Discover openworm/openworm_docs Open Source project

This is a C++/OpenCL implementation of the PCISPH algorithm supplemented with a set of biomechanics related features applied to C. elegans locomotion

2,659

sibernetic

354

org.geppetto

Geppetto is an open-source platform to build web-based applications to visualize and simulate neuroscience data and models.

Unified, simple data access python library for data & facts about C. elegans anatomy

209

owmeta

NeuroML based C elegans model, contained in a neuroConstruct project, as well as c302

152

CElegansNeuroML

c302

wormbrowser

The Worm Browser -- a 3D browser of the cellular anatomy of the c. elegans

A testing pipeline that allows us to run a behavioural phenotyping of our virtual worm running the same test statistics the Schafer Lab used on their worm data.

open-worm-analysis-toolbox

Model of C elegans body wall muscle based on Boyle & Cohen 2008

muscle_model

A repository containing code for a number of tutorials on the Hodgkin Huxley model, including an interactive Jupyter notebook

hodgkin_huxley_tutorial

Artificial biological neural network

bionet

Neuromechanical model of C. Elegans

CyberElegans

Geppetto Java frontend bundle

org.geppetto.frontend

robots

C. elegans robots

openworm.github.io

OpenWorm main website

HTML

org.geppetto.core

Geppetto core bundle

OpenWorm Browser for iOS, based on the open-3d-viewer, which was based on Google Body Browser

openwormbrowser-ios

Objective-C

Blender2NeuroML

Conversion script to bring neuron models created in Blender into NeuroML format

Python Library to create, load, edit and save a Geppetto Model

pygeppetto

Tools and curated datasets to build quantitative models of C. elegans ion channels

ChannelWorm

Compilation of information and code bases related to open-source trackers for C. elegans

tracker-commons

Scala

ChannelWorm2

Tools and curated datasets to build quantitative models of C. elegans ion channels

NeuroML Model Bundle for Geppetto

org.geppetto.model.neuroml

Generic simulation bundle for Geppetto

org.geppetto.simulation

PCI SPH Solver bundle for Geppetto

org.geppetto.solver.sph

Transforms Sibernetic output into a COLLADA animation

skeletonExtraction

behavioral syntax analysis based on the paper of Andre Brown

WormWorx

C. elegans simulator

behavioral_syntax

Movement Analysis on the cloud

movement_cloud

SegWorm is Matlab code from Dr. Eviatar Yemini built as part of the WormBehavior database (http://wormbehavior.mrc-lmb.cam.ac.uk/)

SegWorm

MATLAB

org.geppetto.frontend.jupyter

Geppetto Jupyter Notebook Extension

Interface between Sibernetic and NEURON simulator

sibernetic_NEURON

PCI SPH Model Bundle for Geppetto

org.geppetto.sibernetic

Python project allowing to create a recording for Geppetto

org.geppetto.recording

Tools to produce, analyse and compare both simulated and recorded neuronal datasets

neuronal-analysis

Repo for Google Summer of Code Open Data Project 2019

OpenData

Repository to host Geppetto documentation

org.geppetto.docs

SPH Simulator bundle for Geppetto

org.geppetto.simulator.sph

Generates starting scene configuration for the Sibernetic simulation engine

sibernetic_config_gen

The web client of a Geppetto application

geppetto-client

jLEMS based simulator for Geppetto

org.geppetto.simulator.jlems

Yet Another RDF-Object Mapper

YAROM

SWC Model Interpreter for Geppetto

OpenWormData

TeX

org.geppetto.model.swc

org.geppetto.model

HeuristicWorm

Maven repository for Geppetto

org.geppetto.maven

org.geppetto.simulator.external

Geppetto bundle to add support for external neuronal simulators (NEURON, etc.)

owmeta-core

Core library for owmeta

org.geppetto.model.nwb

Sample Geppetto application

geppetto-application

Electrophysiological recordings of neuron ASH from Wormsense Lab

WormsenseLab_ASH

Some tests on using the NeuroPAL datasets

NeuroPAL

Sample simulations for Geppetto

org.geppetto.samples

C. elegans pharyngeal muscle cell (pm3) model, capable of generating Ca2+ slow action potential (NEURON, NMODL).

pharyngeal_muscle_model

tests

OpenWorm tests across various repos

org.wormsim.frontend

WormSim frontend bundle

DataSources and utilities for movement data in OpenWorm

owmeta-movement

Persistance bundle for Geppetto

org.geppetto.persistence

org.geppetto.templatebundle

org.geppetto.datasources

C. elegans muscle model from Johnson & Mailler 2015

JohnsonMailler_MuscleModel

HTML

org.geppetto.simulator.libroadrunner

libRoadRunner simulator bundle for Geppetto

owmeta-modeldb

A service providing enhanced notifications of published research in Open Worm

openworm-scholar

Geppetto repository for packaged bower components

org.geppetto.bower

org.geppetto.testbackend

Wormsim repository for packaged bower UI components

owmeta-bundles

Bundles for owmeta

org.wormsim.bower

owmeta-pytest-plugin

Pytest plugin for testing with owmeta-core

An online book focusing on the mathematical concepts and models of the OpenWorm project.

worm-math-book

owmeta types for SciUnit and NeuronUnit

owmeta-sciunit

org.geppetto.frontend.nodejs

Geppetto Node.js backend

Multi devices sibernetic engine

jenkins

Groovy

multi-dev-sibernetic

The OpenWorm organisation template repository.

.github

End to end process of the Framework including a BitTorrent Client, Access Control and Data Integrity checks.

bt-gsoc-2019