OpenWorm (@openworm)

Top repositories

1

OpenWorm

Repository for the main Dockerfile with the OpenWorm software stack and project-wide issues
Python
2,659
star
2

sibernetic

This is a C++/OpenCL implementation of the PCISPH algorithm supplemented with a set of biomechanics related features applied to C. elegans locomotion
C
354
star
3

org.geppetto

Geppetto is an open-source platform to build web-based applications to visualize and simulate neuroscience data and models.
Python
209
star
4

owmeta

Unified, simple data access python library for data & facts about C. elegans anatomy
Python
152
star
5

CElegansNeuroML

NeuroML based C elegans model, contained in a neuroConstruct project, as well as c302
Jupyter Notebook
134
star
6

c302

The c302 framework
Python
68
star
7

wormbrowser

The Worm Browser -- a 3D browser of the cellular anatomy of the c. elegans
JavaScript
49
star
8

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.
Python
48
star
9

muscle_model

Model of C elegans body wall muscle based on Boyle & Cohen 2008
Jupyter Notebook
47
star
10

openworm_docs

Documentation for OpenWorm, i.e. docs.openworm.org
Python
44
star
11

hodgkin_huxley_tutorial

A repository containing code for a number of tutorials on the Hodgkin Huxley model, including an interactive Jupyter notebook
Python
36
star
12

bionet

Artificial biological neural network
C++
31
star
13

CyberElegans

Neuromechanical model of C. Elegans
C++
31
star
14

org.geppetto.frontend

Geppetto Java frontend bundle
Java
29
star
15

robots

C. elegans robots
C
24
star
16

openworm.github.io

OpenWorm main website
HTML
24
star
17

org.geppetto.core

Geppetto core bundle
Java
23
star
18

openwormbrowser-ios

OpenWorm Browser for iOS, based on the open-3d-viewer, which was based on Google Body Browser
Objective-C
22
star
19

Blender2NeuroML

Conversion script to bring neuron models created in Blender into NeuroML format
Python
17
star
20

pygeppetto

Python Library to create, load, edit and save a Geppetto Model
Python
14
star
21

ChannelWorm

Tools and curated datasets to build quantitative models of C. elegans ion channels
JavaScript
12
star
22

tracker-commons

Compilation of information and code bases related to open-source trackers for C. elegans
Scala
11
star
23

ChannelWorm2

Tools and curated datasets to build quantitative models of C. elegans ion channels
Jupyter Notebook
10
star
24

org.geppetto.model.neuroml

NeuroML Model Bundle for Geppetto
Java
9
star
25

org.geppetto.simulation

Generic simulation bundle for Geppetto
Java
9
star
26

org.geppetto.solver.sph

PCI SPH Solver bundle for Geppetto
Java
9
star
27

skeletonExtraction

Transforms Sibernetic output into a COLLADA animation
C++
7
star
28

WormWorx

C. elegans simulator
C
6
star
29

behavioral_syntax

behavioral syntax analysis based on the paper of Andre Brown
Jupyter Notebook
5
star
30

movement_cloud

Movement Analysis on the cloud
Python
5
star
31

SegWorm

SegWorm is Matlab code from Dr. Eviatar Yemini built as part of the WormBehavior database (http://wormbehavior.mrc-lmb.cam.ac.uk/)
MATLAB
5
star
32

org.geppetto.frontend.jupyter

Geppetto Jupyter Notebook Extension
Python
5
star
33

sibernetic_NEURON

Interface between Sibernetic and NEURON simulator
Python
5
star
34

org.geppetto.sibernetic

PCI SPH Model Bundle for Geppetto
Java
5
star
35

org.geppetto.recording

Python project allowing to create a recording for Geppetto
Python
5
star
36

neuronal-analysis

Tools to produce, analyse and compare both simulated and recorded neuronal datasets
Jupyter Notebook
4
star
37

OpenData

Repo for Google Summer of Code Open Data Project 2019
Jupyter Notebook
4
star
38

org.geppetto.docs

Repository to host Geppetto documentation
Python
4
star
39

org.geppetto.simulator.sph

SPH Simulator bundle for Geppetto
Java
4
star
40

sibernetic_config_gen

Generates starting scene configuration for the Sibernetic simulation engine
Python
4
star
41

geppetto-client

The web client of a Geppetto application
JavaScript
4
star
42

org.geppetto.simulator.jlems

jLEMS based simulator for Geppetto
Java
3
star
43

YAROM

Yet Another RDF-Object Mapper
Python
3
star
44

OpenWormData

TeX
3
star
45

org.geppetto.model.swc

SWC Model Interpreter for Geppetto
Java
3
star
46

org.geppetto.model

Java
3
star
47

HeuristicWorm

C++
3
star
48

org.geppetto.maven

Maven repository for Geppetto
3
star
49

org.geppetto.simulator.external

Geppetto bundle to add support for external neuronal simulators (NEURON, etc.)
Python
3
star
50

owmeta-core

Core library for owmeta
Python
3
star
51

org.geppetto.model.nwb

Java
3
star
52

geppetto-application

Sample Geppetto application
JavaScript
3
star
53

WormsenseLab_ASH

Electrophysiological recordings of neuron ASH from Wormsense Lab
Jupyter Notebook
3
star
54

NeuroPAL

Some tests on using the NeuroPAL datasets
Jupyter Notebook
3
star
55

org.geppetto.samples

Sample simulations for Geppetto
JavaScript
3
star
56

pharyngeal_muscle_model

C. elegans pharyngeal muscle cell (pm3) model, capable of generating Ca2+ slow action potential (NEURON, NMODL).
C
3
star
57

tests

OpenWorm tests across various repos
Jupyter Notebook
3
star
58

org.wormsim.frontend

WormSim frontend bundle
JavaScript
3
star
59

owmeta-movement

DataSources and utilities for movement data in OpenWorm
Python
2
star
60

org.geppetto.persistence

Persistance bundle for Geppetto
Java
2
star
61

org.geppetto.templatebundle

Java
2
star
62

org.geppetto.datasources

Java
2
star
63

JohnsonMailler_MuscleModel

C. elegans muscle model from Johnson & Mailler 2015
HTML
2
star
64

org.geppetto.simulator.libroadrunner

libRoadRunner simulator bundle for Geppetto
Java
2
star
65

owmeta-modeldb

Python
2
star
66

openworm-scholar

A service providing enhanced notifications of published research in Open Worm
Python
2
star
67

org.geppetto.bower

Geppetto repository for packaged bower components
JavaScript
2
star
68

org.geppetto.testbackend

Java
2
star
69

owmeta-bundles

Bundles for owmeta
2
star
70

org.wormsim.bower

Wormsim repository for packaged bower UI components
2
star
71

owmeta-pytest-plugin

Pytest plugin for testing with owmeta-core
Python
2
star
72

worm-math-book

An online book focusing on the mathematical concepts and models of the OpenWorm project.
Jupyter Notebook
2
star
73

owmeta-sciunit

owmeta types for SciUnit and NeuronUnit
Python
2
star
74

org.geppetto.frontend.nodejs

Geppetto Node.js backend
JavaScript
2
star
75

jenkins

Groovy
1
star
76

multi-dev-sibernetic

Multi devices sibernetic engine
C++
1
star
77

.github

The OpenWorm organisation template repository.
Python
1
star
78

bt-gsoc-2019

End to end process of the Framework including a BitTorrent Client, Access Control and Data Integrity checks.
Python
1
star
79

Newsletter

A repository containing a newsletter with regular OpenWorm updates
1
star
80

owmeta-core-data

owmeta repository for the owmeta-core schema
1
star