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  PyRates — A code-generation tool for modeling dynamical systems in biology and beyond

Gast, R., Knösche, T. R., & Kennedy, A. (2023). PyRates — A code-generation tool for modeling dynamical systems in biology and beyond. PLoS Computational Biology, 19(12): e1011761. doi:10.1371/journal.pcbi.1011761.

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 Creators:
Gast, Richard1, 2, Author
Knösche, Thomas R.3, Author                 
Kennedy, Ann1, 2, Author
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1Department of Neuroscience, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA, ou_persistent22              
2Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, MD, USA, ou_persistent22              
3Methods and Development Group Brain Networks, MPI for Human Cognitive and Brain Sciences, Max Planck Society, ou_2205650              

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 Abstract: The mathematical study of real-world dynamical systems relies on models composed of differential equations. Numerical methods for solving and analyzing differential equation systems are essential when complex biological problems have to be studied, such as the spreading of a virus, the evolution of competing species in an ecosystem, or the dynamics of neurons in the brain. Here we present PyRates, a Python-based software for modeling and analyzing differential equation systems via numerical methods. PyRates is specifically designed to account for the inherent complexity of biological systems. It provides a new language for defining models that mirrors the modular organization of real-world dynamical systems and thus simplifies the implementation of complex networks of interacting dynamic entities. Furthermore, PyRates provides extensive support for the various forms of interaction delays that can be observed in biological systems. The core of PyRates is a versatile code-generation system that translates user-defined models into "backend" implementations in various languages, including Python, Fortran, Matlab, and Julia. This allows users to apply a wide range of analysis methods for dynamical systems, eliminating the need for manual translation between code bases. PyRates may also be used as a model definition interface for the creation of custom dynamical systems tools. To demonstrate this, we developed two extensions of PyRates for common analyses of dynamic models of biological systems: PyCoBi for bifurcation analysis and RectiPy for parameter fitting. We demonstrate in a series of example models how PyRates can be used in combination with PyCoBi and RectiPy for model analysis and fitting. Together, these tools offer a versatile framework for applying computational modeling and numerical analysis methods to dynamical systems in biology and beyond.

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Language(s): eng - English
 Dates: 2023-09-152023-12-142023-12-272023-12-27
 Publication Status: Issued
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 Identifiers: DOI: 10.1371/journal.pcbi.1011761
Other: eCollection 2023
PMID: 38150479
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Funding organization : The Michael J. Fox Foundation for Parkinson’s Research (MJFF)
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Funding organization : Aligning Science Across Parkinson’s (ASAP)

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Title: PLoS Computational Biology
  Abbreviation : PLoS Comput Biol
Source Genre: Journal
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Publ. Info: San Francisco, CA : Public Library of Science
Pages: - Volume / Issue: 19 (12) Sequence Number: e1011761 Start / End Page: - Identifier: ISSN: 1553-734X
CoNE: https://pure.mpg.de/cone/journals/resource/1000000000017180_1