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

MSUO Information Technology and Geographical Information Systems: Common Protocols & Procedures. Report to the Marine Safety Umbrella Operation

The Marine Safety Umbrella Operation (MSUO) facilitates the cooperation between Interreg funded Marine Safety Projects and maritime stakeholders. The main aim of MSUO is to permit efficient operation of new projects through Project Cooperation Initiatives, these include the review of the common protocols and procedures for Information Technology (IT) and Geographical Information Systems (GIS). This study carried out by CSA Group and the National Centre for Geocomputation (NCG) reviews current spatial information standards in Europe and the data management methodologies associated with different marine safety projects. International best practice was reviewed based on the combined experience of spatial data research at NCG and initiatives in the US, Canada and the UK relating to marine security service information and acquisition and integration of large marine datasets for ocean management purposes. This report identifies the most appropriate international data management practices that could be adopted for future MSUO projects

Just below the surface: developing knowledge management systems using the paradigm of the noetic prism

In this paper we examine how the principles embodied in the paradigm of the noetic prism can illuminate the construction of knowledge management systems. We draw on the formalism of the prism to examine three successful tools: frames, spreadsheets and databases, and show how their power and also their shortcomings arise from their domain representation, and how any organisational system based on integration of these tools and conversion between them is inevitably lossy. We suggest how a late-binding, hybrid knowledge based management system (KBMS) could be designed that draws on the lessons learnt from these tools, by maintaining noetica at an atomic level and storing the combinatory processes necessary to create higher level structure as the need arises. We outline the “just-below-the-surface” systems design, and describe its implementation in an enterprise-wide knowledge-based system that has all of the conventional office automation features

1st INCF Workshop on Sustainability of Neuroscience Databases

The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability

UK utility data integration: overcoming schematic heterogeneity

In this paper we discuss syntactic, semantic and schematic issues which inhibit the integration of utility data in the UK. We then focus on the techniques employed within the VISTA project to overcome schematic heterogeneity. A Global Schema based architecture is employed. Although automated approaches to Global Schema definition were attempted the heterogeneities of the sector were too great. A manual approach to Global Schema definition was employed. The techniques used to define and subsequently map source utility data models to this schema are discussed in detail. In order to ensure a coherent integrated model, sub and cross domain validation issues are then highlighted. Finally the proposed framework and data flow for schematic integration is introduced

COTS GIS Integration and its Soap-Based Web Services

In the modern geographic information systems, COTS software has been playing a major role. However, deploying heterogeneous GIS software has the tendency to form fragmented data sets and to cause inconsistency. To accomplish data consolidation, we must achieve interoperability between different GIS tools. In my thesis project, I developed Vector and Raster Data Adapters to implement the spatial data consolidation. I deployed ArcIMS to publish the spatial data and metadata onto Internet. Furthermore, the SOAP-Based GIS Web services are implemented to achieve the enterprise information system integration. The contribution of ours in this project is we have streamlined the COTS GIS server, the J2EE coordinator server, the web service provider components, and the COTS web publishing tools into a hybrid web service architecture, in which the enterprise information system integration, the web publishing, and the business-to business online services are uniformed

COTS GIS Integration and its Soap-Based Web Services

In the modern geographic information systems, COTS software has been playing a major role. However, deploying heterogeneous GIS software has the tendency to form fragmented data sets and to cause inconsistency. To accomplish data consolidation, we must achieve interoperability between different GIS tools. In my thesis project, I developed Vector and Raster Data Adapters to implement the spatial data consolidation. I deployed ArcIMS to publish the spatial data and metadata onto Internet. Furthermore, the SOAP-Based GIS Web services are implemented to achieve the enterprise information system integration. The contribution of ours in this project is we have streamlined the COTS GIS server, the J2EE coordinator server, the web service provider components, and the COTS web publishing tools into a hybrid web service architecture, in which the enterprise information system integration, the web publishing, and the business-to business online services are uniformed