Title: BioXyce: A circuit simulation framework for modeling and understanding host pathogen interactions Speaker: Elebeoba May, Org. 1412 (NECIS) Date/Time: Wednesday, May 31, 2006, 3:00 – 4:00 pm (MT) Location: Bldg. 980, Room 95 (SNL-NM), Bldg. 915, Room W133 (SNL-CA) Brief Abstract: Computational methods for describing, understanding, and manipulating biological pathways are being heavily researched [Arkin 2001, Covert et al., 2001, Smolen et al., 2000]. Many researchers are using constructs based in electrical circuit design in the analysis and simulation of biological systems [McAdams and Arkin 2000, Schilling et al., 2000/2001]. For example, Flux Balance Analysis (FBA) uses Kirchhoff’s electrical current conservation laws as a framework for metabolic modeling and analysis. Although several current modeling approaches draw on parallels between electrical circuits and biological circuits, few employ and exploit this parallelism for simulation purposes. We modify and extend the XyceTM electrical circuit simulation tool (developed in 1400), to create a large-scale, parallel, biocircuit simulator. This requires the development of individual circuit elements representing metabolic and genetic substrates and an accurate description of the coupling between elements as demonstrated in the simulation of the tryptophan biosynthesis pathway. Synthesis continues up the functional hierarchy to the construction of whole cells and the large-scale simulation of cell cultures and multi-cellular organisms. We discuss potential applications of this framework, including modeling and simulation of host-pathogen interactions in Mycobacterium tuberculosis infections.CSRI POC: Danny Rintoul, (505) 844-9592 |