My favorites | Sign in
Project Home Downloads Wiki Issues Source
Project Information
Members

The process of constructing and testing models, particularly those that incorporate significant prior knowledge, involves multiple steps that are currently very poorly integrated. We have developed SB-Pipeline to create an effective workflow based on open-source code, public standards and modern software practice.

SB-Pipeline is a multi-faceted software platform that pulls together all of the steps involved in collecting and transforming primary data; constructing, annotating and calibrating models; and distributing and sharing simulations and analyses. SB-Pipeline is primarily concerned with data and model management for the purpose of calibration; in existing modeling tools, calibration is an ancillary rather than a primary activity. Conversely, SB-Pipeline does not recreate existing tools for model simulation. Second, SB-Pipeline implements a robust system for tracking the provenance of data, links between data and models, and the origins of model assumptions in data or the literature. Third, SB-Pipeline is a collection of discrete but interoperable software tools, rather than a single integrated system. SB-Pipeline incorporates standard protocols for import and export of data and thus components can be integrated into external packages.

SBPipeline comprises a number of toolboxes to store and handle data and models in systems biology:

DataRail is an open source MATLAB toolbox for managing, transforming, visualizing, and modeling data, in particular the high-throughput data encountered in Systems Biology.

CellNetOptimizer is a MATLAB toolbox for creating logic-based models of signal transduction networks, and training them agains high-throughput biochemical data.

SbWiki is a wiki-based system which utilizes Semantic Web technologies and a lightweight data entry and cataloging framework to support collaborative management of unstructured and semi-structured Systems Biology data.

Powered by Google Project Hosting