Transactions on computational systems biology XIII

Preface. The many facets of life are reflected by the multitude of dimensions of systems biology research at present. Current modeling and analysis approaches to a systematic understanding of biological phenomena range from quantitative to qualitative, from discrete to continuous, from deterministic to stochastic, from concrete detailed biological case studies to abstract bio-inspired computing paradigms. This special issue of the Transactions on Computational Systems Biology on Computational Models for Cell Processes also mirrors the rich variety of the field. The volume is based on the CompMod workshop that took place in Eindhoven, the Netherlands, on November 2, 2009. Previously held in Turku, Finland, the workshop was organized for the second time, now as a satellite event of the 16th International Symposium on Formal Methods, part of FMweek, running from November 2 to 6, 2009 in Eindhoven. The CompMod workshop aims to foster a platform gathering researchers in formal methods and related fields interested in the wealth of challenges and opportunities in systems biology. A specific interest is expressed for papers discussing biological processes requiring special tools and techniques not investigated so far in the context of formal methods, as well as extensions of formal methods formalisms introduced to improve their applicability to biology. For this special issue there has been an additional open call for paper submissions, with a separate peer-reviewing process. The papers included illustrate the broad span of aspects of modeling and analysis of biological systems: evolution of a cell population with selection based on toxin resistance; a quantitative and tool-supported interpretation of flow abstraction in the Systems Biology Graphical Notation; an analytic approach to dynamic simulation of deformable biological structures; a new stochastic simulation algorithm reconsidering the delay-as-duration principle; a process algebraic case study on ammonium transport in plant-fungus symbiosis; iterative variable elimination for steady state equations using algebraic modules in the analysis of metabolic networks. From different points of view and following various approaches the papers cover a wide range of topics in Systems Biology, addressing the dynamics we begin to unravel and computational principles that we start to identify. This issue also includes two regular papers by Wallace and Wallace on the heritability of complex diseases and by Paulev´e et al. on the dynamics of gene regulatory networks