Shapiro 9724164 The workshop will bring together the concepts and approaches of two fields--molecular biology and theoretical computer science--for the study of molecular computing/decision-making networks in cells. The focus will be on molecular networks in a small number of well-analyzed microbial systems. All of these networks are analogues of computing networks formed by multiple interacting agents, and we now have powerful experimental tools to investigate the properties of the molecules which constitute their nodes. What is needed now are formal methods for describing and analyzing the behavior of the ensembles. The idea is to use the real networks that are found in microbes to derive formal models/representations with predictive powers. The predictions, in turn, can be tested by returning to the microbes. Truly creative modeling will require new concepts in theoretical computer science. The genesis and testing based on actual microbial systems will ensure that the theoretical results are firmly tied to real phenomena. The goal of the workshop therefore is to begin converting our molecular knowledge into computer theoretic understanding of how these networks function. For example, we need to determine how to represent the analog processing capabilities of proteins that interact with multiple ligands, and we need to find the best vocabulary for translating experimentally-determined molecular properties, such as binding and catalytic constants, into components of computational algorithms. To do so will require intense collective discussions of a small number of real cases involving representatives of many perspectives, both biological and computational. The results of the workshop should have applications to biotechnology, for example in the area of metabolic engineering.
