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The assumption is that making such recommendations will serve to focus the developers' effort on a smaller number of packages. The primary motivation here was to select or recommend certain packages over others specifically within the GMOD context. In late 2006 the GMOD developers took note of the large number of middleware packages in use and elected to embark on a short-term study to evaluate and compare these packages. However, a consensus view has not emerged with respect to middleware, and there are certainly a number of different middleware packages that have been used in the GMOD world, coming from within this world and from the larger world of open source. Despite this diversity certain applications and schemas have emerged as key supported components in GMOD, such as the GBrowse application and the Chado schema, to name just two.

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This applies to applications, database schemas, as well as to middleware, a software layer that mediates the exchange of data between the applications and the databases. One of the key characteristics of the GMOD software project is the variety of approaches and components that it supports.

Specific examples of how one would use a given middleware package.

Strengths & weaknesses of different Middleware packages.To generate this central reference document for Middleware projects, including:.To guide GMOD to a uniform Middleware layer.To facilitate discussion on the best methods.To educate GMOD programmers on methods and practices for Middleware.This one day meeting had the following general goals: This document represents the consensus of the workshop and shows the individual presentations.Ī group of some 50 GMOD developers gathered at the annual meeting to discuss middleware. The attendees reassembled in a general discussion group to discuss the presentations and to develop a consensus statement. Each presenter described the features of the package, both positive and negative, and showed how the package would be used to address a specific set of test problems.

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Such recommendations will focus the efforts of the MODs on specific packages and lead to code re-use and more feature-rich middleware.Īfter an introductory presentation attendees listened to a series of presentations on the different Middleware packages. The workshop attendees were tasked to make specific recommendations. On January 19 2007, representatives of the major model organism databases (MODs) and other interested parties met to discuss and compare Middleware packages used by developers working for the MODs. Middleware for Chado databases Participants

4.2.5 Presentation by Pinglei Zhou and Josh Goodman.

We recommend that implementors of Perl-based GMOD tools seriously consider Modware for their middleware interface to Chado, and that the implementors of Java-based tools collaborate to create a Java API that parallels Modwares.

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The hand-edited layer will serve the common cases in detail while the auto-generated layer retains the full flexibility of the Chado schema for the cases that fall outside the hand-edited API. The approach taken by Modware, which starts from an auto-generated interface and then adds a hand-coded API layer, is both comprehensible and powerful. The consensus from the meeting was that while fully automatic tools are convenient, that there is considerable value in creating a hand-crafted predictable API that reflects the biological data closely. Of the tools presented, Modware, built on top of Chado::AutoDBI, was the most mature and feature-rich. The second class involved hand-coding an API to create an object-oriented interface to Chado. The first class, which includes Hibernate (Java), iBatis (Java), and Chado::AutoDBI (Perl) examines the relational schema and configuration files to create the middleware automatically, or create a relational schema and middleware automatically from a data model ( InterMine). This meeting was designed to review the experiences each group has had with its particular solution and to recommend a 'best practice.'Īll participants had developed some type of Object-Relational Mapping (ORM) tool. This is a summary and detailed notes from the Chado Middleware Bake Off held at the January 2007 GMOD Meeting.Īlthough GMOD uses the Chado schema for its underlying database, each group has developed a separate interface to their databases.