Part V: Appendix (Section 14) UK Grid Services and Activities
A.7. Material from Pilot Projects
A.7.3 myGrid
myGrid Component Inventory
Document Class: Note
Author: Nick Sharman
Institution: University of Manchester
Date: 2003-07-29
Pages: 115
A.7.3.1Introduction
This note describes the components (including clients, services, APIs and tools) that we expect to produce in the myGrid project.
A.7.3.2Generic e-Science Components
A.7.3.2.1Service Registry
The myGrid Service Registry federates a set service registries of interest to a (virtual) organization. The federated registries may be general-purpose or specific to a particular (scientific) community. It is thus a single point of contact for service discovery for the virtual organization.
The myGrid Service Registry supports the widely-used UDDI interface, extended by the ability to attach and retrieve additional metadata to service registrations and their elements (such as particular operations). The myGrid Service Registry allows its users to establish multiple views that provide access to a user-defined subset of the registered services. These views can be specific to individual scientists (thus supporting
personalization) or to further, more specialized, discovery services. A.7.3.2.2
Semantic Service Discovery Service
The myGrid Semantic Service Discovery Service is a specialized discovery service that establishes a view over the myGrid Service Registry to capture services that support a semantic annotation under some set of OWL ontologies. It allows its users to search for services that satisfy some concept expressed as an OWL expression. A.7.3.2.3
Service Ontology
The myGrid Service Ontology is an OWL ontology that allows its users to describe Web and Grid services. For practical use, this ontology will need to be combined with one or more domain ontologies: the myGrid project will provide an initial bioinformatics/biology
A.7.3.2.4
Service Description & Publication Tool
The myGrid Service Description & Publication Tool allows it users to construct semantic service descriptions in terms of some ontology and attach them to new or existing service registrations in the myGrid Service Registry. A.7.3.2.5
Notification Service
The myGrid Notification Service is a general purpose topic-based publish-and-subscribe intermediary. It will be used in myGrid to support workflow progress monitoring and service registration and database update
notifications.
A.7.3.2.6
Workflow Enactment Service
The myGrid Workflow Enactment Service supports the execution of e-Science processes as possibly long- running workflows. The service:
•
Captures an execution trace and intermediate results to create a record of provenance for its results•
Allows the composed service providers to be discovered dynamically at execution timeA.7.3.2.7
Workflow Editor
The myGrid Workflow Editor is a tool that allows the graphical creation and modification of workflow
definitions that can be executed by the myGrid Workflow Enactment Service. It serves as both a standalone tool and as a plugin for the myGrid e-Science Workbench.
A.7.3.2.8
Information Repository
The myGrid Information Repository manages the information (data & metadata) for an organization or
organizational unit. The stored information is organized into projects and experiments. The myGrid Information Repository provides facilities similar to a networked filestore. However, all entities stored in the repository can be qualified by a semantic (OWL-based) concept and an indication of concrete format, and can be described and related by annotation objects that are themselves first-class entities. Other entity types recognized by the Repository include workflow definitions and provenance records.
A.7.3.2.9
E-Science Gateway Service
The myGrid e-Science Gateway Service provides applications with a unified API and point of access to an organization or organizational unit’s instances of the key myGrid services, including the Service Registry, Workflow Enactment Service and Information Repository.
The clients of the tool can include domain-specific applications as well as generic e-Science applications such as the myGrid e-Science Workbench and e-Science Web Portal.
A.7.3.2.10
E-Science Workbench
The myGrid e-Science Workbench is a rich interactive tool (based on the NetBeans framework,
www.netbeans.org) through which a scientist interacts with myGrid and other Web and Grid services and the data and metadata in the myGrid Information Repository via the e-Science Gateway Service.
A.7.3.2.11
E-Science Web Portal
The myGrid e-Science Web Portal is a less-capable alternative to the e-Science Workbench. It supports a subset of the Workbench’s functionality and can be used where remote access or a zero-footprint solution is useful (for example, via PDAs or mobile phones).
A.7.3.2.12
Distributed Query Processing Service
The myGrid Distributed Query Processing Service (developed jointly with the North-East Regional e-Science Centre) provides on OGSA-DAI-based interface that supports distributed queries over any SQL and ODMG OQL-capable data sources that themselves support the OGSA-DAI interface. In myGrid, it will be used to federate myGrid Information Repositories owned by members of a virtual organization, and to execute queries involving any collection of Information Repositories and domain-specific databases.
A.7.3.2.13
E-Science Application Framework
The myGrid e-Science Application Framework is a component model for flexible, simple and future-proof deployment and use of services on the Grid. It comprises:
•
A server-side API that allows a business logic to be deployed according to different standards; our implementation is based on Enterprise Java Beans and we deploy services as Web Services, OGSA Grid Services and EJBs•
A nested container model allowing deployers to identify non-business-logic functionality that needs to be deployed in order to facilitate the integration of the service in virtual organizationsA.7.3.3Bioinformatics-specific Components
A.7.3.3.1Bioinformatics Ontology
The myGrid Bioinformatics Ontology, is an OWL ontology that, when composed with the myGrid Service Ontology, allows users to describe and discover services, workflows and data by their semantics.
A.7.3.3.2
SOAPLAB
SOAPLAB is a set of Web Services that provide programmatic access to applications on remote systems. Its interface is based on the OMG’s CORBA-based Biomolecular Sequence Analysis specification, and in myGrid is used to give access to bioinformatics applications such as the EMBOSS suite (see
www.hgmp.mrc.ac.uk/Software/EMBOSS).
A.7.3.4Miscellaneous Components
A.7.3.4.1AntMerge: build-file construction tool
The myGrid project, like many other Java-based projects, uses Ant to execute reliable and reproducible component builds (see http://ant.apache.org). Ant’s build-files can be come complex, so to reduce the effort needed to develop and maintain robust build files over the myGrid component set, the project has developed a tool to compose build files from a suite of generic build file parts and a component-specific part.