Netscan: A procedure for generating reaction networks by size

Bertrand Clarke; Glenn Fawcett; Jay E. Mittenthal

doi:10.1016/j.jtbi.2004.03.026

Netscan: A procedure for generating reaction networks by size

Bertrand Clarke, Glenn Fawcett, Jay E. Mittenthal

Statistics

Research output: Contribution to journal › Article › peer-review

Abstract

In this paper, we describe an algorithm which can be used to generate the collection of networks, in order of increasing size, that are compatible with a list of chemical reactions and that satisfy a constraint. Our algorithm has been encoded and the software, called Netscan, can be freely downloaded from ftp://ftp.stat.ubc.ca/pub/riffraff/Netscanfiles, along with a manual, for general scientific use. Our algorithm may require pre-processing to ensure that the quantities it acts on are physically relevant and because it outputs sets of reactions, which we call canonical networks, that must be elaborated into full networks.

Original language	English (US)
Pages (from-to)	591-602
Number of pages	12
Journal	Journal of Theoretical Biology
Volume	230
Issue number	4 SPEC. ISS.
DOIs	https://doi.org/10.1016/j.jtbi.2004.03.026
State	Published - Oct 21 2004

Keywords

Network assembly
Network identification
Reaction network

ASJC Scopus subject areas

Statistics and Probability
Modeling and Simulation
Biochemistry, Genetics and Molecular Biology(all)
Immunology and Microbiology(all)
Agricultural and Biological Sciences(all)
Applied Mathematics

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10.1016/j.jtbi.2004.03.026

Cite this

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title = "Netscan: A procedure for generating reaction networks by size",

abstract = "In this paper, we describe an algorithm which can be used to generate the collection of networks, in order of increasing size, that are compatible with a list of chemical reactions and that satisfy a constraint. Our algorithm has been encoded and the software, called Netscan, can be freely downloaded from ftp://ftp.stat.ubc.ca/pub/riffraff/Netscanfiles, along with a manual, for general scientific use. Our algorithm may require pre-processing to ensure that the quantities it acts on are physically relevant and because it outputs sets of reactions, which we call canonical networks, that must be elaborated into full networks.",

keywords = "Network assembly, Network identification, Reaction network",

author = "Bertrand Clarke and Glenn Fawcett and Mittenthal, {Jay E.}",

note = "Funding Information: The first author's work was supported by NSERC Operating Grant with RGPIN #138122-00. The authors wish to thank Gary Catt of Caracal Consulting, profusely, for invaluable help navigating the computing labyrinth. The authors thank Ann Condon for pointing out the connection between network assembly and the minimum cover problem. ",

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Netscan: A procedure for generating reaction networks by size

Abstract

Keywords

ASJC Scopus subject areas

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