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. Comments

Graph theory has become a very critical component in many applications in the computing field including networking and security. Unfortunately, it is also amongst the most complex topics to understand and apply. In this paper, we review some of the key applications of graph theory in network security. We first cover some algorithmic aspects, then present network coding and its relation to routing.

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REPORT DOCUMENTATION PAGEForm Public reporting burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data sources, gathering and maintaining the data needed, and completing and reviewing this collection of information. Send comments regarding this burden estimate or any other aspect of this collection of information, including suggestions for reducing this burden to Washington Headquarters Services, Directorate for Information Operations and Reports, 1215 Jefferson Davis Highway, Suite 1204, Arlington, VA 22202-4302, and to the Office of Management and Budget, Paperwork Reduction Project (0704-0188), Washington, DC 20503 AGENCY USE ONLY (Leave blank)2. REPORT DATE JUNE 2005 REPORT TYPE AND DATES COVEREDFinal Sep 01 -Dec 04 TITLE AND SUBTITLE INTEGRATION OF ANALYTIC AND SYNTHETIC BIOSYSTEM MODELS AND DATA AUTHOR(S)Jonathan Delatizky and Jonathan Webb FUNDING NUMBERSC -F30602-01-C-0210 PE -61101E PR -BIOC TA -M3 WU -04 PERFORMING ORGANIZATION NAME(S) AND ADDRESS(ES)BBN Technologies 10 Moulton Street Cambridge Massachusetts 02138-1119 PERFORMING ORGANIZATION REPORT NUMBERN/A SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES)Defense 12b. DISTRIBUTION CODE ABSTRACT (Maximum 200 Words)This effort, funded under DARPA's Biocomputing (BioComp) program, was directed at providing data services for the BioSpice infrastructure. BioSpice is an environment akin to the Electrical Engineering SPICE modeling and simulation package, in which an open environment and standards-based modularity enable an enormous range of tools for the development and understanding of electronic circuits to be applied without restrictions resulting from proprietary or closed interfaces. BBN also teamed with the University of Pennsylvania to develop an intuitive tool called BioSketchpad, for creating and parameterizing models and connecting the resulting models to a simulator. A modeling language (Systems Biology Markup Language (SBML), was also developed for representing interesting molecular biology models and to support model interchange between different tools. The SBML effort required collaboration with a separate systems biology development effort (which had created the first version of SBML) that was an outgrowth of other research efforts. BBNT's role was envisaged as supporting the system integrator, SRI, and the numerous biologists and modelers who would be developing and integrating simulators, analytical tools, models, and other elements, in data management and data flow within the BioSpice system as it evolved. NUMBER OF PAGES OverviewIn the first year of the program, BBNT performed the following tasks in support of this role:• Surveyed existing database systems used by biologists and modelers and published a listing categorizing databases by content, organization, and access mechanisms • Stood up and ran a database working group, with participation from most performers under the program, to assess BioSpice needs for data management an...