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Modeling Biomolecular Site Dynamics pp 1–32Cite as

A Pycellerator Tutorial

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Part of the book series: Methods in Molecular Biology ((MIMB,volume 1945))

Abstract

We present a tutorial on using Pycellerator for biomolecular simulations. Models are described in human readable (and editable) text files (UTF8 or ASCII) containing collections of reactions, assignments, initial conditions, function definitions, and rate constants. These models are then converted into a Python program that can optionally solve the system, e.g., as a system of differential equations using ODEINT, or be run by another program. The input language implements an extended version of the Cellerator arrow notation, including mass action, Hill functions, S-Systems, MWC, and reactions with user-defined kinetic laws. Simple flux balance analysis is also implemented. We will demonstrate the implementation and analysis of progressively more complex models, starting from simple mass action through indexed cascades. Pycellerator can be used as a library that is integrated into other programs, run as a command line program, or in iPython notebooks. It is implemented in Python 2.7 and available under an open source GPL license.

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Author information

Authors and Affiliations

  1. Department of Mathematics, California State University, Northridge, CA, USA

    Bruce E. Shapiro

  2. Departments of Computer Science and Mathematics, University of California, Irvine, CA, USA

    Eric Mjolsness

Authors
  1. Bruce E. Shapiro
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  2. Eric Mjolsness
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Corresponding author

Correspondence to Bruce E. Shapiro .

Editor information

Editors and Affiliations

  1. Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA

    William S. Hlavacek

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Shapiro, B.E., Mjolsness, E. (2019). A Pycellerator Tutorial. In: Hlavacek, W. (eds) Modeling Biomolecular Site Dynamics. Methods in Molecular Biology, vol 1945. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-9102-0_1

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  • DOI: https://doi.org/10.1007/978-1-4939-9102-0_1

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-9100-6

  • Online ISBN: 978-1-4939-9102-0

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