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by Corrado Priami (Editor in Chief), Rainer Breitling (Guest Editor), David Gilbert (Guest Editor)
Inspired by the interesting contributions to the 6th Conference on Compu- tional Methods in Systems Biology (CMSB 2008) and the Dagstuhl Seminar 09091on"FormalMethods inMolecular Biology"inFebruary2009, papershave been selected for this special issue of the journal TransactionsonComputational Systems Biology, under the title Modeling Methodologies. The special issue starts with a position paper on "Biomodel Engineering - from Structure to Behavior", which discusses the potential that concepts from traditional computing science hold for creating more powerful models of biol- ical systems and identi?es venues for challenging future research. The technical contributions of the special issue covera broadrangeof mod- ing methodologies that have recently been developed in computational systems biology. First, twonewmodelinglanguagesarepresented.The"Attributed?-Calculus withPriorities"presentsacombinationofaconcurrentprocesslanguage, i.e., the ?-calculus, and a sequential core language, i.e., the ?-calculus; being equipped withprioritiesthelanguageenablesthedescriptionofdiversespatialphenomena, di?erent kinetics, as well as an individual-based and population-based modeling of biological systems. It is shown how the di?erent dialects of the ? calculus, including the pi@-calculus, can be expressed. Its stochastic semantic is ?rmly rooted in CMTC's and is re?ected in the stochastic simulator.
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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 of the journal focuses on the topic of modeling methodologies. It starts with a position paper by the guest editors, entitled Biomodel Engineering - from Structure to Behavior, which is followed by the technical contributions covering a broad range of modeling methodologies. Two papers focus on new modeling languages, and these are followed by an article presenting a case study demonstrating the value of the qualitative network approach. With the remaining three contributions, the special issue leaves the area of qualitative modeling, to move toward quantitative programming with the BlenX language and the application of more theoretical process calculi.
