Netscan: A procedure for generating reaction networks by size

Bertrand Clarke, Glenn Fawcett, Jay E. Mittenthal

Research output: Contribution to journalArticlepeer-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 languageEnglish (US)
Pages (from-to)591-602
Number of pages12
JournalJournal of Theoretical Biology
Volume230
Issue number4 SPEC. ISS.
DOIs
StatePublished - 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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