OpenWorm is an open source project dedicated to creating the world’s first virtual organism in a computer, a C. elegans nematode. Throughout the years we have built a network of relationships with with many biologists and neuroscientists interested in C. elegans. This page presents the scientific data and resources produced by the OpenWorm community for the benefit of experimental and computational scientists working in this area.

Existing Scientific Collaborations

The entire C. elegans experimental community that assembles at the yearly GSA C. elegans meeting is incredibly welcoming and supportive. We've received data and help from C. elegans biologists including Dr. Sreekanth Chalasani at the Salk Institute, Dr. Michael Francis at UMass Medical School, Dr. William Schafer at University of Cambridge and Dr. Andrew Leifer at Princeton University. We've been inspired and received help on worm simulations from the lab of Dr. Netta Cohen at Leeds University and her students. The original source for many of the 3D images of the worm's body is the Virtual Worm project at WormBase, specifically Dr. Christian Grove at CalTech.

The OpenWorm project has produced various resources to make it easier to explore the anatomy of the C. elegans, and has released early versions of applications which will enable the biophysical simulation of the worm and its interactions with its environment.

OpenWorm Documentation

All of the documentation for the project in a single site.

OpenWorm Browser

The OpenWorm browser exposes through a web interface the anatomical model of C. elegans developed as part of the Virtual Worm project at Caltech. The application allows pealing different layers of the worm revealing distinct groups for the nervous system, the muscle cells, the organs and the cuticle. All the cells of the worm are searchable through the user interface.

OpenWorm Browser (Free web application)
OpenWorm Browser iOS

NeuroML C. elegans Connectome

The team has produced a model of the connectome of the C. elegans in NeuroML, a standard for describing computational models of neurons and networks. The model has been generated by post-processing the morphology of the nervous system available in the Blender file produced by the Virtual Worm project with an ad-hoc Python script written for this purpose and released in the open-source. This model is a work in progress and although it represents the first full multi-compartmental model of the network of an entire organism it still lacks characterization of the biophysical properties of the neurons. Current efforts are directed towards integrating the synapses in the model, more informations about this can be found here. The NeuroML model can be found and explored in 3D through Open Source Brain; OSB Explorer allows scientists to expose the property of the neurons and navigate their connections by simply clicking on them.

C. elegans connectome on Open Source Brain

Sibernetic

OpenWorm has been developing Sibernetic, a C++ implementation of the Predictive-corrective Incompressible Smooth Particle Hydrodynamics (PCI-SPH) algorithm based on the work of Solenthaler. The algorithm has been extended to model contractile matter and membranes for simulating the muscle tissue of the C. elegans. The implementation uses OpenCL to distribute the computation of the particle system on both CPUs and GPUs in a parallelized way.

Sibernetic sources
Sibernetic video

Geppetto

OpenWorm has been developing Geppetto, a web-based multi-algorithm, multi-scale simulation platform engineered to support the simulation of complex biological systems and their surrounding environment. The platform aims at integrating multiscale models whose simulation depends on a variety of algorithms which need to interoperate. Great focus has been put on the engineering of the platform, aiming at having a robust and generic solution that can be applied to different class of models. OpenWorm aims to make progresses of the OpenWorm simulation available to scientist and general public through Geppetto. Geppetto at present supports a simulator for LEMS, a domain agnostic language specification aimed at describing dynamic models, and Sibernetic, the fluid dynamics simulator also developed as part of the project. The visualisation engine of Geppetto has been reused in Open Source Brain Explorer and allows a variety of neuronal models to be seamlessly visualised in 3D through the web browser.

Geppetto documentation
Geppetto sources
Geppetto website

Other activities

OpenWorm is contributing the development of computational neuronal models to Open Source Brain. The group page with all the projects can be found here.

This is a list of online resources related to C. elegans which we have found useful in the OpenWorm project. If you know of other resources we should include here, please get in contact!

We have created a collection of references that have significantly influenced our work.

A list of publications by members of the OpenWorm community related to the initiative can be found here.

Members of the OpenWorm community are active participants in and presenters at scientific workshops and conferences. You can find a list of past and future events we have contributed to here.

There are numerous ways to interact with the project on our Contacts page.

Want to help curate this page, propose an edit or add a resource? Drop us a line!