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SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches

View ORCID ProfileG.V. HarshaRani, View ORCID ProfileS. Moza, View ORCID ProfileN. Ramakrishnan, View ORCID ProfileU.S. Bhalla
doi: https://doi.org/10.1101/2020.08.04.232371
G.V. HarshaRani
1Neurobiology, National Centre for Biological Sciences, TIFR, Bangalore 560065, India
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S. Moza
1Neurobiology, National Centre for Biological Sciences, TIFR, Bangalore 560065, India
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N. Ramakrishnan
2Discovery Analytics Center, Department of Computer Science, Virginia Tech, Arlington, VA 20148, USA
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U.S. Bhalla
1Neurobiology, National Centre for Biological Sciences, TIFR, Bangalore 560065, India
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  • For correspondence: bhalla@ncbs.res.in
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ABSTRACT

Bistable biochemical switches are key motifs in cellular state decisions and long-term storage of cellular ‘memory’. There are a few known biological switches that have been well characterized, however these examples are insufficient for systematic surveys of properties of these important systems. Here we present a resource of all possible bistable biochemical reaction networks with up to 6 reactions between 3 molecules, and 3 reactions between 4 molecules. Over 35,000 reaction topologies were constructed by identifying unique combinations of reactions between a fixed number of molecules. Then, these topologies were populated with rates within a biologically realistic range. The Searchable Web Interface for Topologies of CHEmical Switches (SWITCHES, https://switches.ncbs.res.in) provides a bistability and parameter analysis of over 7 million models from this systematic survey of chemical reaction space. This database will be useful for theoreticians interested in analyzing stability in chemical systems and also experimentalists for creating robust synthetic biological switches.

Availability and Implementation Freely available on the web at https://switches.ncbs.res.in. Website implemented in PHP, MariaDB, Graphviz, and Apache, with all major browsers supported.

Supplementary Information Not applicable.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • ↵* Contact: Email: bhalla{at}ncbs.res.in, Institutional address: National Centre for Biological Sciences, TIFR, Bellary Road, Bangalore 560065, India.

  • https://switches.ncbs.res.in

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted August 05, 2020.
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SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches
G.V. HarshaRani, S. Moza, N. Ramakrishnan, U.S. Bhalla
bioRxiv 2020.08.04.232371; doi: https://doi.org/10.1101/2020.08.04.232371
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SWITCHES: Searchable Web Interface for Topologies of CHEmical Switches
G.V. HarshaRani, S. Moza, N. Ramakrishnan, U.S. Bhalla
bioRxiv 2020.08.04.232371; doi: https://doi.org/10.1101/2020.08.04.232371

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