A Profile of Today's SBML-Compatible Software

Computational systems biologists today have a healthy selection of software resources to help them do research. Many software packages, especially those concerned with computational modeling, have adopted SBML (the Systems Biology Markup Language) as a machine-readable format to permit users to exchange models. Our group has a keen interest in understanding the landscape of SBML support. To help us ascertain the state of modern SBML-compatible software, in mid-2011 we initiated a survey of software packages that support SBML. Here we report the preliminary survey results. Based on 81 packages for which we have data so far, we summarize the trends in six areas: (1) What are the major types of functionality offered by the software systems? (2) What mathematical frameworks do they support? (3) What are their SBML-specific capabilities? (4) What other standards do they support besides SBML? (5) What are their characteristics with respect to run-time environments? And finally, (6) what are the availability and licensing terms?

[1]  Catherine M Lloyd,et al.  CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.

[2]  H. Sauro,et al.  Standard Biological Parts Knowledgebase , 2011, PloS one.

[3]  Michael L. Hines,et al.  NeuroML: A Language for Describing Data Driven Models of Neurons and Networks with a High Degree of Biological Detail , 2010, PLoS Comput. Biol..

[4]  Sarah M. Keating,et al.  Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. , 2004, Systems biology.

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

[6]  U. Brandes,et al.  GraphML Progress Report ? Structural Layer Proposal , 2001 .

[7]  Sang Yup Lee,et al.  MFAML: a standard data structure for representing and exchanging metabolic flux models , 2005, Bioinform..

[8]  Informatika.  GNU Lesser General Public License , 2010 .

[9]  Melanie I. Stefan,et al.  BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models , 2010, BMC Systems Biology.

[10]  Michael Hucka,et al.  LibSBML: an API Library for SBML , 2008, Bioinform..

[11]  A. González,et al.  GNU General Public License v3: A Legal Analysis , 2006 .

[12]  Nicolas Le Novère,et al.  SED-ML - An XML Format for the Implementation of the MIASE Guidelines , 2008, CMSB.

[13]  Yen-Chih Peng,et al.  A Research of Software Combination under Free Software License- Focusing on GNU General Public License Version 3 , 2010 .

[14]  Leonidas G Alexopoulos,et al.  Setting the Standards for Signal Transduction Research , 2011, Science Signaling.

[15]  Kei-Hoi Cheung,et al.  BioPAX – A community standard for pathway data sharing , 2010, Nature Biotechnology.

[16]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[17]  Markus J. Herrgård,et al.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology , 2008, Nature Biotechnology.

[18]  Sarala M. Wimalaratne,et al.  The Systems Biology Graphical Notation , 2009, Nature Biotechnology.

[19]  Michael Hucka,et al.  The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core , 2010 .

[20]  Laure Petrucci,et al.  The Petri Net Markup Language: Concepts, Technology, and Tools , 2003, ICATPN.