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BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts

Poole, William and Pandey, Ayush and Shur, Andrey and Tuza, Zoltan A. and Murray, Richard M. (2020) BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts. . (Unpublished) https://resolver.caltech.edu/CaltechAUTHORS:20200804-104555959

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Abstract

Biochemical interactions in systems and synthetic biology are often modeled with Chemical Reaction Networks (CRNs). CRNs provide a principled modeling environment capable of expressing a huge range of biochemical processes. In this paper, we present a software toolbox, written in python, that complies high-level design specifications to CRN representations. This compilation process offers three advantages. First, the building of the actual CRN representation is automatic and outputs Systems Biology Markup Language (SBML) models compatible with numerous simulators. Second, a library of modular biochemical components allows for different architectures and implementations of biochemical circuits to represented succinctly with design choices propogated throughout the underlying CRN automatically. This prevents the often occurring mismatch between high-level designs and model dynamics. Third, high-level design specification can be embedded into diverse biomolecular environments, such as cell-free extracts and in vivo milieus. With these advantages offered by BioCRNpyler, users can quickly build and test multitude of models in different environments. Finally, our software toolbox has a parameter database, which allows users to rapidly prototype large models using very few parameters which can be customized later.


Item Type:Report or Paper (Discussion Paper)
Related URLs:
URLURL TypeDescription
https://doi.org/10.1101/2020.08.02.233478DOIDiscussion Paper
https://github.com/BuildACell/BioCRNPylerRelated ItemCode
ORCID:
AuthorORCID
Pandey, Ayush0000-0003-3590-4459
Murray, Richard M.0000-0002-5785-7481
Additional Information:The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. Posted August 03, 2020. We would like to thank the Caltech BE240 class and the Murray Biocircuits lab for extensive testing of this software and discussions of relevant models, library of parts, and parameters. In particular, we would like to thank Matthieu Kratz, Liana Merk, and Ankita Roychoudhury for contributing to the software library. The authors W.P. and A.P. are supported by NSF grant number: CBET-1903477. A.P. is also supported by the Defense Advanced Research Projects Agency (Agreement HR0011-17-2-0008). The content of the information does not necessarily reflect the position or the policy of the Government, and no official endorsement should be inferred.
Funders:
Funding AgencyGrant Number
NSFCBET-1903477
Defense Advanced Research Projects Agency (DARPA)HR0011-17-2-0008
Record Number:CaltechAUTHORS:20200804-104555959
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20200804-104555959
Official Citation:BioCRNpyler: Compiling Chemical Reaction Networks from Biomolecular Parts in Diverse Contexts. William Poole, Ayush Pandey, Zoltan Tuza, Andrey Shur, Richard M Murray. bioRxiv 2020.08.02.233478; doi: https://doi.org/10.1101/2020.08.02.233478
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:104725
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:04 Aug 2020 18:59
Last Modified:04 Aug 2020 18:59

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