Programmable models of growth and mutation of cancer-cell populations

In this paper we propose a systematic approach to construct mathematical models describing populations of cancer-cells at different stages of disease development. The methodology we propose is based on stochastic Concurrent Constraint Programming, a flexible stochastic modelling language. The methodology is tested on (and partially motivated by) the study of prostate cancer. In particular, we prove how our method is suitable to systematically reconstruct different mathematical models of prostate cancer growth - together with interactions with different kinds of hormone therapy - at different levels of refinement.Comment: In Proceedings CompMod 2011, arXiv:1109.104

Generalized Communicating P Systems Working in Fair Sequential Model

In this article we consider a new derivation mode for generalized communicating P systems (GCPS) corresponding to the functioning of population protocols (PP) and based on the sequential derivation mode and a fairness condition. We show that PP can be seen as a particular variant of GCPS. We also consider a particular stochastic evolution satisfying the fairness condition and obtain that it corresponds to the run of a Gillespie's SSA. This permits to further describe the dynamics of GCPS by a system of ODEs when the population size goes to the infinity.Comment: Presented at MeCBIC 201

StochKit-FF: Efficient Systems Biology on Multicore Architectures

The stochastic modelling of biological systems is an informative, and in some cases, very adequate technique, which may however result in being more expensive than other modelling approaches, such as differential equations. We present StochKit-FF, a parallel version of StochKit, a reference toolkit for stochastic simulations. StochKit-FF is based on the FastFlow programming toolkit for multicores and exploits the novel concept of selective memory. We experiment StochKit-FF on a model of HIV infection dynamics, with the aim of extracting information from efficiently run experiments, here in terms of average and variance and, on a longer term, of more structured data.Comment: 14 pages + cover pag

Design Environments for Complex Systems

The paper describes an approach for modeling complex systems by hiding as much formal details as possible from the user, still allowing verification and simulation of the model. The interface is based on UML to make the environment available to the largest audience. To carry out analysis, verification and simulation we automatically extract process algebras specifications from UML models. The results of the analysis is then reflected back in the UML model by annotating diagrams. The formal model includes stochastic information to handle quantitative parameters. We present here the stochastic -calculus and we discuss the implementation of its probabilistic support that allows simulation of processes. We exploit the benefits of our approach in two applicative domains: global computing and systems biology

A modular hybrid simulation framework for complex manufacturing system design

For complex manufacturing systems, the current hybrid Agent-Based Modelling and Discrete Event Simulation (ABM–DES) frameworks are limited to component and system levels of representation and present a degree of static complexity to study optimal resource planning. To address these limitations, a modular hybrid simulation framework for complex manufacturing system design is presented. A manufacturing system with highly regulated and manual handling processes, composed of multiple repeating modules, is considered. In this framework, the concept of modular hybrid ABM–DES technique is introduced to demonstrate a novel simulation method using a dynamic system of parallel multi-agent discrete events. In this context, to create a modular model, the stochastic finite dynamical system is extended to allow the description of discrete event states inside the agent for manufacturing repeating modules (meso level). Moreover, dynamic complexity regarding uncertain processing time and resources is considered. This framework guides the user step-by-step through the system design and modular hybrid model. A real case study in the cell and gene therapy industry is conducted to test the validity of the framework. The simulation results are compared against the data from the studied case; excellent agreement with 1.038% error margin is found in terms of the company performance. The optimal resource planning and the uncertainty of the processing time for manufacturing phases (exo level), in the presence of dynamic complexity is calculated