Published May 6, 2020 | Version v1
Software Open

Using optimal control to understand complex metabolic pathways

Authors/Creators

  • 1. Bioprocess Engineering Group, Spanish National Research Council, IIM-CSIC, C/Eduardo Cabello 6, 36208 Vigo (Spain)

Description

Software source code for the paper:
Tsiantis, Nikolaos, Banga, Julio R. Using optimal control to understand complex metabolic pathways. BMC Bioinformatics 21, 472 (2020). https://doi.org/10.1186/s12859-020-03808-8

Bioprocess Engineering Group, 
IIM-CSIC (Spanish National Research Council), 
C/Eduardo Cabello 6, 36208 Vigo (Spain)

Contact: nikolaostsiantis@gmail.com, julio@iim.csic.es


In order to run the scripts to reproduce the results shown in the paper,
you will need a Matlab installation under Windows (Linux not tested, although it should run). 


Requirements:
- Matlab version R2015b or later (tested with version R2015b using a 64-bit Windows 7 Professional operating system
 with Intel(R) Xeon(R) CPU E5-2630 @ 2.30GHz and 16GB RAM.)
- Matlab toolboxes: Optimization Toolbox, Symbolic Toolbox
- ICLOCS version 1.2.1 available at http://www.ee.ic.ac.uk/ICLOCS/ICLOCS_Old.htm
  and documented at http://www.ee.ic.ac.uk/ICLOCS/user_guide.pdf 
- ICLOCS also requires: SUNDIALS TB, CVODES (check ICLOCS documentation for their installation)
- AMIGO2, available from https://sites.google.com/site/amigo2toolbox/home 

Installation:
- install Matlab and the recommended toolboxes, and make sure they can be executed normally
- install AMIGO2 and test it running the included examples
- install ICLOCS and test it running the included examples
 

Notes

Contact: nikolaostsiantis@gmail.com, julio@iim.csic.es . This research has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No 675585 (MSCA ITN "SyMBioSys") and from the Spanish Ministry of Science, Innovation and Universities and the European Union FEDER under project grant SYNBIOCONTROL (DPI2017-82896-C2-2-R). Nikolaos Tsiantis is a Marie Sklodowska-Curie Early Stage Researcher at IIM-CSIC (Vigo, Spain) under the supervision of Prof Julio R. Banga. The funding bodies played no role in the design of the study, the collection and analysis of the data or in the writing of the manuscript.

Files

OCP_metabolic_pathways_v05May2020.zip

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Additional details

Funding

European Commission
SyMBioSys - Systematic Models for Biological Systems Engineering Training Network 675585

References