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Salto v1.0 ------------------------------------------------------------------------------------------------------------------- (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). ------------------------------------------------------------------------------------------------------------------- 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. ------------------------------------------------------------------------------------------------------------------- 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.
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Salto - automatically generate, explore, and optimize neuron models.
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