DAPPER: a data-mining resource for protein-protein interactions.

BACKGROUND: The identification of interaction networks between proteins and complexes holds the promise of offering novel insights into the molecular mechanisms that regulate many biological processes. With increasing volumes of such datasets, especially in model organisms such as Drosophila melanogaster, there exists a pressing need for specialised tools, which can seamlessly collect, integrate and analyse these data. Here we describe a database coupled with a mining tool for protein-protein interactions (DAPPER), developed as a rich resource for studying multi-protein complexes in Drosophila melanogaster. RESULTS: This proteomics database is compiled through mass spectrometric analyses of many protein complexes affinity purified from Drosophila tissues and cultured cells. The web access to DAPPER is provided via an accelerated version of BioMart software enabling data-mining through customised querying and output formats. The protein-protein interaction dataset is annotated with FlyBase identifiers, and further linked to the Ensembl database using BioMart's data-federation model, thereby enabling complex multi-dataset queries. DAPPER is open source, with all its contents and source code are freely available. CONCLUSIONS: DAPPER offers an easy-to-navigate and extensible platform for real-time integration of diverse resources containing new and existing protein-protein interaction datasets of Drosophila melanogaster.This work was supported financially by grants from the Cancer Research UK (CRUK), the Biotechnology and Biological Sciences Research Council and the Medical Research Council to DMG (C3/A11431, BB/I013938/1, G1001696), by a Cancer Research UK Career Development Fellowship to YK (C40697/A12874), and by Cancer Research UK grants to PPD (C12296/A8039 and C12296/A12541). ZL is on leave from the Biological Research Centre of the Hungarian Academy of Sciences (Institute of Biochemistry, Szeged, Hungary) and was supported by a Long-Term Fellowship of the Federation of European Biochemical Societies (FEBS)

1st INCF Workshop on NeuroImaging Database Integration

The goal of this meeting was to map existing neuroimaging databases, particularly databases containing primary data, and to identify mechanisms that could facilitate integrated use of such databases, including possible fusion of databases. The report provides an overview of existing neuroimaging databases that were discussed during the workshop and examines the feasibility of database federations. The report includes several recommendations for future developments

Modular HLA RTI services: The GRIDS approach

The Generic Runtime Infrastructure for Distributed Simulation (GRIDS) has been developed to investigate modularity issues in distributed simulation. It could be argued that although the HLA RTI is a widespread solution to distributed simulation, it cannot include all possible services. This paper investigates an approach to extending the distributed simulation services available in the HLA RTI. One example of this is bridging support for HLA/DIS legacy integration. This paper therefore presents GRIDS, how GRIDS can be used to provide modular service support for the HLA RTI, and a case study on legacy integration to demonstrate our approach

Empirical analysis of the integration activity of business structures in the regions of Russia

The article investigates the integration activity of business structures in the regions of Russia. A wide variety of approaches to study the problems and prospects of economic integration and the current dispute on the role of integration processes in the regional economic development determined the complexity in the review of the concepts «integration» and «integration activities» in order to form objective conditions to analyse the integration activity of business structures in the Russian regions. The monitoring of the current legal system of the Russian Federation carried out in the area of statistics and compiling statistical databases on mergers and acquisitions showed the absence of formal executive authority dealing with the compiling collections of information on the integration activity at the regional level. In this connection, the data of Russian information and analytical agencies made the information base of the research. As research tools, we used methods of the analysis of structural changes, methods of the analysis of economic differentiation and concentration, methods of non-parametric statistics. The article shows the close relationship between the social and economic development of the subjects of Russia and integrated business structures functioning on its territory. An investigation of the integration activity structure and dynamics in the subjects of the Russian Federation based on statistical data for the period from 2003 to 2012 has revealed the increasing heterogeneity of the integration activity of business structures in the regions of Russia. The hypothesis of a substantial divergence of the mergers and acquisitions of corporate structures in Russian regions has been confirmed by high values of the Gini coefficient, the Herfindahl index and the decile coefficient of differentiation. The research results are of practical importance, since they can be used to improve the existing federal programs aimed at evening-out disproportions in the social and economic development of Russian regions. The qualitative infrastructure formation of the merger and acquisition market and the development of regional policies in order to increase the competitiveness of Russian regions can be possible on the basis of the analysis presented

Security oriented e-infrastructures supporting neurological research and clinical trials

The neurological and wider clinical domains stand to gain greatly from the vision of the grid in providing seamless yet secure access to distributed, heterogeneous computational resources and data sets. Whilst a wealth of clinical data exists within local, regional and national healthcare boundaries, access to and usage of these data sets demands that fine grained security is supported and subsequently enforced. This paper explores the security challenges of the e-health domain, focusing in particular on authorization. The context of these explorations is the MRC funded VOTES (Virtual Organisations for Trials and Epidemiological Studies) and the JISC funded GLASS (Glasgow early adoption of Shibboleth project) which are developing Grid infrastructures for clinical trials with case studies in the brain trauma domain

Federation views as a basis for querying and updating database federations

This paper addresses the problem of how to query and update so-called database federations. A database federation provides for tight coupling of a collection of heterogeneous component databases into a global integrated system. This problem of querying and updating a database federation is tackled by describing a logical architecture and a general semantic framework for precise specification of such database federations, with the aim to provide a basis for implementing a federation by means of relational database views. Our approach to database federations is based on the UML/OCL data model, and aims at the integration of the underlying database schemas of the component legacy systems to a separate, newly defined integrated database schema. One of the central notions in database modelling and in constraint specifications is the notion of a database view, which closely corresponds to the notion of derived class in UML. We will employ OCL (version 2.0) and the notion of derived class as a means to treat (inter-)database constraints and database views in a federated context. Our approach to coupling component databases into a global, integrated system is based on mediation. The first objective of our paper is to demonstrate that our particular mediating system integrates component schemas without loss of constraint information. The second objective is to show that the concept of relational database view provides a sound basis for actual implementation of database federations, both for querying and updating purposes.