Research program
Systems Biology: modeling, languages and analysis (Sybilla)
University Co-ordinator
Università degli Studi di BOLOGNA -
SCIENZE DELL'INFORMAZIONE - BOLOGNA(BO)
Research Unit Leader
Roberto GORRIERI
Description
The research Unit of the University of Bologna (UB for short) intends to use the specific competence, rather complementary in the whole propject team, about process algebra, Petri nets and stochastic models in order to investigate fundamental issues in the modelling of biological systems, such as inhibitors and activators/catalysers of biochemical reactions. 1. The first goal of the UB research unit is to study and to compare the different process calculi that have been proposed so far for modelling biological systems, in order to single out their similarities and differences, testing them on case studies reported in the recent literature. The final outcome should be the proposal of a novel calculus that better suites the needs for system biology modelling. This goal will be accomplished in year 1.2. Based on the specific knowledge in studying Petri nets with inhibitior arcs (Busi is one of the leading expert in this area, e.g., [BP00]), the second goal of the UB research unit is to extend basic process calculi with the notion of inhibitable interaction which should correspond to the inhibiting role played by some enzymes in biochemical reactions. This idea already appeared in some literature that uses Petri nets as basic model [MFD+03], but it is completely new in the process calculi community. We expect to come with novel versions of the most popular formalisms (e.g., bio-pi and bio-ambient) extended to include the feature of inhibitors and activators/catalysers. This goal will be started in year 1 and accomplished in year 2.3. As we have specific competence on how to relate Petri nets and process algebras (e.g. [BG95]), we intend to use this competence in order to study the relationship between the diverse approaches to system biology based on Petri nets and to relate them also with the process algebra based. This goal will be started in year 1 and accomplished in year 2.4. Furthermore, we intend to take advantage of our competence in stochastic models (see e.g. [BrG02]) in order to extend some of the basic languages and models to include also probabilistic information on the way interaction is conducted, in a line similar to [PRSS01]. Indeed, it is sometimes more realistic to regard a biopathway as a hybrid system of discrete and continuous events. The focus will be on probabilistic extension of models with inhibitors/catalyzers as well as on the process calculus that comes out as the result of goal 1. This task will be accomplished in year 2.5. Finally, we will address the issue of defining suitable semantic relations between "specifications" of biological systems and actual "implementations", in the style of what has been done in the theory of complex concurrent, distributed systems. Suitable notions of equivalence and simulation will be studied and experimented on some realistic case studies. Moreover, we intend to study the problem of synthesizing biological systems starting from their observational behaviour, as done in the theory of Petri nets [BP97]. This task will be started in year 1 and accomplished in year 2.[BG95] N.Busi, R.Gorrieri. A Petri Net Semantics for pi-calculus, in CONCUR'95, Theories of Concurrency: Unification and Extension (S.Smolka ed), LNCS 962, Springer, 145-159, Philadelphia (USA), 1995.[BrG02] M.Bravetti, R.Gorrieri. The Theory of Interactive Generalised Semi-Markov Processes, Theoretical Computer Science, volume 282(1):5-32, 2002.[BP97] N.Busi, G.M.Pinna: Synthesis of Nets with Inhibitor Arcs. CONCUR 1997: 151-165[BP00] N.Busi, G.M.Pinna. Comparing Truly Concurrent Semantics for Contextual Place/Transition Nets with Inhibitor and Read Arcs. Fundam. Inform. 44(3): 209-244 (2000)[MFD+03] H.Matsuno, S.Fujita, A.Doi, M.Nagasaki, S.Miyano. Towards Biopathway Modeling and Simulation. Springer LNCS 2679:3-22, 2003.[PRSS01] C.Priami, A.Regev, E.Shapiro, W.Silverman. Applications of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80:25-31, 2001.
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