components | — |
| bionet | 2015-04-26 | 32 | Artificial biological neural network | DD017 (neural network architecture) |
Maintenance Status Legend¶
| Status | Meaning |
|---|---|
| Active | Commits within last 3 months, actively developed |
| Maintained | Commits within last year, stable and working |
| Research | External research code forked into OpenWorm; recent but not under active OpenWorm development; directly reusable for DDs |
| Deferred | Working code, intentionally deferred to a later phase (e.g., OWMeta to Phase 3+) |
| Inactive | Post-2020 activity but no current DD priority; not broken, just not in the critical path |
| Archived | Pre-2020, historical or experimental; may need modernization |
| ARCHIVED | Explicitly superseded or deprecated, do not use |
- Total OpenWorm GitHub Repositories: 109
- Active / Maintained: ~20
- Research Models & Data: ~17
- Geppetto Platform (dormant): 5
- OWMeta Ecosystem (deferred): 9
- Inactive: ~14
- Archived (pre-2020): ~21
-
Other (educational, outreach, etc.): ~23
-
Maintained by: Integration L4 Maintainer (when appointed)
- Next Update: After Phase A (add any new repos created for organ DDs)