661 research outputs found
Membrane Systems and Time Petri Nets
We investigate the relationship of time Petri nets and di erent variants of
membrane systems. First we show that the added feature of \time" in time Petri nets
makes it possible to simulate the maximal parallel rule application of membrane systems
without introducing maximal parallelism to the Petri net semantics, then we de ne local
time P systems and explore how time Petri nets and the computations of local time P
systems can be related
Computational Techniques for the Structural and Dynamic Analysis of Biological Networks
The analysis of biological systems involves the study of networks from different omics such as genomics, transcriptomics, metabolomics and proteomics. In general, the computational techniques used in the analysis of biological networks can be divided into those that perform (i) structural analysis, (ii) dynamic analysis of structural prop- erties and (iii) dynamic simulation. Structural analysis is related to the study of the topology or stoichiometry of the biological network such as important nodes of the net- work, network motifs and the analysis of the flux distribution within the network. Dy- namic analysis of structural properties, generally, takes advantage from the availability of interaction and expression datasets in order to analyze the structural properties of a biological network in different conditions or time points. Dynamic simulation is useful to study those changes of the biological system in time that cannot be derived from a structural analysis because it is required to have additional information on the dynamics of the system. This thesis addresses each of these topics proposing three computational techniques useful to study different types of biological networks in which the structural and dynamic analysis is crucial to answer to specific biological questions. In particu- lar, the thesis proposes computational techniques for the analysis of the network motifs of a biological network through the design of heuristics useful to efficiently solve the subgraph isomorphism problem, the construction of a new analysis workflow able to integrate interaction and expression datasets to extract information about the chromo- somal connectivity of miRNA-mRNA interaction networks and, finally, the design of a methodology that applies techniques coming from the Electronic Design Automation (EDA) field that allows the dynamic simulation of biochemical interaction networks and the parameter estimation
Recommended from our members
A review of modelling and verification approaches for computational biology
This paper reviews most frequently used computational modelling approaches and formal verification techniques in computational biology. The paper also compares a number of model checking tools and software suits used in analysing biological systems and biochemical networks and verifiying a wide range of biological properties
Multi-level model for the investigation of oncoantigen- driven vaccination effect
BACKGROUND: Cancer stem cell theory suggests that cancers are derived by a population of cells named Cancer Stem Cells (CSCs) that are involved in the growth and in the progression of tumors, and lead to a hierarchical structure characterized by differentiated cell population. This cell heterogeneity affects the choice of cancer therapies, since many current cancer treatments have limited or no impact at all on CSC population, while they reveal a positive effect on the differentiated cell populations. RESULTS: In this paper we investigated the effect of vaccination on a cancer hierarchical structure through a multi-level model representing both population and molecular aspects. The population level is modeled by a system of Ordinary Differential Equations (ODEs) describing the cancer population's dynamics. The molecular level is modeled using the Petri Net (PN) formalism to detail part of the proliferation pathway. Moreover, we propose a new methodology which exploits the temporal behavior derived from the molecular level to parameterize the ODE system modeling populations. Using this multi-level model we studied the ErbB2-driven vaccination effect in breast cancer. CONCLUSIONS: We propose a multi-level model that describes the inter-dependencies between population and genetic levels, and that can be efficiently used to estimate the efficacy of drug and vaccine therapies in cancer models, given the availability of molecular data on the cancer driving force
Petri Net modelling approach for analysing the behaviour of Wnt/[inline-formula removed] -catenin and Wnt/Ca 2+ signalling pathways in arrhythmogenic right ventricular cardiomyopathy.
Arrhythmogenic right ventricular cardiomyopathy (ARVC) is an inherited heart muscle disease that may result in arrhythmia, heart failure and sudden death. The hallmark pathological findings are progressive myocyte loss and fibro fatty replacement, with a predilection for the right ventricle. This study focuses on the adipose tissue formation in cardiomyocyte by considering the signal transduction pathways including Wnt/[inline-formula removed]-catenin and Wnt/Ca2+ regulation system. These pathways are modelled and analysed using stochastic petri nets (SPN) in order to increase our comprehension of ARVC and in turn its treatment regimen. The Wnt/[inline-formula removed]-catenin model predicts that the dysregulation or absence of Wnt signalling, inhibition of dishevelled and elevation of glycogen synthase kinase 3 along with casein kinase I are key cytotoxic events resulting in apoptosis. Moreover, the Wnt/Ca2+ SPN model demonstrates that the Bcl2 gene inhibited by c-Jun N-terminal kinase protein in the event of endoplasmic reticulum stress due to action potential and increased amount of intracellular Ca2+ which recovers the Ca2+homeostasis by phospholipase C, this event positively regulates the Bcl2 to suppress the mitochondrial apoptosis which causes ARVC
Spiking neural P systems: matrix representation and formal verification
YesStructural and behavioural properties of models are very important in development of complex systems and applications. In this paper, we investigate such properties for some classes of SN P systems. First, a class of SN P systems associated to a set of routing problems are investigated through their matrix representation. This allows to make certain connections amongst some of these problems. Secondly, the behavioural properties of these SN P systems are formally verified through a natural and direct mapping of these models into kP systems which are equipped with adequate formal verification methods and tools. Some examples are used to prove the effectiveness of the verification approach.EPSRC research grant EP/R043787/1; DOST-ERDT research grants; Semirara Mining Corp; UPD-OVCRD
A Study of the PDGF Signaling Pathway with PRISM
In this paper, we apply the probabilistic model checker PRISM to the analysis
of a biological system -- the Platelet-Derived Growth Factor (PDGF) signaling
pathway, demonstrating in detail how this pathway can be analyzed in PRISM. We
show that quantitative verification can yield a better understanding of the
PDGF signaling pathway.Comment: In Proceedings CompMod 2011, arXiv:1109.104
- …