Tutorials

Here, we show how to use SimTracker to run a NEURON simulation of a ringdemo network (Tutorial Install SimTracker and run a parallel ring network simulation) and how to use the Network Clamp tool to run a network clamp simulation (Tutorial Network Clamp). Other tutorials are covered in the online documentation, including tutorials on particular functions within SimTracker, how to install SimTracker and its components individually rather than as part of a Docker package, and how to use SimTracker to run large scale parallel NEURON models on supercomputers.

All SimTracker functionality is open to customization. For users who want to customize SimTracker or its outputs, review the MATLAB code, or even run the NEURON code independently of SimTracker, we recommend consulting the online documentation at readthedocs.org <readthedocs.org>.

While working through the tutorials, keep in mind that steps that include the text terminal-$ enter_this_command mean that, at the user’s local terminal, the text after the dollar sign should be entered ( in this example, enter_this_command). Any step that advises entering ”text” somewhere means that only the characters within the quotes, not the quotes themselves, should be entered.

Tutorials:

• Install SimTracker and run a parallel ring network simulation
• Network Clamp a cell using the NetworkClamp tool
• Create a new model repository using SimTracker
• Design, execute and upload a simulation
• Analyzing a simulation
• Organize simulations
• Model Design Characterization
  • Add model cell types and specify model cell numbers and connections
  • Characterize model network components with CellClamp
• Automatically analyze experimental data using CellData
• Characterize model network components with CellClamp
• Add model cell types and specify model cell numbers and connections