Proceedings Fourth International Workshop on Computational Models for Cell Processes

TL;DR

The CompMod 2013 workshop showcased diverse computational modeling approaches for cell processes, emphasizing systems and synthetic biology, with selected papers covering mathematical models, rule-based systems, and literature mining.

Contribution

This volume presents the first collection of selected papers from the CompMod workshop series, highlighting novel modeling techniques and analyses in systems biology.

Findings

Mathematical modeling of PDGF signaling pathway

Rule-based modeling of polymerization reactions

Large-scale biomedical literature text mining

Abstract

The fourth international workshop on Computational Models for Cell Processes (CompMod 2013) took place on June 11, 2013 at the {\AA}bo Akademi University, Turku, Finland, in conjunction with iFM 2013. The first edition of the workshop (2008) took place in Turku, Finland, in conjunction with Formal Methods 2008, the second edition (2009) took place in Eindhoven, the Netherlands, as well in conjunction with Formal Methods 2009, and the third one took place in Aachen, Germany, in conjunction with CONCUR 2013. This volume contains the final versions of all contributions accepted for presentation at the workshop. The goal of the CompMod workshop series is to bring together researchers in Computer Science and Mathematics (both discrete and continuous), interested in the opportunities and the challenges of Systems Biology. The Program Committee of CompMod 2013 selected 3 papers for presentation at the workshop. In addition, we had two invited talks and five informal presentations. The scientific program of the workshop spans an interesting mix of approaches to systems and even synthetic biology, encompassing several different modeling approaches, ranging from quantitative to qualitative techniques, from continuous to discrete mathematics, and from deterministic to stochastic methods. We thank our invited speakers Daniela Besozzi (Universita degli Studi di Milano, Milano, Italy) and Juho Rousu (Aalto University, Finland) for accepting our invitation and for presenting some of their recent results at CompMod 2013. The technical contributions address the mathematical modeling of the PDGF signalling pathway, the canonical labelling of site graphs, rule-based modeling of polymerization reactions, rule-based modeling as a platform for the analysis of synthetic self-assembled nano-systems, robustness analysis of stochastic systems, an algebraic approach to gene assembly in ciliates, and large-scale text mining of biomedical literature.