Published: 30th November 2009
DOI: 10.4204/EPTCS.11
ISSN: 2075-2180

EPTCS 11

Proceedings Third Workshop on
Membrane Computing and Biologically Inspired Process Calculi 2009
Bologna, Italy, 5th September 2009

Edited by: Gabriel Ciobanu

Membrane Systems and Related Process Calculi
Gabriel Ciobanu
1
Bigraphical models for protein and membrane interactions
Giorgio Bacci, Davide Grohmann and Marino Miculan
3
A framework for protein and membrane interactions
Giorgio Bacci, Davide Grohmann and Marino Miculan
19
A Process Calculus for Molecular Interaction Maps
Roberto Barbuti, Andrea Maggiolo-Schettini, Paolo Milazzo, Giovanni Pardini and Aureliano Rama
35
Modelling Cell Cycle using Different Levels of Representation
Thomas Anung Basuki, Antonio Cerone and Rafael V. Carvalho
51
A compartmental model of the cAMP/PKA/MAPK pathway in Bio-PEPA
Federica Ciocchetta, Adam Duguid and Maria Luisa Guerriero
71
A Type System for a Stochastic CLS
Mariangiola Dezani-Ciancaglini, Paola Giannini and Angelo Troina
91
New Solutions to the Firing Squad Synchronization Problems for Neural and Hyperdag P Systems
Michael J. Dinneen, Yun-Bum Kim and Radu Nicolescu
107
Drip and Mate Operations Acting in Test Tube Systems and Tissue-like P systems
Rudolf Freund and Marian Kogler
123
Abstract Interpretation for Probabilistic Termination of Biological Systems
Roberta Gori and Francesca Levi
137
Dependencies and Simultaneity in Membrane Systems
G. Michele Pinna and Andrea Saba
155

Membrane Systems and Related Process Calculi

Membrane Systems and Process Calculi

This volume contains the accepted papers at the third Workshop on Membrane Computing and Biologically Inspired Process Calculi held in Bologna on 5th September 2009. The papers are devoted to both membrane computing and biologically inspired process calculi, as well as to other related formalisms. The papers are selected by the programme committee due to their quality and relevance. These papers lead to an exciting meeting by highlighting some interesting problems and stimulating the search for novel ways of describing biological phenomena. In addition, we had an invited talk Pi in the Sky: Spatial Process Algebra for Developmental Biology given by Luca Cardelli.

Membrane systems were introduced as a class of distributed parallel computing devices inspired by the observation that any biological system is a complex hierarchical structure, with a flow of materials and information that underlies their functioning. The emphasis is on the computational properties of the model, and it makes use of automata, languages, and complexity theoretic tools. On the other hand, certain calculi such as mobile ambients and brane calculi work with similar notions (compartments, membranes). These calculi are used to model and analyze the various biological systems. The workshop on Membrane Computing and Biologically Inspired Process Calculi brings together researchers working in these fields to present their recent work and discuss new ideas concerning the formalisms, their properties and relationships. We thank the authors of the papers and the invited speaker who together contribute to the success of the workshop in reaching its aim, namely to bring together researchers working in these fields in order to present their recent work and discuss new ideas concerning the formalisms, their properties and relationships.

We express our gratitude to the Programme Committee members and external referees that spent a considerable amount of their time refereeing the submitted papers by using high scientific standards. Since good editorial work is made by good referees, it is my duty and pleasure to mention the Programme Committee members:

Luca Cardelli (Microsoft Research, UK) Vincenzo Manca (Verona, Italy)
Matteo Cavaliere (Trento, Italy) Emanuela Merelli (Camerino, Italy)
Gabriel Ciobanu (Iasi, Romania), Chair Marino Miculan (Udine, Italy)
Erzsebet Csuhaj-Varju (Budapest, Hungary) Gheorghe Paun (Bucharest, Romania)
Jean-Louis Giavitto (Evry, France) Cristian Versari (Bologna, Italy)
Maciej Koutny (Newcastle, UK) Claudio Zandron (Milano, Italy)

Many thanks to the local organizers coordinated by Ivan Lanese. We thank the team of EasyChair system used to manage our submissions and reviews, and Rob van Glabbeek for his help in preparing this volume.

The first edition of MeCBIC was co-organized by Nadia Busi. The third MeCBIC takes place exactly two years after her tragic death (on 5th September 2007). Nadia was also a professor at the University of Bologna (the venue of MeCBIC 2009) for many years. This is why we can consider the third edition of MeCBIC as a scientific commemoration and reverence to Nadia.


Gabriel Ciobanu
October 2009