Visual Programming for Modeling and Simulation of Biomolecular Regulatory Networks

In this paper we introduce our new tool BIOSKETCHPAD that allows visual programming and modeling of biological regulatory networks. The tool allows biologists to create dynamic models of networks using a menu of icons, arrows, and pop-up menus, and translates the input model into CHARON, a modeling language for modular design of interacting multi-agent hybrid systems. Hybrid systems are systems that are characterized by continuous as well as discrete dynamics. Once a CHARON model of the underlying system is generated, we are able to exploit the various analysis capabilities of the CHARON toolkit, including simulation and reachability analysis. We illustrate the advantages of this approach using a case study concerning the regulation of bioluminescence in a marine bacterium

An enrichment method for temperature-sensitive and auxotrophic mutants of yeast

An enrichment procedure that exploits the difference in heat-sensitivity between exponentially growing and stationary phase cells has been developed for the isolation of yeast mutants. Enrichments of up to 12-fold for temperature-sensitive lethal mutants and of up to 15-fold for auxotrophs have been obtained with single cycles of selection. Still higher enrichments (to frequencies of greater than 90% and 80% for temperature-sensitive lethals and auxotrophs, respectively) have been obtained with multiple cycles of selection. The method requires no special parent strain, and seems adaptable to the selection of a wide variety of types of mutants.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47545/1/438_2004_Article_BF00274022.pd

Hierarchical Organization in Complex Networks

Many real networks in nature and society share two generic properties: they are scale-free and they display a high degree of clustering. We show that these two features are the consequence of a hierarchical organization, implying that small groups of nodes organize in a hierarchical manner into increasingly large groups, while maintaining a scale-free topology. In hierarchical networks the degree of clustering characterizing the different groups follows a strict scaling law, which can be used to identify the presence of a hierarchical organization in real networks. We find that several real networks, such as the World Wide Web, actor network, the Internet at the domain level and the semantic web obey this scaling law, indicating that hierarchy is a fundamental characteristic of many complex systems

A Calculus of Chemical Systems

In recent years various calculi have been proposed for modelling biological systems, typically intracellular pathways. These calculi generally fall into one of two camps: ones based on process calculi, such as Milner’s pi-calculus [24], and rule-based ones. Examples of the former include [31, 32, 30]; examples of the latter include BIOCHAM, κ, BioNet