title: Computational Modeling, Formal Analysis, and Tools for Systems Biology.
abstract: As the amount of biological data in the public domain grows, so does the range of modeling and analysis techniques employed in systems biology. In recent years, a number of theoretical computer science developments have enabled modeling methodology to keep pace. The growing interest in systems biology in executable models and their analysis has necessitated the borrowing of terms and methods from computer science, such as formal analysis, model checking, static analysis, and runtime verification. Here, we discuss the most important and exciting computational methods and tools currently available to systems biologists. We believe that a deeper understanding of the concepts and theory highlighted in this review will produce better software practice, improved investigation of complex biological processes, and even new ideas and better feedback into computer science.
authors.affiliation: Faculty of Informatics, Technische Universität Wien, Vienna, Austria.
authors.forename: Ezio
authors.initials: E
authors.lastname: Bartocci
authors.affiliation: Computer Laboratory, University of Cambridge, Cambridge, United Kingdom.
authors.forename: Pietro
authors.initials: P
authors.lastname: Lió
mesh_terms: D003198:Computer Simulation; D008954:Models, Biological; D012984:Software; D049490:Systems Biology