Category Cross-Omics>Pathway Analysis/Tools

Abstract ProMoT (Process Modeling Tool) is a software product for the construction and manipulation of complex technical and biological systems.

ProMoT has its origins in process engineering.

Together with the 'simulation environment' Diana (see below) it provides capabilities for the development of dynamic models based on 'differential-algebraic equations', and their simulation and further analysis.

For the application in Systems Biology key features of ProMoT are the development of modular models, the use of specialized modeling- libraries, and the support for model-exchange via the international standard Systems Biology Markup Language (SBML).

Of specific importance for successful work in interdisciplinary teams is the availability of ‘graphical methods’ for model editing and exploration, because this defines a common language for direct communication about models without the need for in-depth mathematical knowledge.

ProMoT already implements graphical tools for both the implementation, and the exploration and visualization of models.

ProMoT has being used as a 'modeling tool' Not only for the setup of 'dynamic models', but also for the visual construction of 'Boolean models' that can be analyzed with CellNetAnalyzer (see G6G Abstract Number 20331).

Diana -- Diana (Dynamic simulation and numeric analysis tool) is a 'simulation environment' for the processing of 'differential-algebraic equation' models.

It is the successor of Diva.

Diana offers simulation, parameter analysis, parameter estimation and bifurcation analysis and implements several recent improvements in the fields of nonlinear analysis, optimization and state estimation compared to Diva.

The Diana project is done in close cooperation with the Donezk Technical University.

ProMoT features/capabilities include:

1) Object oriented modeling --

Modeling can be done in an object oriented fashion (use of super classes and inheritance).

2) Modularity and hierarchy --

Models can be decomposed into hierarchies and modules.

This results in specialized modeling libraries and flexible models, which can be reused and easily connected.

3) Advanced visual capabilities --

Models can be easily setup using a visual editor. Advanced visualization techniques support the user while exploring and navigating the model.

4) SBML support --

Models can be exchanged via SBML. ProMoT supports SBML import and export (SBML Level 2 Version 1, except events).

5) Open source --

ProMoT is an open source project and free for download.

Note: For additional info on ProMoT see the paper entitled: Visual setup of 'logical models' of signaling and regulatory networks with ProMoT; BMC Bioinformatics 2006; 7: 506; doi: 10.1186/1471-2105-7-506.

System Requirements

Requirements and licensing.


Manufacturer Web Site ProMoT

Price Contact manufacturer.

G6G Abstract Number 20332

G6G Manufacturer Number 101743