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OpenWorm (@openworm)

openworm

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OpenWorm

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues

sibernetic

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

org.geppetto

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

owmeta

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

CElegansNeuroML

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

Jupyter Notebook

c302

The c302 framework

wormbrowser

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

open-worm-analysis-toolbox

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.

muscle_model

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

Jupyter Notebook

openworm_docs

Documentation for OpenWorm, i.e. docs.openworm.org

hodgkin_huxley_tutorial

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

bionet

Artificial biological neural network

CyberElegans

Neuromechanical model of C. Elegans

org.geppetto.frontend

Geppetto Java frontend bundle

robots

C. elegans robots

openworm.github.io

OpenWorm main website

org.geppetto.core

Geppetto core bundle

openwormbrowser-ios

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

Blender2NeuroML

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

pygeppetto

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

ChannelWorm

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

tracker-commons

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

ChannelWorm2

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

Jupyter Notebook

org.geppetto.model.neuroml

NeuroML Model Bundle for Geppetto

org.geppetto.simulation

Generic simulation bundle for Geppetto

org.geppetto.solver.sph

PCI SPH Solver bundle for Geppetto

skeletonExtraction

Transforms Sibernetic output into a COLLADA animation

WormWorx

C. elegans simulator

behavioral_syntax

behavioral syntax analysis based on the paper of Andre Brown

Jupyter Notebook

movement_cloud

Movement Analysis on the cloud

SegWorm

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

org.geppetto.frontend.jupyter

Geppetto Jupyter Notebook Extension

sibernetic_NEURON

Interface between Sibernetic and NEURON simulator

org.geppetto.sibernetic

PCI SPH Model Bundle for Geppetto

org.geppetto.recording

Python project allowing to create a recording for Geppetto

neuronal-analysis

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

Jupyter Notebook

OpenData

Repo for Google Summer of Code Open Data Project 2019

Jupyter Notebook

org.geppetto.docs

Repository to host Geppetto documentation

org.geppetto.simulator.sph

SPH Simulator bundle for Geppetto

sibernetic_config_gen

Generates starting scene configuration for the Sibernetic simulation engine

geppetto-client

The web client of a Geppetto application

org.geppetto.simulator.jlems

jLEMS based simulator for Geppetto

YAROM

Yet Another RDF-Object Mapper

OpenWormData

org.geppetto.model.swc

SWC Model Interpreter for Geppetto

org.geppetto.model

HeuristicWorm

org.geppetto.maven

Maven repository for Geppetto

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

geppetto-application

Sample Geppetto application

WormsenseLab_ASH

Electrophysiological recordings of neuron ASH from Wormsense Lab

Jupyter Notebook

NeuroPAL

Some tests on using the NeuroPAL datasets

Jupyter Notebook

org.geppetto.samples

Sample simulations for Geppetto

pharyngeal_muscle_model

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

tests

OpenWorm tests across various repos

Jupyter Notebook

org.wormsim.frontend

WormSim frontend bundle

owmeta-movement

DataSources and utilities for movement data in OpenWorm

org.geppetto.persistence

Persistance bundle for Geppetto

org.geppetto.templatebundle

org.geppetto.datasources

JohnsonMailler_MuscleModel

C. elegans muscle model from Johnson & Mailler 2015

org.geppetto.simulator.libroadrunner

libRoadRunner simulator bundle for Geppetto

owmeta-modeldb

openworm-scholar

A service providing enhanced notifications of published research in Open Worm

org.geppetto.bower

Geppetto repository for packaged bower components

org.geppetto.testbackend

owmeta-bundles

Bundles for owmeta

org.wormsim.bower

Wormsim repository for packaged bower UI components

owmeta-pytest-plugin

Pytest plugin for testing with owmeta-core

worm-math-book

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

Jupyter Notebook

owmeta-sciunit

owmeta types for SciUnit and NeuronUnit

org.geppetto.frontend.nodejs

Geppetto Node.js backend

jenkins

multi-dev-sibernetic

Multi devices sibernetic engine

.github

The OpenWorm organisation template repository.

bt-gsoc-2019

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

Newsletter

A repository containing a newsletter with regular OpenWorm updates

owmeta-core-data

owmeta repository for the owmeta-core schema