Formal methods and Systems Biology: the Calculus of Looping Sequences.

Relatore
Paolo Milazzo - Dipartimento di Informatica - Universita' di Pisa
Data e ora
martedì 22 gennaio 2008 alle ore 16.45 - Inizio alle 16:45, Caffe' e biscotti alle 16:30.
Luogo
Ca' Vignal - Piramide, Piano 0, Sala Verde
Referente
Roberto Giacobazzi
Referente esterno
Data pubblicazione
10 gennaio 2008
Dipartimento
 

Riassunto

In the last few years many formalisms, originally developed by computer
scientists to model systems of interacting components, have been applied to
Biology. Among these, there are Petri Nets, Hybrid Systems, and the
pi-calculus. Moreover, formalisms such as P Systems, originally developed
to study new computational paradigms inspired by Biology, have recently
found application to the description of biological phenomena.

The first advantage of using formal models to describe biological systems is
that they avoid ambiguities. In fact, ambiguity is often a problem of the
notations used by biologists. Moreover, the formal modeling of biological
systems allows the development of simulators and the verification of
properties of the described systems by means of tools (such as model
checking,
behavioural equivalences, type systems and static analyses) which are well
established and widely used in other application fields of Computer Science,
but unknown to biologists.

In this talk I will describe a formalism, called Calculus of Looping
Sequences (CLS), for the description of biological systems. CLS is based on
term rewriting and it is a rather simple formalism that allows describing
proteins, DNA, membranes and other macromolecules. CLS is equipped
with a labeled semantics and with bisimulation relations that can be used
to compare the behaviour of two biological systems and to prove properties
of such systems. Extensions of CLS have been defined to take into account
quantitative (stochastic) aspects of the dynamics of the described systems
and to describe biomolecular systems by taking into account interactions
at a less abstract level, namely at the level of the individual interaction
sites of proteins and dna. I will briefly describe these extensions by
highlighting the benefits of the use of formal methods in the biological
application domain.





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