Systems Biology

KBase – The Department of Energy Systems Biology Knowledgebase (KBase) is an emerging software and data environment designed to enable researchers to collaboratively generate, test and share new hypotheses about gene and protein functions, perform large-scale analyses on a scalable computing infrastructure, and model interactions in microbes, plants, and their communities.

LEfSeLEfse (LDA Effect Size) is an algorithm for high-dimensional biomarker discovery and explanation that identifies genomic features (genes, pathways, or taxa) characterizing the differences between two or more biological conditions.

IMPIMP (Integrative Multi-species Prediction) is a web server that enables biologists to analyze their experimental results in the functional context of gene-gene networks from multiple organisms. Biologists can use IMP to direct functional experiments by identifying novel gene participants in a pathway or additional processes that a gene of interest participates in.