This workflow has been developed to tackle the challenge of building and analyzing biochemical pathway models, combining pre-existing tools and custom-made software.
At the root of our implementation is the SBtab format, a file format that can store biochemical models and associated data in an easily readable and expandable way.
We have also developed tools to convert the SBtab format into several formats that can be used in MATLAB®, NEURON, STEPS and Copasi.
Using MATLAB® we have developed custom scripts for parameter estimation, global sensitivitiy analysis, and diagnostics tools that can be used for model development.
We demonstrate all these features using an example model, a modified version of the D1 MSN subcellular cascade model from Nair et al 20161. Code to run this model in MATLAB®, NEURON, and Subcellular aplication(STEPS) can be found on the "MATLAB®", "NEURON" and "BioNetGen and Steps folders" respectively.
Model simulation, using MATLAB®, subcellular aplication(STEPS), or NEURON
Analysis of selected parameter sets, using MATLAB®
Parameter optimization, using MATLAB®
Global Sensitivity analysis, using MATLAB®
SBtab(.xlsx) to SBtab(.tsv), using MATLAB®
SBtab(.xlsx) to MATLAB® SimBiology™(.m, .sbproj), using MATLAB®
MATLAB® SimBiology™ to SBML(.xml), using MATLAB®
SBtab(.tsv) to VFGEN(.vf), using R
SBtab(.tsv) to Mod(.mod), using R
SBtab(.tsv) to SBML(.xml), using R
Santos, João P. G., et al. A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Cold Spring Harbor Laboratory, Nov. 2020, doi:10.1101/2020.11.17.385203.
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