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

Systems biology driven software design for the research enterprise

<p>Abstract</p> <p>Background</p> <p>In systems biology, and many other areas of research, there is a need for the interoperability of tools and data sources that were not originally designed to be integrated. Due to the interdisciplinary nature of systems biology, and its association with high throughput experimental platforms, there is an additional need to continually integrate new technologies. As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools.</p> <p>Results</p> <p>We illustrate an approach, through the discussion of a purpose built software architecture, which allows disparate groups to reuse tools and access data sources in a common manner. The architecture allows for: the rapid development of distributed applications; interoperability, so it can be used by a wide variety of developers and computational biologists; development using standard tools, so that it is easy to maintain and does not require a large development effort; extensibility, so that new technologies and data types can be incorporated; and non intrusive development, insofar as researchers need not to adhere to a pre-existing object model.</p> <p>Conclusion</p> <p>By using a relatively simple integration strategy, based upon a common identity system and dynamically discovered interoperable services, a light-weight software architecture can become the focal point through which scientists can both get access to and analyse the plethora of experimentally derived data.</p

IC-Service: A Service-Oriented Approach to the Development of Recommendation Systems

Recommendation systems have proven to be useful in various application domains. However, current solutions are usually ad-hoc systems which are tightly-coupled with the application domain. We present the IC-Service, a recommendation service that can be included in any system in a loosely coupled way. The implementation follows the principles of service oriented computing and provides a solution to various problems arising in recommendation systems, e.g. to the problem of meta-recommendation systems development. Moreover, when properly configured, the IC-Service can be used by different applications (clients), and several independent instances of the IC-Service can collaborate to produce better recommendations. Service architecture and communication protocols are presented. The paper describes also ongoing work and applications based on the IC-Service

Framework for Interoperable and Distributed Extraction-Transformation-Loading (ETL) Based on Service Oriented Architecture

Extraction. Transformation and Loading (ETL) are the major functionalities in data warehouse (DW) solutions. Lack of component distribution and interoperability is a gap that leads to many problems in the ETL domain, which is due to tightly-coupled components in the current ETL framework. This research discusses how to distribute the Extraction, Transformation and Loading components so as to achieve distribution and interoperability of these ETL components. In addition, it shows how the ETL framework can be extended. To achieve that, Service Oriented Architecture (SOA) is adopted to address the mentioned missing features of distribution and interoperability by restructuring the current ETL framework. This research contributes towards the field of ETL by adding the distribution and inter- operability concepts to the ETL framework. This Ieads to contributions towards the area of data warehousing and business intelligence, because ETL is a core concept in this area. The Design Science Approach (DSA) and Scrum methodologies were adopted for achieving the research goals. The integration of DSA and Scrum provides the suitable methods for achieving the research objectives. The new ETL framework is realized by developing and testing a prototype that is based on the new ETL framework. This prototype is successfully evaluated using three case studies that are conducted using the data and tools of three different organizations. These organizations use data warehouse solutions for the purpose of generating statistical reports that help their top management to take decisions. Results of the case studies show that distribution and interoperability can be achieved by using the new ETL framework

The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*

Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain specialists from web service providers, client software developers, Open Bio* projects, the BioMoby project and researchers of emerging areas where a standard exchange data format is not well established, for an intensive collaboration entitled the BioHackathon 2008. The meeting was hosted by the Database Center for Life Science (DBCLS) and Computational Biology Research Center (CBRC) and was held in Tokyo from February 11th to 15th, 2008. In this report we highlight the work accomplished and the common issues arisen from this event, including the standardization of data exchange formats and services in the emerging fields of glycoinformatics, biological interaction networks, text mining, and phyloinformatics. In addition, common shared object development based on BioSQL, as well as technical challenges in large data management, asynchronous services, and security are discussed. Consequently, we improved interoperability of web services in several fields, however, further cooperation among major database centers and continued collaborative efforts between service providers and software developers are still necessary for an effective advance in bioinformatics web service technologies