FindSim - A Framework for Integrating Neuronal Data and Signaling Models

Welcome

This is the website for the code and user documentation of the FindSim project. The published paper is here. The related FindSimWeb project provides a web interface to search, view, edit, and run FindSim experiments.

FindSim is a Python/MOOSE framework to map experimental protocols and readouts to models of neurophysiology and cellular signaling. FindSim simulates the experiment, checks how it fits the data, and provides tools for parameter analysis and optimization. These are designed to run from the command line, and in batch mode for large parallel optimization runs.

The workflow for FindSim is to identify/build a model, select an experiment, codify it, and run the experiment on the model. With the additional tools one can do a parameter exploration and sensitivity analysis, and single or multi-parameter optimization.

Core

The core FindSim program performs the workflow above: It takes a model, and runs an experiment on it. It reports how well the model output matches the experimental readouts. When run in console mode, it can plot out the experimental and simulated results. It can also run in batch mode, and as a subsidiary program for other tools.

Utilities

FindSim provides a variety of tools:
-to simulate and test experiments (in both, single and batch mode),
-single- and multi-parameter sensitivity analysis and,
-model optimization.

Welcome to FindSim

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