Published: 15th November 2012
DOI: 10.4204/EPTCS.100
ISSN: 2075-2180


Proceedings 6th Workshop on
Membrane Computing and Biologically Inspired Process Calculi
Newcastle, UK, 8th September 2012

Edited by: Gabriel Ciobanu

Preface: Biologically Inspired Formalisms
Gabriel Ciobanu
Invited Paper: Membrane Systems and Petri Net Synthesis
Jetty Kleijn, Maciej Koutny, Marta Pietkiewicz-Koutny and Grzegorz Rozenberg
A Process Calculus for Spatially-explicit Ecological Models
Margarita Antonaki and Anna Philippou
GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology
Adrien Basso-Blandin and Franck Delaplace
Combining Insertion and Deletion in RNA-editing Preserves Regularity
E.P. de Vink, H. Zantema and D. Bošnački
Towards modular verification of pathways: fairness and assumptions
Peter Drábik, Andrea Maggiolo-Schettini and Paolo Milazzo
Implementing the Stochastics Brane Calculus in a Generic Stochastic Abstract Machine
Marino Miculan and Ilaria Sambarino
Parallel BioScape: A Stochastic and Parallel Language for Mobile and Spatial Interactions
Adriana Compagnoni, Mariangiola Dezani-Ciancaglini, Paola Giannini, Karin Sauer, Vishakha Sharma and Angelo Troina
RNA interference and Register Machines (extended abstract)
Masahiro Hamano

Biologically Inspired Formalisms

This EPTCS issue contains the papers presented at the 6th Membrane Computing and Biologically Inspired Process Calculi (MeCBIC), a satellite workshop of the 23rd International Conference on Concurrency Theory (CONCUR) held on 8th September 2012 in Newcastle upon Tyne.

The modelling and the analysis of biological systems has attracted the interest of several research communities. The notion of compartments appears in rule-based formalisms as membrane computing, and in several process calculi (bio-ambients, brane calculi, etc.). Multiset rewriting appears both in membrane computing and Petri nets. A cross fertilization of various research areas leads to deeper investigations of the relations between these related formalisms, trying also to understand their similarities and differences. MeCBIC started as an workshop devoted to membrane computing and biologically inspired process calculi. In the last years, it also attracted papers dealing with (bio-inspired) Petri nets, emphasizing the links between Petri nets and membrane systems. Membrane computing deals with the computational properties, making use of automata, formal languages, and complexity results. Petri nets are used to model and analyse several biological systems by using advanced software tools. Certain process calculi, such as mobile ambients and brane calculi, describe the compartments and their interactions, emphasizing on behaviour equivalences and stochastic aspects.

The main aim of the workshop is to bring together researchers working in these biologically inspired formalisms (membrane systems, Petri nets, ambient and brane calculi, various stochastic approaches) in order to present their recent results and to discuss new ideas concerning these formalisms, their properties and relationships. Topics presented at MeCBIC include (but are not limited to):

The submitted papers describe biologically inspired models and languages, as well as various properties and links between different models. They include various stochastic approaches, spatial interactions, modular verification of pathways, behaviour-based languages in synthetic biology, and RNA-induced transcriptional aspects.

The papers were reviewed by at least three referees. Many thanks for the evaluation process go to all the members of the Programme Committee:

   Bogdan AmanRoberto BarbutiLuca CardelliGabriel Ciobanu
Erik de VinkJean-Louis GiavittoJane HillstonJetty Kleijn
Jean KrivineEmanuela MerelliPaolo MilazzoGethin Norman
G. Michele PinnaFranck PommereauJason StegglesAngelo Troina.

We express our gratitude to the invited speakers Maciej Koutny and Vincent Danos for their interesting talks. Maciej Koutny presents the automated synthesis from behavioural specifications for a number of Petri net models relevant from the point of view of membrane systems. Vincent Danos defines a class of local stochastic rewrite rules on directed site trees, giving a compact presentation of coarse-grained differential systems describing the dynamics of these rules.

Many thanks to Bogdan Aman, Jason Steggles and local organizers for their help.

Gabriel Ciobanu
Iaşi, Romania