Project Goals

This page contains the original description of our project goals, as it was submitted to the Italian Ministry of Education, University and Research in February 2009 in the basic research programme (PRIN). For a more up-to-date description of our workplan please see the project presentation in the Our Documents section.

The project was approved at the end of January 2010 and, notwithstanding an evaluation of 59 out of 60 with an excellence label, received a funding of 13.800 euros against a requested funding of 101.200 euros (a ratio of 13.6%).

The project started in March 2010 and will end in March 2012.

The Project Team is made up by 3 research units:

- the Mathematics Department of University of Roma “Tor Vergata”, coordinating the project. The Project Coordinator is Enrico Nardelli.

- the Biology Department of University of Roma “Tor Vergata”. The Unit Coordinator is Manuela Helmer Citterich.

- the Science Department of University of Chieti-Pescara “Gabriele D’Annunzio”. The Unit Coordinator is Fabio Fioravanti.

Original description of Simbiosys project goals

The main objective of this project is, working on real-life biological case studies, to develop a methodology and a tool for the automatic translation of models of biological systems specified using SBML (Systems Biology Markup Language) to models based on Statecharts. This objective will be accomplished by means of
(i) the translation of semiformal models of biological systems to Statecharts models,
(ii) the development of an integrated environment for modeling and simulation of biological systems modeled using Statecharts.

This will allow us to use in a straightforward manner the semiformal description of models which the community of systems biology researchers have recently started to develop, to derive from it a graphical representation based on Statecharts, and to perform simulations on the derived model. We aim to develop a software tool for visually modeling the behavior of a complex biological system by using Statecharts and for simulating it. This tool will also allow one to use and refine models of biological systems translated from SBML-based models.

According to our knowledge of the scientific literature, this is one of the first attempts to automatically translate SBML-based models to formal computational models based on Statecharts, and characterizes the high innovation degree of this research project.

The availability of opensource tools for Statecharts-based modeling, simulation and verification of the temporal evolution of biological systems will allow us to define an integrated simulation environment which a large scientific community will be able to use:
(i) to detect possible discrepancies between the constructed model and expected results,
(ii) to predict the behavior of the system under conditions for which experimental data are not available and
(iii) to verify theses about the behavior of the system using computer-based simulations (“in silico”) before performing laboratory experiments (“in vitro”, “in vivo” or through comparison with data already present in biomedical literature).
In an iterative engineering process, this can contribute to correct the model of the biological system and to suggest new laboratory experiments.

The software which will be developed in this research project will be made available using an opensource license. The choice of this type of license will allow the scientific community to use the software free of charge, to customize it and to make it evolve according to the community needs, thus increasing its longevity. This represents a significant strong point of the software which we will develop, because this flexibility, which is strongly needed by the scientific community, is almost missing from industrial closed-source software products for Statecharts-based modeling of reactive systems, which, in addition, have not been specifically designed to be used in a bioinformatics environment.

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