Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis
ABSTRACT Summary: Over past decades, constraint-based modelling has emerged as an important approach to obtain referential information about mechanisms behind biological phenotypes and identify physiological and perturbed metabolic states at genome-scale. However, application of this novel approach...
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ftciteseerx:oai:CiteSeerX.psu:10.1.1.1035.4824 2023-05-15T17:53:21+02:00 Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis Longfei Mao Wynand S Verwoerd The Pennsylvania State University CiteSeerX Archives application/pdf http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1035.4824 http://bioinformatics.oxfordjournals.org/content/early/2013/12/27/bioinformatics.btt723.full.pdf en eng http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1035.4824 http://bioinformatics.oxfordjournals.org/content/early/2013/12/27/bioinformatics.btt723.full.pdf Metadata may be used without restrictions as long as the oai identifier remains attached to it. http://bioinformatics.oxfordjournals.org/content/early/2013/12/27/bioinformatics.btt723.full.pdf text ftciteseerx 2020-02-16T01:14:58Z ABSTRACT Summary: Over past decades, constraint-based modelling has emerged as an important approach to obtain referential information about mechanisms behind biological phenotypes and identify physiological and perturbed metabolic states at genome-scale. However, application of this novel approach to systems biology in biotechnology is still hindered by the functionalities of the existing modelling software. To augment the usability of the constraint-based approach for various use scenarios, we present ORCA, a Matlab package, which extends the scope of established Constraint-Based Reconstruction and Analysis metabolic modelling and includes three unique functionalities: (i) a framework method integrating three analyses of multi-objective optimization, robustness analysis and fractional benefit analysis, (ii) metabolic pathways identification with futile loop elimination and (iii) a dynamic flux balance analysis framework incorporating kinetic constraints. Availability and implementation: ORCA is freely available to academic users and is downloadable from https://sourceforge.net/ projects/exorca/; a mini-tutorial is supplied in the package for training purposes as well as a software manual. Text Orca Unknown |
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ABSTRACT Summary: Over past decades, constraint-based modelling has emerged as an important approach to obtain referential information about mechanisms behind biological phenotypes and identify physiological and perturbed metabolic states at genome-scale. However, application of this novel approach to systems biology in biotechnology is still hindered by the functionalities of the existing modelling software. To augment the usability of the constraint-based approach for various use scenarios, we present ORCA, a Matlab package, which extends the scope of established Constraint-Based Reconstruction and Analysis metabolic modelling and includes three unique functionalities: (i) a framework method integrating three analyses of multi-objective optimization, robustness analysis and fractional benefit analysis, (ii) metabolic pathways identification with futile loop elimination and (iii) a dynamic flux balance analysis framework incorporating kinetic constraints. Availability and implementation: ORCA is freely available to academic users and is downloadable from https://sourceforge.net/ projects/exorca/; a mini-tutorial is supplied in the package for training purposes as well as a software manual. |
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The Pennsylvania State University CiteSeerX Archives |
format |
Text |
author |
Longfei Mao Wynand S Verwoerd |
spellingShingle |
Longfei Mao Wynand S Verwoerd Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis |
author_facet |
Longfei Mao Wynand S Verwoerd |
author_sort |
Longfei Mao |
title |
Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis |
title_short |
Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis |
title_full |
Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis |
title_fullStr |
Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis |
title_full_unstemmed |
Systems biology ORCA: a COBRA toolbox extension for model-driven discovery and analysis |
title_sort |
systems biology orca: a cobra toolbox extension for model-driven discovery and analysis |
url |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1035.4824 http://bioinformatics.oxfordjournals.org/content/early/2013/12/27/bioinformatics.btt723.full.pdf |
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Orca |
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Orca |
op_source |
http://bioinformatics.oxfordjournals.org/content/early/2013/12/27/bioinformatics.btt723.full.pdf |
op_relation |
http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.1035.4824 http://bioinformatics.oxfordjournals.org/content/early/2013/12/27/bioinformatics.btt723.full.pdf |
op_rights |
Metadata may be used without restrictions as long as the oai identifier remains attached to it. |
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1766161059936206848 |