COSBI, The Microsoft Research – University of Trento Centre for Computational and Systems Biology

Description of organization

COSBI, The Microsoft Research – University of Trento Centre for Computational and Systems Biology is a non-profit organization founded in 2005 as a joint venture between Microsoft Research and the University of Trento. COSBI's mission is to conduct research and development activities of conceptual approaches, programming languages and supporting software tools for modeling, analysis and simulation in the areas of medical sciences, biology, bioinformatics and more in general on complex systems. COSBI is primarily oriented to the research in innovative computer-science technologies and applications, following a multi-disciplinary approach whose objective is to integrate the foundational aspects of computer science with biological research.

COSBI proposes and propels the paradigm of algorithmic systems biology. On the ground of this paradigm COSBI defines algorithmic abstractions of real biological phenomena through programming languages and computing techniques. The algorithmic modelling is a mechanisms-oriented methodology of creating and simulating predictive models of causal, spatial and temporal relationships among entities and interactions of biological processes at any level of abstraction. In addition to modelling and simulation, COSBI expertise covers knowledge and network inference from -omics data network analysis of large interactomes data mining and creation of ad hoc algorithms to analyse experimental data. COSBI produced an in silico research platform, COSBI LAB: an integrated artificial laboratory designed to perform in silico life science experiments. COSBI LAB platform allows efficient model building, simulation, and analysis of biological processes at any scale: from the molecular scale of the biochemical intracellular processes to the meso-scale of inter-cellular and tissue processes. COSBI software platform tackles two main computational challenges: processing, integrating, and predicting data concerning biological processes; and tailoring models to each individual to reflect their own physiological and genetic uniqueness in responding to environmental factors and medical treatments.

Previous experience

Corrado Priami is professor of Computer Science at the University of Trento and he is COSBI President and CEO. He is one of the inventors of the paradigm of Algorithmic Systems Biology and he developed new programming languages and new computational paradigms, as well as ad hoc stochastic and hybrid simulation techniques for complex biochemical and biological reaction systems.

Those same results, besides constituting the scientific foundation of COSBI, are recognized as fundamental in the field of systems biology by an expanding international community, which is using them to model the behavior of biological systems (the CMSB conference is a milestone of this).

On the basis of the theoretical studies and the new paradigm proposed by Corrado Priami, through cooperative, multidisciplinary research projects COSBI developed a computational foundation for systems biology. COSBI produced software prototypes for modelling and simulation (BetaWB, Lime, Redi), model calibration (KInfer), and network analysis (Graph).

Thanks to these studies, COSBI took part in several research projects such as "FIRB: computational tools for systems biology", "NOBEL: molecular modeling of gene regulation, transcription and translation", and the European project "VENUS-C: Virtual multidisciplinary EnviroNments USing Cloud infrastructures".

In 2009, the framework platform for biological modeling, analysis and simulation implemented by COSBI researchers won the first international competition on Formal Methods in Molecular Biology that took place at the Leibniz-Zentrum Für Informatik in Dagstuhl, Germany.

Profile of staff members

Paola Lecca received a B.S. in Theoretical Physics from the University of Trento (Italy) in 1997 and a PhD in Computer Science in 2006 from the International Doctorate School in Information and Communication Technologies at the University of Trento. Paola Lecca is the Principal Investigator of the research area "Inference and Data Manipulation". She is leading and coordinating the research activities concerning the design and the development of data-driven techniques knowledge inference and predictive modelling and the data mining from multiple sources.

Webpage

Centre for Computational and Systems Biology (COSBI)

Five recent publications relevant to the project

1 - P. Lecca, A. Palmisano, A. Ihekwaba, C. Priami. Calibration of dynamic models of biological systems with KInfer, Eur. Biophysics J., 39:1019-1039, 2010

2 - P. Lecca, A. Ihekwaba, L. Dematte', C. Priami. Stochastic simulation of the spatio-temporal dynamics of reaction-diffusion systems: the case for the bicoid gradient, Journal of Integrative Bioinformatics, 7, 2010

3 - A. Ihekwaba, P. Nguyen, C. Priami. Elucidation of Functional Consequences of Signalling Pathway Interactions, BMC Bioinformatics, 10, 2009

4 - M. Guerriero, A. Dudka, N. Underhill-Day, J. Heath, C. Priami. Narrative-based computational modelling of the Gp130/JAK/STAT signalling pathway BMC Systems Biology 2009, 3:40, BMC Systems Biology, 2009

5 - C. Priami. Algorithmic Systems Biology, Communications of the ACM, 52:80-88, 2009.