The last several decades have witnessed a vast accumulation of biological data and data analysis. Many of these data sets represent only a small fraction of the system's behavior, making the visualization of full system behavior difficult. A more complete understanding of a biological system is gained when different types of data (and/or conclusions drawn from the data) are integrated into a larger-scale representation or model of the system. Ideally, this type of model is consistent with all available data about the system, and it is then used to generate additional hypotheses to be tested. Computer-based methods intended to formulate models that integrate various events and to test the consistency of these models with respect to the laboratory-based observations on which they are based are potentially very useful. In addition, in contrast to informal models, the consistency of such formal computer-based models with laboratory data can be tested rigorously by methods of formal verification. We combined two formal modeling approaches in computer science that were originally developed for non-biological system design. One is the inter-object approach using the language of live sequence charts (LSCs) with the Play-Engine tool, and the other is the intra-object approach using the language of statecharts and Rhapsody as the tool. Integration is carried out using InterPlay, a simulation engine coordinator. Using these tools, we constructed a combined model comprising three modules. One module represents the early lineage of the somatic gonad of C. elegans in LSCs, while a second more detailed module in statecharts represents an interaction between two cells within this lineage that determine their developmental outcome. Using the advantages of the tools, we created a third module representing a set of key experimental data using LSCs. We tested the combined statechart-LSC model by showing that the simulations were consistent with the set of experimental LSCs. This small-scale modular example demonstrates the potential for using similar approaches for verification by exhaustive testing of models by LSCs. It also shows the advantages of these approaches for modeling biology.
Abstract. We describe InterPlay, a simulation engine coordinator that supports cooperation and interaction of multiple simulation and execution tools, thus helping to scale-up the design and development cycle of reactive systems. InterPlay involves two main ideas. In the first, we concentrate on the inter-object design approach involving LSCs and the Play-Engine tool, enabling multiple Play-Engines to run in cooperation. This makes possible the distributed design of large-scale systems by different teams, as well as the refinement of parts of a system using different Play-Engines. The second idea concerns combining the inter-object approach with the more conventional intraobject approach, involving, for example, statecharts and Rhapsody. InterPlay makes it possible to run the Play-Engine in cooperation with Rhapsody, and is very useful when some system objects have clear and distinct internal behavior, or in an iterative development process where the design is implementation-oriented and the ultimate goal is to end up with an intra-object implementation.
Abstract. We describe InterPlay, a simulation engine coordinator that supports cooperation and interaction of multiple simulation and execution tools, thus helping to scale-up the design and development cycle of reactive systems. InterPlay involves two main ideas. In the first, we concentrate on the inter-object design approach involving LSCs and the Play-Engine tool, enabling multiple Play-Engines to run in cooperation. This makes possible the distributed design of large-scale systems by different teams, as well as the refinement of parts of a system using different Play-Engines. The second idea concerns combining the inter-object approach with the more conventional intraobject approach, involving, for example, statecharts and Rhapsody. InterPlay makes it possible to run the Play-Engine in cooperation with Rhapsody, and is very useful when some system objects have clear and distinct internal behavior, or in an iterative development process where the design is implementation-oriented and the ultimate goal is to end up with an intra-object implementation.
Staff exchanges, such as the one described in this report, are intended to facilitate communication and collaboration among scientists and engineers at Department of Energy (DOE) laboratories, in U.S. industry, and academia. Funding support for these exchanges is provided by the DOE, Office of Energy Research, Laboratory Technology Transfer Program. Funding levels for each exchange typically range from $20,000 to $40,000. The exchanges offer the opportunity for the laboratories to transfer technology and expertise to industry, gain a pei'spective on industry's problems, and develop the basis for further cooperative efforts through Cooperative Research and Development Agreements (CRADAs) or other mechanisms. Purpose/Objective The original objective of the exchange between Pacific Northwest Laboratory (PNL) and Chemical Waste Management, Inc. (CWM) was the transfer of PNL technology and expertise in computational chemistry and waste fiow/treatment modeling to CWM. However, as the exchange progressed, this objective was broadened and modified somewhat to better address the needs of CWM. Identification and characterization of a broader portfolio of PNL's environmental remediation technologies with a high potential for rapid application to CWM's businesses became the focus of the exchange. This expansion in objectives resulted in a wider involvement of both CWM and PNL staff in the exchange. Summary of Activities Mr. Dan Barak, the primary CWM exchange participant and other representatives of CWM made several visits to PNL. The first visit was in August 1992. This visit focused on logistics of the staff exchange and included some general discussions about technical areas of interest to CWM. Mr. Barak was also linked into PNL's E-MAIL system to facilitate communication with PNL staff. The second visit occurred over a 2-week peric_din September and October 1992. During this visit, Mr. Barak held technical discussions regarding 14 PNL technologies (listed in Appendix A) that were of potential interest to CWM. In addition, Mr. Barak provided technical input to PNL personnel on a chemical process modeling program that PNL is developing under the sponsorship of the DOE Office of Energy Efficiency and Renewable Energy, Office of Industrial Technologies. Of the 14 technologies discussed, Mr. Barak identified tb_ following as being of the highest interest to CWM: • Six Phase Soil Heating (In-Situ Heating)-a low-temperature approach (-212°F) used in conjunction with soil vapor extraction for removal of volatile and semi-volatile organics from soils • High Energy Corona (Electrical Corona Destruction)-use of a high voltage coronato oxidize organics in gas streams • RAAS/ReOptTM-remedialinvestigationtechnology _d expert system software designedto help remedial investigation/feasibilitystudies • TEESTM-a catalytic techniquethat produces methanefrom biological wastes (cellulose, food processing, etc.) • PST-a process for treating petroleumsludge that uses heat and pressure to break emulsions resulting in distinct oil/water/solid ph...
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