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ACM Transactions on Modeling and Computer Simulation (TOMACS) - Special Issue on Computational Methods in Systems Biology, Volume 25 Issue 2, April 2015



Section: Special Issue on Computational Methods in Systems Biology

Guest Editors’ Introduction to Special Issue on Computational Methods in Systems Biology
Ashutosh Gupta, Thomas Henzinger
Article No.: 7
DOI: 10.1145/2745799

Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks
Jakob Ruess, John Lygeros
Article No.: 8
DOI: 10.1145/2688906

Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of the molecular interactions cannot be ignored. This has motivated recent research effort into methods for...

Computing Cumulative Rewards Using Fast Adaptive Uniformization
Frits Dannenberg, Ernst Moritz Hahn, Marta Kwiatkowska
Article No.: 9
DOI: 10.1145/2688907

The computation of transient probabilities for continuous-time Markov chains often employs uniformization, also known as the Jensen method. The fast adaptive uniformization method introduced by Mateescu et al. approximates the probability by...

Simulating Organogenesis: Algorithms for the Image-Based Determination of Displacement Fields
Clemens Arthur Schwaninger, Denis Menshykau, Dagmar Iber
Article No.: 10
DOI: 10.1145/2688908

Recent advances in imaging technology now provide us with 3D images of developing organs. These can be used to extract 3D geometries for simulations of organ development. To solve models on growing domains, the displacement fields between...

Constrained Community-Based Gene Regulatory Network Inference
Ferdinando Fioretto, Agostino Dovier, Enrico Pontelli
Article No.: 11
DOI: 10.1145/2688909

The problem of gene regulatory network inference is a major concern of systems biology. In recent years, a novel methodology has gained momentum, called community network approach. Community networks integrate predictions from...

Model Reconstruction for Moment-Based Stochastic Chemical Kinetics
Alexander Andreychenko, Linar Mikeev, Verena Wolf
Article No.: 12
DOI: 10.1145/2699712

Based on the theory of stochastic chemical kinetics, the inherent randomness of biochemical reaction networks can be described by discrete-state continuous-time Markov chains. However, the analysis of such processes is computationally expensive...

Spatial-Temporal Modelling and Analysis of Bacterial Colonies with Phase Variable Genes
Ovidiu Pârvu, David Gilbert, Monika Heiner, Fei Liu, Nigel Saunders, Simon Shaw
Article No.: 13
DOI: 10.1145/2742546

This article defines a novel spatial-temporal modelling and analysis methodology applied to a systems biology case study, namely phase variation patterning in bacterial colony growth. We employ coloured stochastic Petri nets to construct the model...

Hybrid Simulations of Heterogeneous Biochemical Models in SBML
Hui Ju K. Chiang, François Fages, Jie Hong R. Jiang, Sylvain Soliman
Article No.: 14
DOI: 10.1145/2742545

Models of biochemical systems presented as a set of formal reaction rules can be interpreted in different formalisms, most notably as either deterministic Ordinary Differential Equations, stochastic continuous-time Markov Chains, Petri nets, or...