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Tools

The Software Environment for BIological Network Inference (SEBINI) Website

The Software Environment for BIological Network Inference (SEBINI) project at Pacific Northwest National Laboratory (PNNL) is building a software platform to provide an interactive environment for the deployment and evaluation of algorithms used to reconstruct the structure of biological regulatory and interaction networks. SEBINI can be used to compare and train network inference methods on artificial networks and simulated gene expression perturbation data. It also allows the analysis within the same framework of experimental high-throughput expression data using the suite of (trained) inference methods; hence SEBINI should be useful to software developers wishing to evaluate, compare, refine, or combine inference techniques, and to bioinformaticians analyzing experimental data. SEBINI provides a platform that aids in more accurate reconstruction of biological networks, with less effort, in less time.

Collective Analysis of Biological Interaction Networks Software (CABIN) Website

CABIN was developed at Pacific Northwest National Laboratory (PNNL) as a plugin to Cytoscape [Genome Research 13(11):2498-2504], which is an open source network visualization and analysis tool. CABIN promotes analytical reasoning for integrating evidence of interaction data from multiple sources by the use of interactive visual interfaces. Multiple coordinated views within CABIN foster exploratory data analysis by users, accommodating expert domain knowledge. The functionalities available within CABIN maximize human perception and understanding of uncertain and complex data, facilitating high-quality human judgment with limited investment of the user's time.