CMSB is an annual series of conferences, initiated in 2003, on the design of computational methods for modeling and analyzing biological systems, networks, data, and on their applications to study cases. The conference brings together computer scientists, biologists, mathematicians, engineers, and physicists interested in a system-level understanding of biological processes, their control by experimental or therapeutic means, or even their design or optimization by synthetic biology means.
This selection of CMSB 2011 is composed of eight papers that will be published in two parts in two TCBB issues. The first part, published in this issue, contains five papers.
One central challenge in systems biology is model calibration, i.e., the fitting of models to data and the inference of parameters that cannot be measured. "Evaluation of Design Strategies for Time Course Experiments in Genetic Networks: Case Study of the XlnR Regulon in Aspergillus niger" by Jimmy Omony, Astrid R. Mach-Aigner, Leo H. de Graaff, Gerrit van Straten, and Anton J.B. van Boxtel considers the design of experiments that maximize the information contained in mRNA time courses for the construction of genetic networks. This article presents, through a study of the XlnR regulon in Asparagus niger, the use of parameter sensitivity analysis, Fisher Information Matrix, and the E-modified criterion to optimize experimental design. This study case shows that a second inducer impulse, instead of a single impulse, just before the disappearance of the first impulse, optimizes the estimation of the kinetic parameters. This paper received the best student paper award at CMSB 2011.
"The Phosphorylation of the Heat Shock Factor as a Modulator for the Heat Shock Response" by Eugen Czeizler, Vladimir Rogojin, and Ion Petre studies the phosphorylation-mediated transcription of heat-shock proteins, which are responsible for chaperoning protein refolding after a prolonged elevated heat in eukaryotes. This paper presents several mechanistic models obtained by refinement, all based on ordinary differential equations, and investigates three alternative phosphorylation mechanisms for the regulation of heat shock factors. Only the models based on