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Projects Overview

OpenWorm Projects

Projects and Design Documents

OpenWorm's projects are now formally specified in Design Documents (DDs). Each repository implements one or more DDs:

Repository Design Documents Status Role
c302 DD002, DD003, DD005-DD009, DD014-DD015 Active Neural circuit, muscle models, organ systems
Sibernetic DD001, DD004 Active Body physics, SPH engine
ConnectomeToolbox DD016 Active Connectome data access (cect API)
Worm3DViewer DD012 Active Visualization (Trame evolution)
open-worm-analysis-toolbox DD010, DD017 Revival needed Tier 3 behavioral validation
OpenWorm (meta-repo) DD011 Proposed Integration, Docker stack
DevoWorm Phase 6, DD004, DD005 Active Developmental dynamics, morphogenesis
Geppetto DD012 (historical) Dormant Web platform (superseded by Trame)

See Integration Map for the complete dependency graph.

Currently active projects

Projects still maintained, less active

NeuroMechanical Modeling - Sibernetic

Sibernetic implements DD001 (Body Physics Architecture) — the formal specification for SPH-based body mechanics including the PCISPH algorithm, ~100K particles, and fluid-structure interaction. See DD001 for the complete spec including particle types, validation criteria, and integration contract.

Sibernetic is the home of the C++ code base that implements the core of the model. We have implemented an algorithm called Smoothed Particle Hydrodynamics (SPH) to simulate the body of the worm and its environment using GPUs.

To get a quick idea of what this looks like, check out the latest movie. In this movie you can see a simulated 3D C. elegans being activated in an environment. Its muscles are located around the outside of its body, and as they contract, they exert forces on the surrounding fluid, propelling the body forward via undulatory thrust.

More detailed information is available on the Sibernetic project page.

c302 Neural Modeling Framework

c302 implements DD002 (Neural Circuit Architecture) — the multi-level Hodgkin-Huxley framework for all 302 neurons. It also serves as the foundation for DD005 (cell-type specialization), DD006 (neuropeptides), DD007-DD009 (organ circuits), DD014 (egg-laying), and DD015 (touch response).

c302 generates NeuroML2 networks at multiple levels of biophysical detail (Levels A-D), with Level C1 (HH + graded synapses) as the recommended default for coupling with Sibernetic.

More detailed information is available on the c302 project page.

Visualization

The visualization platform is evolving per DD012 (Dynamic Visualization Architecture):

  • Phase 1: Trame viewer (PyVista + live server)
  • Phase 2: Interactive layers with validation overlays
  • Phase 3: Three.js + WebGPU static site at wormsim.openworm.org (WormSim 2.0)

Geppetto served this role historically (2014-2020) and is preserved as archival reference.

Movement Analysis and Validation

The Movement Analysis project implements DD010 (Validation Framework) — the 3-tier validation system that ensures our simulation matches real worm behavior. The analysis toolbox is being revived per DD017.

More detailed information is available on the Movement analysis project page and the Validation page.

Optimization and Parameter Fitting

Now formalized in DD013 (Hybrid Mechanistic-ML Framework) — differentiable simulation with gradient descent, neural surrogates for 1000x speedup, and foundation model predictions for channel kinetics.

More detailed information is available on the Optimization project page.

Data Collection and Representation

Formalized in DD008 (Data Integration Pipeline) and DD016 (Connectome Data Access) — the ConnectomeToolbox (cect) is the canonical API for connectome data.

More detailed information is available on the Data representation project page.

DevoWorm — Developmental Modeling

The DevoWorm project (devoworm.weebly.com, github.com/devoworm) focuses on developmental dynamics, digital morphogenesis, and developmental plasticity in C. elegans. DevoWorm's embryogenetic connectome analysis, differentiation trees, and CompuCell3D morphogenesis models form the foundation for Phase 6 (Developmental Modeling) of the simulation roadmap — the "Worm That Grows" milestone. DevoWorm's work also connects to DD004 (cell identity during body growth) and DD005 (temporal dynamics of cell-type specification).

More detailed information is available on the DevoWorm project page.

Community Outreach

The effort to build the OpenWorm open science community is always ongoing. See the contributor progression model ([DD011](contributing/contributor-progression.md)) for the L0-L5 path.

More detailed information is available on the Community project page.

Muscle-Neuron Integration

Now formalized in DD002 (neural) + DD003 (muscle) + DD005 (cell-type specialization). The goal of creating biologically-realistic ion channel models from experimental data is specified with quantitative criteria and CeNGEN single-cell transcriptomics as the primary data source.

More detailed information is available on the Muscle-Neuron integration project page.

C. elegans robot

The goal of this project is twofold:

  1. To build a robot that simulates sensory-motor functions of a C. elegans nematode worm, including foraging for food.
  2. To specify parts and instructions that will help anyone to build the robot.

More detailed information is available on the C. elegans robot project page.