Salto v1.0
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(c) Charles CH Cohen, 2014-present
The contents of this package are released to the public under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International license (CC BY-NC-ND 4.0, in English).
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Automated generation, GUI-based exploration, and multiscale optimization of neuron models.
Current version: fully-operational and tested for fixed timestep voltage recording applications, with both passive and active biophysical elements, including notably evoked action potentials (the example used in this version).
In development: a version for variable timestep applications, across passive and active bioelectric mechanisms, for voltage responses to both short and long pulse current stimuli.
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To run a model for the first time:
- Download and install NEURON (github.com/neuronsimulator).
- Download Salto (github.com/cccohen/Salto).
- Import cellular morphology via getmorph.hoc.
- Load morphology and identify recorded sections with loadmorph.hoc.
- Run setup.hoc
- This process should be performed once per cell
- Once setup.hoc is completed, the model may be opened with openmodel.hoc
-------------------------------Contents-------------------------------
getmorph.hoc
- Import cellular morphology (in ASCII format or other)
loadmorph.hoc
- Load cellular morphology in 3D.
- Identify cellular locations of interest by section name and sublocation (0-1).
setup.hoc
- Quintessential starting point to create a model cell.
- Requires recording setup information and data.
- Initialize the model cell (mode, axon type, session options, etc).
compilemod.hoc
- Compile or recompile mod files.
- Required for running any model.
- Run once after setup or download to a new machine.
openmodel.hoc
- View and test the model.
- Try different parameter combinations.
- Run optimizations.
- etc.
- Typical entry point after setup.
- Broadest option for model interaction.
resetmode.hoc
- Switch mode from passive to active and vice versa.
resetses.hoc
- Reset session data (recording information) to mode-appropriate default options.
resetaxon.hoc
- Switch between model axon options.
- Available options include no myelin, single cable and double cable.
*modeltype*.type
- Describes current model setup. Composed of three parts separated by dashes.
- First part: active ("act") or passive ("pas").
- Second part: selected cellular location(s) of interest combination. SO = soma, AX = axon, DE = dendrite.
- Third part: axon model type. NOMY = no myelin, SC = single cable, DC = double cable, etc.
- Updated after opening openmodel.hoc.
startopt.hoc
- Run massive optimization of passive parameters using custom optimization procedure.
- May be run in parallel at the NSG (https://www.nsgportal.org/) or other configered machines.
- Saves simulation results in an "outdir", in a subfolder entitled *modeltype*
extractopt.hoc
- Extract and rank optimized solutions returned by startopt.hoc.
- Required to be run before resubmitting startopt, finish unfinished optimizations.
- Note: unfinished optimizations due to lack of simulation time may also be finished first by adding simulation time. This is usually set at setup, but may also be changed thereafter in /ses/time.dat by increasing maxtime (time unit is s).
playopt.hoc
- Play optimized and ranked solutions of current model setup.
- startopt.hoc and rankopt.hoc must have returned first.
- To start playing a solution set, select it by clicking on the corresponding checkbox.
- Solutions will play from best to worst.
- To stop at a particular solution, uncheck the corresponding checkbox by clicking on it.