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  4. Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models
 
research article

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Weilandt, Daniel R.  
•
Salvy, Pierre  
•
Masid, Maria  
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December 10, 2022
Bioinformatics

Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and analyze large-scale models efficiently. The toolbox presented here provides the means to implement, parameterize and analyze large-scale kinetic models intuitively and efficiently.Results: We present a Python package (SKiMpy) bridging this gap by implementing an efficient kinetic modeling toolbox for the semiautomatic generation and analysis of large-scale kinetic models for various biological domains such as signaling, gene expression and metabolism. Furthermore, we demonstrate how this toolbox is used to parameterize kinetic models around a steady-state reference efficiently. Finally, we show how SKiMpy can implement multispecies bioreactor simulations to assess biotechnological processes.

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Type
research article
DOI
10.1093/bioinformatics/btac787
Web of Science ID

WOS:000899775400001

Author(s)
Weilandt, Daniel R.  
Salvy, Pierre  
Masid, Maria  
Fengos, Georgios  
Denhardt-Erikson, Robin
Hosseini, Zhaleh  
Hatzimanikatis, Vassily  
Date Issued

2022-12-10

Publisher

OXFORD UNIV PRESS

Published in
Bioinformatics
Subjects

Biochemical Research Methods

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Biotechnology & Applied Microbiology

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Computer Science, Interdisciplinary Applications

•

Mathematical & Computational Biology

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Statistics & Probability

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Biochemistry & Molecular Biology

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Computer Science

•

Mathematics

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uncertainty

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metabolism

Editorial or Peer reviewed

REVIEWED

Written at

EPFL

EPFL units
LCSB  
Available on Infoscience
January 16, 2023
Use this identifier to reference this record
https://infoscience.epfl.ch/handle/20.500.14299/193888
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