Running Simulations

From Whole Brain Catalog

Contents 1 Neuron Simulations 1.1 Animating Growth Simulations 1.2 Animating Spike Firing Simulations 1.3 Submitting NeuroConstruct Project for Simulations

[edit] Neuron Simulations

For the neuron simulations, the files must be specially formatted. Please contact the Whole Brain Catalog team for details on how to use your own data by posting to our forums or sending an email to contact (at) wholebraincatalog (dot) org

[edit] Animating Growth Simulations

Whole Brain Catalog allows users to view neurogenesis and cell growth data. To do this, you will first need an appropriately formatted data file (this is not bundled with the software). We are providing a sample set of data from the Lab of Dr. Rusty Gage, click the link to download the data.

1. Get growth data. (You may use the sample set from the link above)
2. Unzip the data from the file
3. Navigate to the cells in Whole Brain Catalog
4. Select the View menu on menubar
5. Select 'Grow All Neurons'
6. Navigate to, and select the XML file you wish to view ( If you are using the data we are providing, the file to locate is Growth_3_GranuleCell.xml )

[edit] Animating Spike Firing Simulations

Whole Brain Catalog allows users to view firing action potentials. To do this, you will first need an appropriately formatted data file (this is not bundled with the software). We are providing four sample set of data obtained through the NeuroConstruct project for the Granule Cell Network, Thalamocortical Network, Rothman's Pyramidal Cell Network and the Mainen Pyramidal Cell.

• Sample - Test Phase Firing Data for Granule Cell Network
• Sample - Test Phase Firing Data for Thalamocortical Network
• Sample - Test Phase Firing Data for Rhotman Network
• Sample - Test Phase Firing Data for Mainen Pyramidal Cell

We are also including a sample set of data obtained from the Gage lab for the Dentate Gyrus Network.

• Sample - Test Phase Firing Data for Dentate Gyrus Network

1. Get firing data. (You may use the sample sets from the links above)
2. Unzip the data from the file to a folder
3. Navigate to network. You can do this by opening the "Cells" tree under the "data type" panel found on the left hand side of the Whole Brain Catalog Window and checking on the box next to the network name.
4. Double click on a cell that is checked (For example, MF_3D_20 if you are animating the Granule Cell Network)
5. You will zoom to the network. You may use the "-" key to zoom out once you have clicked on the 3d window.
6. Select a cell corresponding to the Network from the "data type" panel or from the scene.
7. A pop-up menu will show, select the "Animate Network" option.
8. A window will pop up prompting you to choose the simulation data. Navigate to, and select a time-series formatted file. All files in this folder will be used for the simulation, so you can choose any file. ( For example, if you are using the data we are providing for the Granule Cell Network, the file to locate is GrC_3D_0.xml )
9. Right click on a network cell and choose "Animate Network" from the pop up menu to turn animations off.

[edit] Submitting NeuroConstruct Project for Simulations

Whole Brain Catalog allows users to submit Neuro Construct models for simulation. The above video, "Simulation roundtrip", shows this process in detailed.