Welcome to the Workbench Framework Home Page
The Workbench Framework is designed to provide a "content management system on steroids" for Biologists. In other words,we wanted to capture the configurability and functionality of content management systems like Drupal and Wordpress so scientists can manage their data and communicate easily, while at the same providing access to as many public data and software resources as possible. The result is a flexible, configurable software environment that presents user data in an intellectual context. We have constructed this software in service of a project called SWAMI: the Next Generation Biology Workbench. However, by design, the Workbench Framework is a scalable and portable architecture, so it can be used a point of departure in creating other Workbenches for other Biology groups.. The Workbench Framework has now been used to launch a second portal, the CIPRES Portal V 2.0, proof of concept for the flexibility of the architecture with respect to toolkit and community served.
We have focused on finding ways to engage the community of biologist/developers, and to give biologists who are not developers the opportunity to participate in the creation of portals. By aggregating intellectual capital and computational resources in a single location, we hope to promote formation of on-line communities, make it easier for scientists to do their work, and to improve the speed communication and distribution of resources throughout the community. This kind of engagement will allow users to access the full depth and breadth of community experience.
Our first effort to achieve community engagement was to create tools that allow anyone in the community to create and/or edit a portal interface for any analytical tool in a given portal. Just as Wikipedia provides the community with tools to create and edit any topic in a public forum, we created a tool called webtooldev to allow users to create and/or edit any of the interfaces in any portal built with the Workbench Framework (currently SWAMI or CIPRES Portal 2.0). Once a finished interface is created, it can be vetted and exposed immediately in a production environment and supported by our group, just as is done in Wikipedia. The resulting interfaces will also be compatible with any installation running PISE XML (with one or two minor adjustments).
A high level description of the Workbench Framework has been presented. The current implementation consists of a Core Software Development Kit that is highly generic in the way it manages data searching and tools. The SDK manages specific data sets and analytical tools using information recorded in a central registry. A schematic diagram of the SDK can be viewed here. The NGBW SDK is designed to be easily deployed in new environments, so that developers can customize its features to their home environment. Our goal is to engage with the community, rather than to hand down edicts. Accordingly, we are happy to receive input and advice on how we could do better, and are receptive to forming partnerships with other groups.
The Core architecture will support a wide variety of View Layers. We currently offer an interface based on Apache Struts2. It is served via a Tomcat installation, which meets our current needs with a minimum of overhead. The interfaces used in our view layer were derived from the PISE project XML documents. Our current process is to transform PISE XML into NGBW XML, which is then converted into .jsp pages. If we add a tool that does not have a PISE interface, we create the new interface in PISE XML format, and then pull it forward into NGBW format. The reason for this is pragmatic: our PISE XML interfaces will be returned to the PISE project, and will be more easily pulled forward into the Mobyle project. Our pages are XHTML/CSS compliant.
Our current RDBMS solution is MySQL, which is used for storing user data items. Currently we store data from public providers in flat file format, and index it using the Apache Lucene engine. The resulting indices are used for text string searching of the flat files. We are still considering data integration solutions using RDBMS, but so far the overhead in keeping data current in relational format has been too great for our resources.
Our routine development is done in a Subversion repository. Access to our software and to information about our software will be provided upon request. We can also provide API's and assistance in mounting new tools in our workbench, or help you understand how to do it in yours. Documentation to help in such efforts is being created now, and will be posted here.
Who are we?
The Workbench Framework is part of an ongoing effort to create web portals for biology that are community specified, and that promote a closer relationship between developers, computational biologists, and biological researchers.The Workbench Framework was built with funding from NIH 5R01GM073931. The webtooldev server was created under funding provided by NSF EF 03-31648 and NIH 5R01GM073931.