Running the NeuroML connectome in NeuroConstruct
The NeuroML conversion of the Virtual Worm Blender files has been imported into a neuroConstruct project.
This page provides instructions for obtaining the latest version of neuroConstruct, getting the latest CElegans project and generating/visualising the cells and connections.
Install neuroConstruct and the CElegans project
There is a quick-start zip file containing neuroConstruct and the C. elegans connectome project. Installation instructions are in the file README.txt inside the zip file.
If you have any problems installing the quick-start package, please e-mail openworm-bundle -at- magic-cookie.co.uk with a description of what went wrong.
If you are a developer, or need the very latest changes, you may prefer to install from the GitHub repositories instead. See the advanced installation instructions at the end of this page for details.
Open the project
Run neuroConstruct as outlined in the installation instructions (using ant run or nC.bat/nC.sh). In the main menu select File -> Open and browse to the location of CElegans.ncx. Select this file and press Open.
The project may take up to 20 seconds to load. When it does load, try clicking on one of the cells in the Cell Types in project box, e.g. ADAL. This will take you to the Cell Types tab and show a summary of the cell's electrical properties (note: these are not yet matched to the real electrophysiological properties of Celegans cells!) and the number of segments in the cell.
Click on View/edit morphology and this will visualise the cell in 3D, see below.
Generate a network
Now generate a subset network. Go to tab Generate, select 'PharyngealNeurons_inputs' from the dropdown and press Generate cell positions and connections. Now go to tab Visualisation and press View with Latest Generated Positions selected in the drop down box. On a Mac, you can hold down the option button, click and drag downwards to zoom in further than the slider allows.
Alternatively, you can generate a network of all 302 neurons. Go to tab Generate and select 'Default Simulation Configuration' from the dropdown and press Generate cell positions and connections.
The image below shows the generated full network.
Executing the network in NEURON simulation environment.
Install the NEURON simulation environment and set the path to NEURON's bin directory containing nrniv within neuroConstruct's menu (Settings->General Preferences and Project Defaults). After generating cell positions (easiest to do this with the PharyngealNeurons_inputs configuration), go to the export tab, the NEURON subtab, and press 'create hoc simulation'. Once this is completed the button will stop being greyed out and the 'Run simulation' button will be available. Clicking this should kick off the simulation run. Once this is completed, the output from the simulation should tell you that results are available in a directory named 'Sim_XX' where XX will be a number. Go back to the Visualisation tab and click 'View Prev Sims in 3D..." Click on the box with the 'Sim_XX' name that applies to the simulation run you did and press 'Load Simulation' at the bottom. Then at the bottom of the Visualisation screen click 'Replay' and the 'Replay simulation'. For PharyngealNeurons_inputs, the color changes will be subtle, but they will be happening.
Check the project
In addition to being able to generate and view the project through the main GUI, a number of Python scripts are provided to test the configuration of the project. These scripts access functionality in the Java implementation of neuroConstruct by using Jython. More details on the Python interface to neuroConstruct can be found here.
A script to test various aspects of the project is CheckProject.py. Running this generates a number of the Simulation Configurations in succession and checks that the expected numbers of cells and connections are created:
cd pythonScripts
~/neuroConstruct/nC.sh -python CheckProject.py
Generate NeuroML from the project
A NeuroML file containing the structure of the cells & all connections can be generated in two ways:
Through the GUI
After generating the network in the GUI as outlined above, go to tab Export, click on Generate all NeuroML scripts. To have a single file with all the NeuroML for cells, channels and network connections, select Generate single NeuroML Level 3 file.
Using a Python script
Go to folder pythonScript and run:
~/neuroConstruct/nC.sh -python GenerateNeuroML.py
Regenerate the connectome in NeuroML format
See here for more details.
Advanced installation instructions
This section describes how to install directly from the GitHub repositories. If you are a developer, or need the very latest changes, this may be a better option than using the quick-start bundle.
Install the latest neuroConstruct
First, get the latest version of neuroConstruct from GitHub. While there are binary installers available on the neuroConstruct download page, it's best to use the latest version of this application from the GitHub repository, as this will most likely be the version in which the C. elegans project was last saved.
For full details on installing neuroConstruct from GitHub, see here: https://github.com/NeuralEnsemble/neuroConstruct/blob/master/INSTALL
Contact p.gleeson -at- ucl.ac.uk if there you have any problems with this.
Getting the latest CElegans neuroConstruct project
The latest CElegans project is being hosted on Github here. You have a number of options for getting the project:
A) Zip file with latest project
Get a zipped file with the project here. Unzip this and go to the CElegans folder.
B) Read only copy of latest project
Install Git and get a read only clone of the Git repository:
git clone git://github.com/openworm/CElegansNeuroML.git
cd CElegansNeuroML/CElegans
You'll always be able to retrieve the latest version of the project with
git pull
C) Fork the project
Fork yourself a personal copy of the project repository. Go to https://github.com/openworm/CElegansNeuroML for more details.