MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory

Luca Marchetti; Vincenzo Manca

doi:10.1093/bioinformatics/btu814

MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory

Bioinformatics. 2015 Apr 15;31(8):1328-30. doi: 10.1093/bioinformatics/btu814. Epub 2014 Dec 10.

Authors

Luca Marchetti¹, Vincenzo Manca²

Affiliations

¹ Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy.
² Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy Department of Computer Science, University of Verona, 37134 Verona, Italy, Center for BioMedical Computing, University of Verona, 37134 Verona, Italy and The Microsoft Research - University of Trento, Centre for Computational and Systems Biology (COSBI), 38068 Rovereto (TN), Italy.

PMID: 25504849
DOI: 10.1093/bioinformatics/btu814

Abstract

MpTheory Java library is an open-source project collecting a set of objects and algorithms for modeling observed dynamics by means of the Metabolic P (MP) theory, that is, a mathematical theory introduced in 2004 for modeling biological dynamics. By means of the library, it is possible to model biological systems both at continuous and at discrete time. Moreover, the library comprises a set of regression algorithms for inferring MP models starting from time series of observations. To enhance the modeling experience, beside a pure Java usage, the library can be directly used within the most popular computing environments, such as MATLAB, GNU Octave, Mathematica and R.

Availability and implementation: The library is open-source and licensed under the GNU Lesser General Public License (LGPL) Version 3.0. Source code, binaries and complete documentation are available at http://mptheory.scienze.univr.it.

Contact: luca.marchetti@univr.it, marchetti@cosbi.eu

Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms*
Humans
Metabolism*
Models, Biological*
Programming Languages*
Software*
Systems Biology / methods*