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System Modeling in Cellular BiologyFrom Concepts to Nuts and Bolts$
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System Modeling in Cellular Biology: From Concepts to Nuts and Bolts

Zoltan Szallasi, Jorg Stelling, and Vipul Periwal

Print publication date: 2006

Print ISBN-13: 9780262195485

Published to MIT Press Scholarship Online: August 2013

DOI: 10.7551/mitpress/9780262195485.001.0001

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PRINTED FROM MIT PRESS SCHOLARSHIP ONLINE (www.mitpress.universitypressscholarship.com). (c) Copyright The MIT Press, 2022. All Rights Reserved. An individual user may print out a PDF of a single chapter of a monograph in MITSO for personal use.date: 21 May 2022

Software Infrastructure for Effective Communication and Reuse of Computational Models

Software Infrastructure for Effective Communication and Reuse of Computational Models

Chapter:
(p.355) 17. Software Infrastructure for Effective Communication and Reuse of Computational Models
Source:
System Modeling in Cellular Biology
Author(s):

Andrew Finney

Michael Hucka

Benjamin J. Bornstein

Sarah M. Keating

Bruce E. Shapiro

Joanne Matthews

Ben L. Kovitz

Maria J. Schilstra

Akira Funahashi

John Doyle

Hiroaki Kitano

Publisher:
The MIT Press
DOI:10.7551/mitpress/9780262195485.003.0017

This chapter describes Systems Biology Markup Language (SBML), a format for representing models in a way that can be used by different software systems to communicate and exchange those models. By supporting SBML as an input and output format, different software tools can all operate on an identical representation of a model, removing opportunities for errors in translation and assuring a common starting point for analyses and simulations. The chapter also discusses some of the resources available for working with SBML as well as ongoing efforts in SBML’s continuing evolution.

Keywords:   Systems Biology Markup Language, SBML, software, system modeling

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