Transactions on Computational Systems Biology XI

ISBN-13: 9783642041853 / Angielski / Miękka / 2009 / 335 str.

Corrado Priami

Opis

Biology is witnessing a transformation towards a more quantitative science, based on the major technological breakthroughs of the past decade. In this transformation, biology is incorporating mathematical modeling techniques and computational approaches towards numerical simulations, model analysis, and quantitativepredictions.An importantgoalis to formalizeandanalyzethe ev- changing inter-connections between components (often on di?erent time and space scales), their in?uence on one another, regulatory patterns, alternative pathways, etc. Formal reasoning rather than empirical observations is the main driving force in this new type of biological research.At the same time, computer science and applied mathematics are faced with considerable methodological challenges in handling an unprecedented level of concurrency, stochastic e?ects, amixoflargeandsmallpopulations, combinatorialexplosionsinthe statespace, model re?nement, and model (de)composition, etc. ThisspecialissueofTransactionsonComputationalSystemsBiologyonC- putationalModels forCellProcessesisbasedonaworkshopwith thesamename that took place in Turku, Finland, on May 27, 2008. The workshop was or- nized as a satellite event of the 15th International Symposium on Formal Me- ods that took place in Turku in the period May 28-31, 2008. This special issue however had an open call for paper submissions, with a separate peer-review process. The accepted papers span an interesting mix of approaches to systems biology, ranging from quantitative to qualitative techniques, from continuous to discrete mathematics, from deterministic to stochastic methods, from compu- tional models for biology to computing paradigms inspired by biology. Overall, they give a good glimpse into some of the exciting current research avenues in computational systems biology

Recenzje

From the reviews:

"It is a multidisciplinary collection of research papers, by researchers, for researchers. The papers target specialists in particular formalisms. ... papers were presented at a satellite workshop of the 15th International Symposium on Formal Methods at Turku, in 2008. The goal of the research is to supplement 'wetlab' science (in vitro or in vivo) by in silico or in numero studies. ... In conclusion, this book is for specialists ... ." (Richard Botting, ACM Computing Reviews, November, 2010)

Spis treści

Computational Models for Cell Processes.- Process Algebra Modelling Styles for Biomolecular Processes.- Simple, Enhanced and Mutual Mobile Membranes.- Bio-PEPA with Events.- In Silico Modelling and Analysis of Ribosome Kinetics and aa-tRNA Competition.- Qualitative and Quantitative Analysis of a Bio-PEPA Model of the Gp130/JAK/STAT Signalling Pathway.- Rule-Based Modelling and Model Perturbation.- Extended Stochastic Petri Nets for Model-Based Design of Wetlab Experiments.- A Projective Brane Calculus with Activate, Bud and Mate as Primitive Actions.- Accepting Networks of Non-inserting Evolutionary Processors.- Discrete Modeling of Biochemical Signaling with Memory Enhancement.- Dynamical Systems and Stochastic Programming: To Ordinary Differential Equations and Back.- Computing Equilibrium Points of Genetic Regulatory Networks.- Code, Context, and Epigenetic Catalysis in Gene Expression.

Blurb

The LNCS journal Transactions on Computational Systems Biology is devoted to inter- and multidisciplinary research in the fields of computer science and life sciences and supports a paradigmatic shift in the techniques from computer and information science to cope with the new challenges arising from the systems oriented point of view of biological phenomena.

This special issue on Computational Models for Cell Processes is based on a workshop with the same name that took place in Turku, Finland, on May 27, 2008. The accepted papers, which have passed through a separate peer-review process, span an interesting mix of approaches to systems biology, ranging from quantitative to qualitative techniques, from continuous to discrete mathematics, from deterministic to stochastic methods, and from computational models for biology to computing paradigms inspired by biology. Also included in this issue are three regular submissions dealing with the relationship between ODEs and stochastic concurrent constraint programming, with the equilibrium points of genetic regulatory networks, and with probability models describing how epigenetic context affects gene expression and organismal development.