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KBase

The Department of Energy’s Systems Biology Knowledgebase (KBase) is an ambitious program to disrupt the way we do biological systems science for prediction and engineering. It is an open-source, extensible platform that runs on DOE high-end infrastructure and supports collaborative, reproducible, reusable, and openly publishable analyses of organisms and their communities to predict and design […]

KBase

The Department of Energy’s Systems Biology Knowledgebase (KBase) is an ambitious program to disrupt the way we do biological systems science for prediction and engineering. It is an open-source, extensible platform that runs on DOE high-end infrastructure and supports collaborative, reproducible, reusable, and openly publishable analyses of organisms and their communities to predict and design their functions.

Microbes Online

A comparative functional genomic database and workbench with advanced tools for phylogenetic analysis and annotation, functional data storage/display/analysis, metabolic analysis and metafunctional genomics. Visit Microbes Online.

RegTransBase

A database of gene regulatory interactions in microbes based on literature and an expertly curated database of transcription factor binding sites underlying a suite of prediction tools. Visit RegTransBase.

RegPrecise

Capture, visualize and analyze transcription factor regulons reconstructed by a comparative genomic approach. Visit RegPrecise.

RegPredict

Genomic reconstruction of transcriptional regulons in groups of closely related prokaryotic genomes. Regulons are described as gene sets with shared regulatory sites. Visit RegPredict.

Simulac

An old but flexible simulator for complex gene expression circuits. Used initially to model complex promoter, elongation, and expression dynamics of the bacteriophage lambda lysis/lysogeny switch. Download Simulac.zip.

Deduce

A now very old but still surprisingly effective correlation-based method of reconstructing molecular reaction networks from time-series data. Download Deduce.zip

Labelled Latent Dirichlet Allocation

This code implements a “soft” clustering methodology we call Labeled Latent Dirichlet Allocation (LLDA). The LLDA model is an instance of a general family of probabilistic models, known as probabilistic graphical models. Probabilistic graphical models provide a general Bayesian framework for representing joint probability distributions over collections of variables, and for computing posterior distributions on […]

Meta Microbes Online

As of October 2010, Meta.MicrobesOnline.org contained over 1600 genomes from bacterial, archaeal, and microeukaryotic isolates, offers combined phylogenetic gene tree analysis of millions of genes from over 150 ecological and organismal metagenomes. These trees are built using our FastTree program, which offers rapid highly accurate tree building, even for very large trees. Such combined analysis […]