COEL: A Web-based Chemistry Simulation Framework

The chemical reaction network (CRN) is a widely used formalism to describe macroscopic behavior of chemical systems. Available tools for CRN modelling and simulation require local access, installation, and often involve local file storage, which is susceptible to loss, lacks searchable structure, and does not support concurrency. Furthermore, simulations are often single-threaded, and user interfaces are non-trivial to use. Therefore there are significant hurdles to conducting efficient and collaborative chemical research. In this paper, we introduce a new enterprise chemistry simulation framework, COEL, which addresses these issues. COEL is the first web-based framework of its kind. A visually pleasing and intuitive user interface, simulations that run on a large computational grid, reliable database storage, and transactional services make COEL ideal for collaborative research and education. COEL's most prominent features include ODE-based simulations of chemical reaction networks and multicompartment reaction networks, with rich options for user interactions with those networks. COEL provides DNA-strand displacement transformations and visualization (and is to our knowledge the first CRN framework to do so), GA optimization of rate constants, expression validation, an application-wide plotting engine, and SBML/Octave/Matlab export. We also present an overview of the underlying software and technologies employed and describe the main architectural decisions driving our development. COEL is available at http://coel-sim.org for selected research teams only. We plan to provide a part of COEL's functionality to the general public in the near future.Comment: 23 pages, 12 figures, 1 tabl

Knowledge Discovery in the SCADA Databases Used for the Municipal Power Supply System

This scientific paper delves into the problems related to the develop-ment of intellectual data analysis system that could support decision making to manage municipal power supply services. The management problems of mu-nicipal power supply system have been specified taking into consideration modern tendencies shown by new technologies that allow for an increase in the energy efficiency. The analysis findings of the system problems related to the integrated computer-aided control of the power supply for the city have been given. The consideration was given to the hierarchy-level management decom-position model. The objective task targeted at an increase in the energy effi-ciency to minimize expenditures and energy losses during the generation and transportation of energy carriers to the Consumer, the optimization of power consumption at the prescribed level of the reliability of pipelines and networks and the satisfaction of Consumers has been defined. To optimize the support of the decision making a new approach to the monitoring of engineering systems and technological processes related to the energy consumption and transporta-tion using the technologies of geospatial analysis and Knowledge Discovery in databases (KDD) has been proposed. The data acquisition for analytical prob-lems is realized in the wireless heterogeneous medium, which includes soft-touch VPN segments of ZigBee technology realizing the 6LoWPAN standard over the IEEE 802.15.4 standard and also the segments of the networks of cellu-lar communications. JBoss Application Server is used as a server-based plat-form for the operation of the tools used for the retrieval of data collected from sensor nodes, PLC and energy consumption record devices. The KDD tools are developed using Java Enterprise Edition platform and Spring and ORM Hiber-nate technologies

A multiarchitecture parallel-processing development environment

A description is given of the hardware and software of a multiprocessor test bed - the second generation Hypercluster system. The Hypercluster architecture consists of a standard hypercube distributed-memory topology, with multiprocessor shared-memory nodes. By using standard, off-the-shelf hardware, the system can be upgraded to use rapidly improving computer technology. The Hypercluster's multiarchitecture nature makes it suitable for researching parallel algorithms in computational field simulation applications (e.g., computational fluid dynamics). The dedicated test-bed environment of the Hypercluster and its custom-built software allows experiments with various parallel-processing concepts such as message passing algorithms, debugging tools, and computational 'steering'. Such research would be difficult, if not impossible, to achieve on shared, commercial systems

A Pure Java Parallel Flow Solver

In this paper an overview is given on the "Have Java" project to attain a pure Java parallel Navier-Stokes flow solver (JParNSS) based on the thread concept and remote method invocation (RMI). The goal of this project is to produce an industrial flow solver running on an arbitrary sequential or parallel architecture, utilizing the Internet, capable of handling the most complex 3D geometries as well as flow physics, and also linking to codes in other areas such as aeroelasticity etc. Since Java is completely object-oriented the code has been written in an object-oriented programming (OOP) style. The code also includes a graphics user interface (GUI) as well as an interactive steering package for the parallel architecture. The Java OOP approach provides profoundly improved software productivity, robustness, and security as well as reusability and maintainability. OOP allows code construction similar to the aerodynamic design process because objects can be software coded and integrated, reflecting actual design procedures. In addition, Java is the programming language of the Internet and thus Java is the programming language of the Internet and thus Java objects on disparate machines or even separate networks can be connected. We explain the motivation for the design of JParNSS along with its capabilities that set it apart from other solvers. In the first two sections we present a discussion of the Java language as the programming tool for aerospace applications. In section three the objectives of the Have Java project are presented. In the next section the layer structures of JParNSS are discussed with emphasis on the parallelization and client-server (RMI) layers. JParNSS, like its predecessor ParNSS (ANSI-C), is based on the multiblock idea, and allows for arbitrarily complex topologies. Grids are accepted in GridPro property settings, grids of any size or block number can be directly read by JParNSS without any further modifications, requiring no additional preparation time for the solver input. In the last section, computational results are presented, with emphasis on multiprocessor Pentium and Sun parallel systems run by the Solaris operating system (OS)