KInfer and BetaWB: tools for supporting the modeling workflow of Biological Systems

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• Alida Palmisano, CoSBi
• Tuesday 31 March 2009, 14:00-15:00
• Small public lecture room, Microsoft Research Ltd, 7 J J Thomson Avenue (Off Madingley Road), Cambridge.

If you have a question about this talk, please contact Dr Fabien Petitcolas.

Abstract: Developing novel quantitative conceptual and computational tools smoothly connecting models and experiments can give to life scientists a deeper understanding of fundamental biological principles. Starting from the analysis of wet experiment data, it is important to standardize and automatize each step of the modeling process in a way that hides from the users the complexity of the technical details of the underlying algorithms and computations as much as possible.

The tools developed in our research group can help biologists to infer the system knowledge contained in experimental measurements, to build a model from those data in order to carry out in-silico experiments (with possible manipulations of the structure of the model), to visualize and analyze the results in order to be able to suggest new experiments and/or solutions.

In this seminar I would like to show, in particular, two tools belonging to our platform on a real relevant biological case study, i.e. the budding yeast cell cycle. I will show how, starting from wet experiment data, we could use KInfer (a tool for kinetic inference) in order to have an estimation of the kinetic parameter of the model, and I will show how the model can be easily translated from the ODE language to BlenX, in order to use the BetaWB framework to perform stochastic simulations that are able to catch behaviors of the biological system that cannot be seen with the standard deterministic approach.

Biography: Short bio Alida Palmisano attended the Faculty of Science at the University of Trento, where she obtained a Bachelor’s degree (2005) and a Master’s degree (2007) in Computer Science. Her thesis, “Formal models of examples of biological synthesis and signal transduction pathways,” focused on building models of real biological systems using Beta-binders formalism and some specific extensions. In 2004 she worked at ITC -irst (Center for Scientific and Technological Research) of Trento. The main goal of her work was the analysis of service-oriented architectures for the development of softwares able to manage the automation of domotic devices.

This talk is part of the CoSBi Computational and Systems Biology Series series.

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