Swami, The Next Generation Biology Workbench

Category Cross-Omics>Knowledge Bases/Databases/Tools

Abstract Swami, The Next Generation Biology Workbench (NGBW) is a free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics.

The NGBW is a re-engineering of the Biology Workbench which was designed by Shankar Subramaniam and his group to provide an integrated environment where tools, user data, and public data resources can be easily accessed.

The NGBW employs best practices from industry and academia to provide high performance analytical tools to the research and education communities.

It is designed to be an organic tool that evolves with the needs of the community. The Workbench project welcomes input and contributions from the general community.

SWAMI for Users -- The NGBW Project was conceived by a domain Biologist as a tool to meet the needs of educators, students, and researchers using modern but well understood and reliable technologies.

Since its inception, the project has been based on a User-guided development model.

In implementing the NGBW, the manufacturer strives to make the development flow from user requirements, and to make choices driven by user needs rather than by specific development goals.

Further, the manufacturer believes that 'Information Technology' is a necessary component of all modern research, and so must be made available to users at all levels of training, independent of location and with minimal barriers to entry.

SWAMI for Developers -- The SWAMI project is designed to meet the needs of Users. At the same time, it is designed to be scalable and portable. Accordingly, it is a pure JAVA implementation that is easy to install, easy to add to, and easy to maintain.

The manufacturer employs open source or free-to-academic tools whenever possible, to minimize the barrier to entry for developers.

The current implementation consists of a Core Software Development Kit (SDK) 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.

The NGBW SDK is designed to be easily deployed in new environments, so that developers can customize its features to their home environment.

The Core architecture will support a wide variety of View Layers. The manufacturer currently offers an interface based on Apache Struts 2 (an extensible framework for creating enterprise-ready Java web applications).

It is served via a Tomcat installation, which meets the manufacturer’s current needs with a minimum of overhead.

The interfaces used in the manufacturers ‘view layer’ were derived from the PISE (a tool to generate Web interfaces for Molecular Biology programs) project Extensible Markup Language (XML) documents.

The manufacturer’s current process is to transform PISE XML into NGBW XML, which is then converted into Java Server Pages (.jsp pages). The manufacturer’s pages are Extensible Hypertext Transfer Markup Language/Cascading Style Sheets (XHTML/CSS) compliant.

The manufacturer’s current Relational Database Management System (RDBMS) solution is MySQL, which is used for storing user data items.

Currently the manufacturer stores data from public providers in a flat file format, and indexes it using the Apache Lucene (a high-performance, full-featured text search engine library written entirely in Java) engine.

The resulting indices are used for text string searching of the flat files.

The manufacturer’s routine development is done in a Subversion (an open source version control system) repository. Access to the manufacturer’s software and to information about this software will be provided upon request.

The manufacturers can also provide Application Programming Interfaces (APIs) and assistance in mounting new tools in the 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 at the manufacturer’s web-site.

SWAMI Toolkit consists of --

1) Nucleic Acid Sequence Tools.

2) Protein Sequence Tools.

3) Phylogeny/Alignment Tools.

4) Structure Tools.

SWAMI Data Resources currently consist of --

1) GenBank® - the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences.

2) Uniprot - a comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

3) Protein Data Bank - an Information Portal to Biological Macromolecular Structures.

System Requirements

Browser compatibility

The authors intend the NGBW project to be compatible with all browsers that have a significant representation in the user base. They currently support the following browsers shown below, and test routinely on them. There are known issues with the Opera browser.


Manufacturer Web Site Swami

Price A free resource for research and education in Bioinformatics, Genomics, Proteomics, and Phylogenetics.

G6G Abstract Number 20247

G6G Manufacturer Number 102356