Related Experiment Video
Updated: Apr 19, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
MpTheory Java library: a multi-platform Java library for systems biology based on the Metabolic P theory
Luca Marchetti1, Vincenzo Manca2
1Department 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.
Unlabelled:
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.
Related Concept Videos
Introduction to Metabolism
Overview of Metabolism
Plant Metabolism
Sunlight, the primary source of energy in plants, is first absorbed by the chlorophyll pigments present in their leaves. Plants then use this energy to carry out photosynthesis, where water is oxidized into oxygen and carbon dioxide...
C4 Pathway and CAM
C4 Pathway
The C4 pathway is used by plants such as...
Mechanistic Models: Overview of Compartment Models
What is Metabolism?
Overview of Protein Metabolism
Amino acids play various roles in the body once they are absorbed into cells. They are restructured...

