Subcellular_workflow_matlab_code

Versione 0.2 (52 KB) da Joao Santos

A workflow developed to tackle the challenge of building and analyzing biochemical pathway models.

https://subcellular-workflow.readthedocs.io/

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Aggiornato 5 apr 2023

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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.

Features:

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®

Conversion tools:

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

Cita come

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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Compatibile con R2020a fino a R2021a

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Run_main.m

Code

default_settings

Code/Analysis

Code/Analysis/Optimization

Code/Analysis/Sensitivity Analysis

Code/General

Code/Import

Code/Plots

Code/Simulation

Code/Standalone

Le versioni che utilizzano il ramo predefinito di GitHub non possono essere scaricate

Versione	Pubblicato	Note della release
0.2	5 apr 2023	Now only relevant matlab code is included
0.1.1	31 mar 2021	fixed description
0.1	24 mar 2021

Per visualizzare o segnalare problemi su questo componente aggiuntivo di GitHub, visita GitHub Repository.

MLA	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.
APA	Santos, J. P. G., Pajo, K., Trpevski, D., Stepaniuk, A., Eriksson, O., Nair, A. G., Keller, D., et al. (2020). A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience. Cold Spring Harbor Laboratory. Retrieved from https://doi.org/10.1101%2F2020.11.17.385203
BibTeX	@article{Santos_2020, doi = {10.1101/2020.11.17.385203}, url = {https://doi.org/10.1101%2F2020.11.17.385203}, year = 2020, month = {nov}, publisher = {Cold Spring Harbor Laboratory}, author = {Jo{\~{a}}o P.G. Santos and Kadri Pajo and Daniel Trpevski and Andrey Stepaniuk and Olivia Eriksson and Anu G. Nair and Daniel Keller and Jeanette Hellgren Kotaleski and Andrei Kramer}, title = {A Modular Workflow for Model Building, Analysis, and Parameter Estimation in Systems Biology and Neuroscience} }