kbase

About the Knowledgebase

Final Implementation Plan now available.

Download document - Final Implementation Plan
Download - Executive Summary

What is the purpose of this website?

This interactive wiki is a forum for the research community to help define requirements for the U.S. Department of Energy (DOE) Systems Biology Knowledgebase (Kbase). Users are encouraged to click on the "How to Participate" link to join the conversation, post comments, and help develop the Knowledgebase. Click on the "Conceptual Design Report" drafting page to see the current status and contribute.

What is the Systems Biology Knowledgebase (Kbase)?

The DOE Office of Biological and Environmental Research (BER) is supporting the development of the Systems Biology Knowledgebase, a cyberinfrastructure to facilitate a new level of scientific inquiry by serving as a central component for the integration of modeling, simulation, experimentation, and bioinformatic approaches. The Knowlegebase would focus on DOE science-application areas and meeting the needs of the DOE Genomic Science program, yet it also would be widely and easily applicable to all systems biology research. In addition to supporting data storage, retrieval, and management capabilities, Kbase also would enable new knowledge acquisition and management, through free and open access to data, analysis tools, and information for the scientific research community. Kbase, therefore, must serve multiple roles, including:

A repository of data and results from high-throughput experiments.
A collection of tools to derive new insights through data synthesis, analysis, and comparison.
A framework to test scientific understanding.
A heuristic capability to improve the value and sophistication of further inquiry.
A foundation for prediction, design, manipulation, and ultimately, engineering of biological systems.

See the Project Plan for more information about the Knowledgebase and the principles guiding its development.

How will the Knowledgebase be developed?

This project will document the requirements necessary for the subsequent development of the Systems Biology Knowledgebase. A series of workshops, pilot projects, and activities exploring options for hardware infrastructure will be used to determine the scope, cost, and schedule for the Knowledgebase.

1. Workshops. To develop a successful open informatics endeavor for DOE systems biology, this project will identify all user groups (e.g., plant and microbial genomic researchers, bioinformaticians, computer scientists, database developers, software engineers, etc.) and elicit their expectations in regards to the opportunities and requirements for developing and managing Kbase. The workshops will also address the cultural transition the informatics community will need to make from individual project based efforts toward research community based informatics.

2. Pilot Projects. In order to explore some possible Systems Biology Knowledgebase implementations and architectures, as well as demonstrate and characterize the range of computational challenges facing Genomic Science projects, part of this project will support the development of pilot projects to address three goals:

Develop benchmarks for existing computational biology and bioinformatics programs on existing architectures,
Develop prototypic computational biology and bioinformatics programs on new architectures including cloud architectures, and
Develop novel and integrative web platforms as possible solutions to bioinformatics problems in anticipation of and to inform a future Systems Biology Knowledgebase.

3. Hardware Infrastructure. Recognizing that there are a range of biocomputing problems and that different computing architectures may be required, an objective of this effort will be to provide access to a range of computing architectures that can be accomplished with available or off-the-shelf products.

What will be the final product of this project?

The final product of this project is the Final Implementation Plan that will document the scope, cost, and schedule of the complete Kbase. This report will be completed and posted on September 30, 2010.

We want Your participation

Lastly, your input to this wiki site (i.e., your comments and suggestions) is needed in order for this project to succeed. If you are interested in helping to shape the future Knowledgebase, please join in. One of the guiding principles for Knowledgebase is open development – meaning anyone can contribute. So please sign up, start contributing, and become part of the first online wiki content systems biology community of its kind. Follow this link to register

Acknowledgement

The Knowledgebase R&D project is sponsored by the Office of Biological and Environmental Research in the DOE Office of Science with American Recovery and Reinvestment Act 2009 funding and performed at Oak Ridge National Laboratory (ORNL). ORNL is managed by UT-Battelle, LLC, for the U.S. Department of Energy under contract DE-AC05-00OR22725.