Bio-Inspired Systems and Calculi with Applications

BISCA DIT-PRJ-07-019

Status NOT active project
DISI role Partner
Project type Research Project
Dimension National
Acquisition date 2007-02-09
Start date 2007-02-09
End date 2009-02-09

Project details

Project astract We plan to develop and use methods typical of computer science for describing, analysing and implementing in silico biological<br/>systems.<br/>Besides offering such a modelization, we expect that the interaction and organization mechanisms of living matter will suggest us<br/>new paradigms of computation and new formalisms beneficial to information technology in general.<br/>In particular, the project will focus on languages and models for specifying biological systems, for simulating their behaviour and<br/>for verifying formally their properties.<br/>We will mainly concentrate on the specification and analysis of intra- and inter-cellular interactions.<br/>The description of these phenomena will include both qualitative aspects, e.g. cause-effect relationships, and quantitative aspects,<br/>e.g. those depending on time and probabilistic distributions typical of biological systems.<br/>Quantitative and qualitative aspects require new enhancements of existing computer-based analysis techniques and the development<br/>of new ones.<br/>We plan to use linguistic mechanisms and models, specifically tailored for describing and manipulating such aspects of living<br/>matter as biochemical reactions, metabolic pathways and membranes.<br/>Therefore we may be required to adapt existing linguistic instruments and models and to develop new ones.<br/>Our ideas and proposals will be tuned, tested and validated over case studies coming from the relevant literature and selected<br/>together with the biologists present in all the research groups involved in this project, as well as with biologists and computer<br/>scientists working in similar topics worldwide, the results of which we envisage to compare with ours.<br/>The feasibility of our approach will be further validated by designing and implementing proof-of-concept prototypical software tools,<br/>based on the theoretical framework developed in the first phase of the investigation.<br/>Our long term goal is twofold.<br/>From the one side, we aim at producing tools and techniques inspired by the biological world, and able to deal with much more<br/>complex Information Technology problems than were addressable with current technology, for example being able to do knowledge<br/>discovery in structurally and behaviourally complex systems functioning in probabilistic environments, or modelling and simulation<br/>tools for handling (partial) knowledge at different levels of detail.<br/>On the other hand, we would like to offer biologists with an environment for attacking problems at a system level that cannot be<br/>addressed without using Information Technology, because biology is a knowledge-intensive domain, involving huge amounts of<br/>data, showing emerging properties.<br/>If succesful, this project will confirm a general understanding in the scientific community, that Infromation Technology will be as<br/>indispensible for biology, and viceversa, as mathematics has been for physics.<br/>In any case, there will certainly be a fruitful cross-fertilization between biology and computer science.
Fundings 94500 €
Partners
  • DIT, Universita' di Trento
  • Universita' di Bologna
  • Universita' di Pisa
  • Universita' di Siena
  • Universita' di Udine
  • DIT

DISI Sub-project details

Project astract The main goals of this local research unit are the definition of a linguistic specification environment for the functionalities of<br/>biological systems, the definition of expression data analysis techniques that leverage biological knowledge expressed in<br/>computational models, and the design and development of prototypes for the simulation and analysis of behaviours and for data<br/>analysis. The long term aim of this research direction is the definition of computer science methods and techniques to address more<br/>and more complex scenarios that cannot be approached by the current information technology. Our shorter term goal is the design<br/>of user-friendly tools that biologists can use to either validate/tune their wet experiments or predict emerging properties or perform<br/>expression data analysis.
Fundings 18000 €
Manager Paola Quaglia
Participating RP