The Institute for Systems Biology (ISB) seeks to develop revolutionary approaches to understanding of biological complexity and the analysis of biological systems. The ISB brings together a multidisciplinary group of scholars and scientists, from biologists, mathematicians and engineers, to computer scientists and physicists, in an interactive and collaborative environment.

The Adaptive Data Management Service Architecture has been designed to support the needs of researchers at the ISB. Its main goals are to:

• support ad-hoc software development within the research enterprise
• facilitate the integration of large heterogeneous data
• enable collaboration between individual researchers and consortiums

Addama (a-duh-mah) provides a variety of REST+JSON web services for integrating web applications, visualizations, data management systems, and computational tools. It also offers a platform for the rapid development and deployment of modern web applications using security and authentication interfaces provided by Google App Engine. Addama software components are used at ISB to support many ad-hoc collaborations, and several large projects.

Addama is built upon existing Open Source Software from trusted sources (e.g. Apache Software Foundation, Spring Framework, Google Code). Its design is based on the latest web and enterprise software principles.

NOTICE: We have migrated our source code repository from SVN to Mercurial (HG). The SVN repository is still available at http://addama.googlecode.com/svn along with tags and branches. New development will be managed through Mercurial.

Addama 3.0 Release

• Simplified service registration interface
• Platform for rapid deployment of web applications
• New user interfaces to browse and query data, and examples for web application developers
• Simplified user access control
• Improved chromosome datasource index service
• Support for RSS feeds and notification channels (push over web sockets)

New downloads and documentation are currently being produced. Contact us for information on this release

Demo

• The latest version of Addama has been deployed to this appspot https://addama-systemsbiology-public.appspot.com

Questions, Comments, Issues

Addama is an open source project that is made available to the community AS IS. We are proud to provide this software to the community. We welcome any input and will prioritize any critical issues that are submitted. We appreciate any contributions that will be generally useful to systems biology, and to the scientific research community.

If you would like to submit a feature or bug request, please use the Issues section of this project.

For more information, please contact codefor@systemsbiology.org.