CoSBiLab: Enabling Simulation-Based Science

Date

October 13, 2010

Speaker

Corrado Priami

Overview

CoSBiLab is a software platform implementing the new conceptual framework of algorithmic systems biology. It is centered on the idea of representing biological elements as programs and elements interaction as message passing between the corresponding programs. This idea is guiding the programming paradigm supported by the new programming language BlenX. This approach is higher level and provides a component-based view of systems rather than reaction-based descriptions that are usually adopted in ODE or rewriting system tools. CoSBiLab allows its users to exploit compositionality and stochasticity addressing in a native way concurrency and complexity.

To make the approach intuitive, CoSBiLab has a tabular interface to model systems and to grasp data from databases so that non-experts can use CoSBiLab; i.e., programming in BlenX without having programming skills. CoSBiLab has also tools that can help inferring missing data, perform network analysis, and visualize simulation outcomes. In addition to the introduction of the conceptual framework, demos will be provided to help in understanding the software that will support the e-scientists of the future in their work.

For more information, see “Algorithmic Systems Biology,” Communications of the ACM, 52(5):80–88, May 2009.

Speakers

Corrado Priami

Corrado Priami obtained his Bachelor’s and PhD degrees in Computer Science at the University of Pisa, and was visiting researcher at the laboratory LIX, École Politechnique, Paris (1995) and the École Normale Supérieure, Paris under an EC Marie Curie TMR grant, and was also a researcher and associate professor at the University of Verona. Currently, he is professor of Computer Science at the University of Trento. The results of his PhD thesis on stochastic pi-calculus were the basis for the foundation of the Microsoft Research – University of Trento Centre for Computational and Systems Biology (CoSBi), of which he is the President and CEO. Those same results 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). Professor Priami was member of the expert group on the EU 7th FP of the CRUI and participated in many projects promoted by the European Commission. He regularly serves on evaluation committees for projects presented by the European Commission, is a reviewer for many international journals, and serves in the review panels of the Science Foundation Ireland for institutes of systems biology and of the Netherlands Organisation for Scientific Research. His research covers computational methods for the modeling, analysis, and simulation of biological systems, programming languages, and formal computational theories. Professor Priami has published more than 120 papers, delivered 40 invited talks and lectures at conferences and universities worldwide, participated on program committees for 21 international conferences, is a member of three steering committees of international conferences, is editor-in-chief of Transactions on Computational Systems Biology and is a member of the editorial board of the journal Bioinformatics Research and Applications. He founded the international conferences “Computational Methods in Systems Biology (CMSB),” and “Converging Sciences,” whose success has been described by many international journals. Professor Priami is currently a member of ISTAG (Information Society Technologies Advisory Group) of the European Commission.