GNV-5 | Integrated Bioinformatics | Node UMA In The INB

GNV-5 | Integrated Bioinformatics | Node UMA in the INB

Our contribution have been focused in the design, development, and testing of the software architecture for data, services and computational resources integration at the INB.

The main lines of the system architecture were specified, addressing the integration problem with the design of a simple but powerful, dynamic and extensible platform to represent, discover, integrate and process the different source of data in a distributed computational Web-services environment.

Description of input/output objects is coordinated and standardized by means of an object-ontology in such a way that services can inter-connect, wiring natural bioinformatics workflows. Automatic interfaces and help system builders have been incorporated into the architecture to standardize and facilitate user communication.

Novel functionality in the area has been incorporated into the architecture to allow data persistence, user authentication, task scheduling, monitoring of long-CPU consuming tasks, workflows and collection of objects for massive use of services, including automatic notification, help and training systems.

PROJECT DETAILS

The GNV-5 contribution has been focused in the design, development, and testing of the software architecture for data, services and computational resources integration at the INB. The main lines of work at GNV-5 have been:

  1. Architecture design
  2. Implementation of the working environment
  3. Elaboration of technical reports about system design
  4. The INB Client development
    1. The user perspective
    2. Administration modules
  5. Grid Management
  6. Services wiring and inter-communication functionality
  7. Workflows
  8. Extension to the BioMOBY protocol: asynchronism, mirroring, error handling, etc.
  9. Quality control procedures

During the first phase of the project (2003-2006) GNV-5 specified the main lines of the system architecture, adressing the integration problem with the design of a simple but powerful, dynamic and extensible platform to represent, recover, process, integrate and discover information. To integrate geographically dispersed resources a Grid-enabled system has been built on top of BioMOBY API, offering a view of the system databases as a single data source with services readily available for enhancing data processing.

Description of input/output objects is coordinated and standardized by means of an object-ontology in such a way that services can inter-connect, wiring natural bioinformatics workflows.

Automatic interfaces and help system builders have been incorporated into the architecture to standardize and facilitate user communication.

Novel functionality in the area has been incorporated into the architecture to allow data persistence, user authentication, task scheduling, monitoring of long-CPU consuming tasks, workflows and collection of objects for massive use of services, including automatic notification, help and training systems.

The system has been implemented and diverse prototypes are available (see links).

To meet the objectives of the INB project we have coordinated an internal muti-disciplinary team composed by several groups of the University of Malaga. The Khaos group from the Computer Sciences dept. covers the ‘semantic web’ side of the project; and from the biological side two groups; the Molecular biology and biotechnology of plants and the Biochemistry Molecular Bases of Cell Proliferation group both at the Dept. of Molecular Biology and Biochemistry; and the Molecular Genetics of plant pathogens group at the Dept. of Cellular Biology and Genetics; cover several important aspect in the development of the platform; especially from the user side they help to obtain a friendly and intuitive interface; and also supervise the ontology committee for a better organization of services and objects. Finally, the computer architecture department acts as coordinator of the group, host the hardware and provide the adequate technology and software development environment for production.

ADITIONAL INFORMATION

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