A Profile of Today´s SBML-Compatible Software

Author

Hucka, Michael ; Bergmann, Frank T. ; Keating, Sarah M. ; Smith, Lucian P.

Author_Institution

California Inst. of Technol., Pasadena, CA, USA

fYear

2011

fDate

5-8 Dec. 2011

Firstpage

143

Lastpage

150

Abstract

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?

Keywords

bioinformatics; data handling; specification languages; SBML; Systems Biology Markup Language; bioinformatics; compatible software; computational modeling; computational system; data handling; machine-readable format; software package; software resource; software system; Analytical models; Biological system modeling; Mathematical model; Software systems; Software tools; Systems biology; application software; bioinformatics; computational systems biology; data handling; open source software; software standards; software tools; systems biology;

fLanguage

English

Publisher

ieee

Conference_Titel

e-Science Workshops (eScienceW), 2011 IEEE Seventh International Conference on

Conference_Location

Stockholm

Print_ISBN

978-1-4673-0026-1

Type

conf

DOI

10.1109/eScienceW.2011.28

Filename

6130743