The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models

MOTIVATION Molecular biotechnology now makes it possible to build elaborate systems models, but the systems biology community needs information standards if models are to be shared, evaluated and developed cooperatively. RESULTS We summarize the Systems Biology Markup Language (SBML) Level 1, a free, open, XML-based format for representing biochemical reaction networks. SBML is a software-independent language for describing models common to research in many areas of computational biology, including cell signaling pathways, metabolic pathways, gene regulation, and others. AVAILABILITY The specification of SBML Level 1 is freely available from http://www.sbml.org/

[1]  H. Gutfreund,et al.  Enzyme kinetics , 1975, Nature.

[2]  Hugh D. Spence,et al.  Minimum information requested in the annotation of biochemical models (MIRIAM) , 2005, Nature Biotechnology.

[3]  H. Sauro,et al.  Conservation analysis in biochemical networks: computational issues for software writers. , 2004, Biophysical chemistry.

[4]  Andy Powell,et al.  Guidelines for implementing Dublin Core in XML , 2003 .

[5]  Eric H Davidson,et al.  New computational approaches for analysis of cis-regulatory networks. , 2002, Developmental biology.

[6]  H. Kitano Systems Biology: A Brief Overview , 2002, Science.

[7]  Bernd Oestereich,et al.  Developing Software with UML: Object-Oriented Analysis and Design in Practice , 2002 .

[8]  E. Mjolsness,et al.  Developmental simultations with cellerator , 2001 .

[9]  W. J. Hedley,et al.  A short introduction to CellML , 2001, Philosophical Transactions of the Royal Society of London. Series A: Mathematical, Physical and Engineering Sciences.

[10]  Emmanuel Barillot,et al.  XML, bioinformatics and data integration , 2001, Bioinform..

[11]  Paul Smaglik,et al.  US grant glues ‘virtual cell’ together , 2000, Nature.

[12]  D. Fell,et al.  A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks , 2000, Nature Biotechnology.

[13]  Alison Abbott,et al.  Alliance of US labs plans to build map of cell signalling pathways , 1999, Nature.

[14]  Igor Goryanin,et al.  Mathematical simulation and analysis of cellular metabolism and regulation , 1999, Bioinform..

[15]  T. Bray,et al.  XML and the Second-Generation WEB , 1999 .

[16]  James C. Schaff,et al.  The Virtual Cell , 1998, Pacific Symposium on Biocomputing.

[17]  C. M. Sperberg-McQueen,et al.  Extensible markup language , 1997 .

[18]  Hans-Erik Eriksson,et al.  UML toolkit , 1997 .

[19]  P Mendes,et al.  Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. , 1997, Trends in biochemical sciences.

[20]  J. H. Hofmeyr,et al.  The reversible Hill equation: how to incorporate cooperative enzymes into metabolic models , 1997, Comput. Appl. Biosci..

[21]  David A. Fell,et al.  SCAMP: A metabolic simulator and control analysis program , 1991 .

[22]  Richard M. Karp,et al.  A n^5/2 Algorithm for Maximum Matchings in Bipartite Graphs , 1971, SWAT.

[23]  J. E. L. Peck,et al.  Revised report on the algorithmic languageAlgol 60 , 1962, Springer Berlin Heidelberg.

[24]  Thomas Cierpka,et al.  A LETTER FROM THE DIRECTORS , 2003 .

[25]  Dan Brickley,et al.  Resource Description Framework (RDF) Model and Syntax Specification , 2002 .

[26]  E. Mjolsness Developmental Simulations with Cellerator , 2001 .

[27]  Elliotte Rusty Harold,et al.  XML in a Nutshell , 2001 .

[28]  Hiroaki Kitano,et al.  Foundations of systems biology , 2001 .

[29]  Herbert M. Sauro,et al.  33 JARNAC: a system for interactive metabolic analysis , 2000 .

[30]  Andreas Kremling,et al.  Application of the process modeling tool PROMOT to the modeling of metabolic networks , 2000 .

[31]  J C Schaff,et al.  Physiological modeling with virtual cell framework. , 2000, Methods in enzymology.

[32]  Masaru Tomita,et al.  E-CELL: software environment for whole-cell simulation , 1999, Bioinform..

[33]  C. J.,et al.  Predicting Temporal Fluctuations in an Intracellular Signalling Pathway , 1998 .

[34]  Barry N. Taylor,et al.  Guide for the Use of the International System of Units (SI) , 1995 .

[35]  Guy L. Steele,et al.  C, a reference manual , 1984 .