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Gostner R.,COSBI | Gostner R.,University of Trento | Baldacci B.,COSBI | Baldacci B.,University of Trento | And 4 more authors.
ACM Computing Surveys | Year: 2014

Modeling biological systems to understand their mechanistic behavior is an important activity in molecular systems biology. Mathematical modeling typically requires deep mathematical or computing knowledge, and this limits the spread of modeling tools among biologists. Graphical modeling languages have been introduced to minimize this limit. Here, we survey the main graphical formalisms (supported by software tools) available to model biological systems with a primary focus on their usability, within the framework of modeling reaction pathways with two-dimensional (2D) (possibly nested) compartments. Considering the main characteristics of the surveyed formalisms, we synthesise a new proposal (Style) and report the results of an online survey conducted among biologists to assess usability of available graphical formalisms. We consider this proposal a guideline developed from what we learned in the survey, which can inform development of graphical formalisms to model reaction pathways in 2D space. © 2014 ACM.

Romanel A.,CoSBi | Romanel A.,University of Trento | Priami C.,CoSBi | Priami C.,University of Trento
Theoretical Computer Science | Year: 2010

We present some decidability and undecidability results for subsets of the BlenX Language, a process-calculi-based programming language developed for modelling biological processes. We show that for a core subset of the language (which considers only communication primitives) termination is decidable. Moreover, we prove that by adding either global priorities or events to this core language, we obtain Turing equivalent languages. The proof is through encodings of Random Access Machines (RAMs), a well-known Turing equivalent formalism, into our subsets of BlenX. All the encodings are shown to be correct. © 2009 Elsevier B.V. All rights reserved.

Larcher R.,CoSBi | Larcher R.,University of Trento | Priami C.,CoSBi | Priami C.,University of Trento | And 2 more authors.
Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) | Year: 2010

The process through which disordered components spontaneously arrange themselves into patterns is called self-assembly. Molecular self-assembly describes the process by which molecules adopt a defined arrangement without external guidance (e.g. formation of membranes and protein complexes). These biological processes are essential to the functioning of cells. We investigate the usage of BlenX, a process calculi based programming language, for modelling molecular self-assembly of filaments, trees and rings. Moreover, we show how these structures can be used to model actin polymerization. © 2010 Springer.

Priami C.,COSBI | Priami C.,University of Trento | Quaglia P.,University of Trento | Zunino R.,COSBI | Zunino R.,University of Trento
Proceedings of the ACM Symposium on Applied Computing | Year: 2012

The main design features of a language for the management of the dynamic reconfiguration of graphs are described. The language is domain-specific to model the behaviour of biological systems. Nodes of graphs are biochemical components, and undirected edges between them represent biochemical bonds. Also, nodes have a finite number of binding sites, and each of them can be the end-point of an edge leading to (exactly one end-point of) another node. A pair of nodes can be connected by multiple edges, each of them representing a particular bond between the involved biochemical entities. Spontaneous events, corresponding to the biological formation/breakage of bonds, can cause graph reconfigurations. Nodes can be programmed to react to them, and consequently change their own propensity to be involved in further events. The event handling routines coded within nodes are executed in a concurrent fashion. This poses the usual problems related to race conditions, deadlock and the like. Language primitives are tailored to cope with these issues. They ensure, e.g., consistency of reconfigurations: each binding site of every node can be connected at most with one single binding site of another node. This extended abstract describes the rationale behind the peculiarities of the language by showing excerpts of programmed nodes that, together with spontaneous events, can drive relevant reconfigurations of graphs. © 2012 ACM.

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