Strengths and Weaknesses of Selected Modeling Methods Used in Systems Biology

The development of multicellular organisms requires the coordinated accomplishment of many molecular and cellular processes, like cell division and differentiation, as well as metabolism. Regulation of those processes must be very reliable and capable of resisting fluctuations of the internal and external environments. Without such homeostatic capacity, the viability of the organism would be compromised. Cellular processes are finely controlled by a number of regulatory molecules. In particular, transcription factors are amongst the proteins that determine the transcription rate of genes, including those involved in development and morphogenesis. For this reason, the molecular mechanisms responsible for the homeostatic capacity and coordinated behavior of the transcriptional machinery have become the focus of several laboratories. Modern techniques of molecular genetics have greatly increased the rate at which genes are recognized and their primary sequences determined. High throughput methods for the identification of gene-gene and protein-protein interactions exist and continue to be refined, raising the prospect of high-throughput determination of networks of interactions in discrete cell types. Still, classic biochemical and physiological studies are necessary to identify the targets, and to understand the functions of the encoded proteins. For such reasons, the rate at which pathways are described is much slower than the rate of genome sequencing. The large quantity of available sequences creates the challenge for molecular geneticists of linking genes and proteins into functional pathways or networks. Biologists are often interested in particular subsets of these very extensive networks obtained with