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The development of detailed, coherent, models of complex biological systems is recognized as a key requirement for integrating the increasing amount of experimental data. In addition, in-silico simulation of bio-chemical models provides an easy way to test different experimental conditions, helping in the discovery of the dynamics that regulate biological(More)
This paper focuses on Beta-binders, a language of processes with typed interaction sites which has been recently introduced to represent biological entities. Here the syntax and semantics of Beta-binders are enriched to achieve a stochastic version of it, in order to obtain quantitative measures on biological phenomena. The relevance of quantitative(More)
A stochastic extension of COWS is presented. First the formalism is given an operational semantics leading to finitely branching transition systems. Then its syntax and semantics are enriched along the lines of Markovian extensions of process calculi. This allows addressing quantitative reasoning about the behaviour of the specified web services. For(More)
Single base level information from next-generation sequencing (NGS) allows for the quantitative assessment of biological phenomena such as mosaicism or allele-specific features in healthy and diseased cells. Such studies often present with computationally challenging burdens that hinder genome-wide investigations across large datasets that are now becoming(More)
The analysis of exonic DNA from prostate cancers has identified recurrently mutated genes, but the spectrum of genome-wide alterations has not been profiled extensively in this disease. We sequenced the genomes of 57 prostate tumors and matched normal tissues to characterize somatic alterations and to study how they accumulate during oncogenesis and(More)
Defining the chronology of molecular alterations may identify milestones in carcinogenesis. To unravel the temporal evolution of aberrations from clinical tumors, we developed CLONET, which upon estimation of tumor admixture and ploidy infers the clonal hierarchy of genomic aberrations. Comparative analysis across 100 sequenced genomes from prostate,(More)
Data protection legislation requires personal data to be collected and processed only for lawful and legitimate purposes. Unfortunately, existing protection mechanisms are not appropriate for purpose control: they only prevent unauthorized actions from occurring and do not guarantee that the data are actually used for the intended purpose. In this paper, we(More)
Biological systems are characterised by a large number of interacting entities whose dynamics is described by a number of reaction equations. Mathematical methods for modelling biological systems are mostly based on a centralised solution approach: the modelled system is described as a whole and the solution technique, normally the integration of a system(More)
The Stochastic Simulation Algorithm (SSA) is a milestone in the realm of stochastic modeling of biological systems, as it inspires all the current algorithms for stochastic simulation. Essentially, the SSA shows that under certain hypothesis the time to the next occurrence of a biochemical reaction is a random variable following a negative exponential(More)