OpenWorm Science

Resources OpenWorm has developed for the C. elegans research community.

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!

Resource Description
C. Elegans Ion Channels Spreadsheet of ion channels
WormAtlas Website with an atlas containing images of worm anatomy
WormBase A comprehensive web-based database of genes, gene expression, proteins, and much more specifically for c. elegans and related species
Virtual Worm project at WormBase 3D Blender files for the anatomy of the C. elegans
C. elegans II Web-based textbook for all things C. elegans. Second edition
WormBook Comprehensive, open-access collection of original, peer-reviewed chapters covering topics related to the biology of Caenorhabditis elegans and other nematodes
WormClassroom WormClassroom is intended to serve as an education portal for the research model organism Caenorhabditis elegans
WormImage Here you can view and download thousands of unpublished electron micrographs and associated data
RNAiDB Provides access to results from RNAi interference studies in C. elegans, including images, movies, phenotypes, and graphical maps
PhenoBank Our aim was to test all C. elegans genes for their role in the first two rounds of mitotic cell division. To this end, we combined genome-wide RNAi screening with time-lapse video microscopy of the early embryo
Worm Interactome DB Worm Interactome version 8 assembles high-quality yeast two-hybrid protein protein interactions in C. elegans
IntAct IntAct provides a freely available, open source database system and analysis tools for molecular interaction data.
BioGrid The Biological General Repository for Interaction Datasets (BioGRID) is an online interaction repository with data compiled through comprehensive curation efforts
INTACT The Kohara lab has been constructing an expression pattern map of the 100Mb genome of the nematode Caenorhabditis elegans through EST analysis and systematic whole mount in situ hybridization. NEXTDB is the database to integrate all information from our expression pattern project
Hope Laboratory Expression Pattern Database Each page in this database is a record of the results of one experiment. For each experiment, a C. elegans genomic DNA fragment has been joined to a reporter gene, either lacZ or gfp and this fusion gene has been used to generate transgenic C. elegans lines
BC C. elegans Gene Expression Consortium Expression patterns for C. elegans promoter:GFP fusions
Stanford Microarray Database A database of microarray experiments
NCBI Gene Expression Omnibus GEO is a public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted. Tools are provided to help users query and download experiments and curated gene expression profiles
EBI ArrayExpress ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies
Protein Data Bank The PDB archive contains information about experimentally-determined structures of proteins, nucleic acids, and complex assemblies
NCBI PubMed PubMed comprises more than 23 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites
Textpresso
Neuroscience Information Framework The Neuroscience Information Framework is a dynamic inventory of Web-based neuroscience resources: data, materials, and tools accessible via any computer connected to the Internet
WormBase Wiki This is the official wiki site for WormBase, the database of the model organism Caenorhabditis elegans and related nematodes
Worm Community Forums Forums for discussing scientific topics with c. elegans scientists
Entrez Gene Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide
MapViewer The 100 Mb genome is organized in six chromosomes and annotation represents more than 20,000 genes. The gene, transcript, and protein annotation is provided by WormBase and NCBI provides ab initio model predictions and calculates alignments to provide the C. elegans UniGene (Cel_UniG) and transcript (Cel_EST) maps
Ensembl The goal of Ensembl is to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web
UCSC Genome Browser Browse the C. elegans Genome
UniProt The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information
InParanoid Ortholog groups with inparalogs
TreeFam TreeFam is a database composed of phylogenetic trees inferred from animal genomes. It provides orthology/parology predictions as well the evolutionary history of genes
Reactome Reactome is a free, open-source, curated and peer reviewed pathway database. Our goal is to provide intuitive bioinformatics tools for the visualization, interpretation and analysis of pathway knowledge to support basic research, genome analysis, modeling, systems biology and education
MetaCyc MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 2097 pathways from more than 2460 different organisms, and is curated from the scientific experimental literature
KEGG Pathway database Wiring diagrams of molecular interactions, reactions, and relations
Gene Ontology The Gene Ontology project is a major bioinformatics initiative with the aim of standardizing the representation of gene and gene product attributes across species and databases. The project provides a controlled vocabulary of terms for describing gene product characteristics and gene product annotation data from GO Consortium members, as well as tools to access and process this data
miRBase The miRBase database is a searchable database of published miRNA sequences and annotation
Toolbox at the EBI We maintain the world’s most comprehensive range of freely available and up-to-date molecular databases. Developed in collaboration with our colleagues worldwide, our services let you share data, perform complex queries and analyse the results in different ways
ExPASy Proteomics Tools Bioinformatics Resource Portal

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 .

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