Bioinformatics publications
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A Comparison of the Pathway Tools Software with the Reactome Software
This document compares SRI’s Pathway Tools (PTools) software with the Reactome software. Both software systems serve the pathway bioinformatics area, including representation and analysis of metabolic pathways and signaling pathways.
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The MetaCyc Database of Metabolic Pathways and Enzymes – A 2019 Update
This article provides an update on the developments in MetaCyc during September 2017 to August 2019, up to version 23.1.
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The MultiOmics Explainer: Explaining Omics Results in the Context of a Pathway/Genome Database
We describe the MultiOmics Explainer, a new tool within the Pathway Tools software suite that leverages what is known about an organism’s metabolic and regulatory network to suggest explanations for…
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Metabolic Route Computation in Organism Communities
We developed an efficient software tool to search for metabolic routes that include metabolic reactions from multiple organisms.
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Using pathway covering to explore connections among metabolites
Pathway Covering is a new algorithm that takes a list of metabolites (compounds) and determines a minimum-cost set of metabolic pathways in an organism that includes (covers) all the metabolites…
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A Comparison of Microbial Genome Web Portals
This article compares the capabilities of the major microbial genome web portals to aid researchers in determining which portal(s) are best suited to their needs.
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How accurate is automated gap filling of metabolic models?
Here we compare the results of applying an automated likelihood-based gap filler within the Pathway Tools software with the results of manually gap filling the same metabolic model.
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The MetaCyc database of metabolic pathways and enzymes
This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.
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Evaluation of reaction gap-filling accuracy by randomization
We report on computational experiments of reaction gap filling in which we generated degraded versions of the EcoCyc-20.0-GEM model by randomly removing flux-carrying reactions from a growing model.
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The Omics Dashboard for interactive exploration of gene-expression data
The Omics Dashboard is a software tool for interactive exploration and analysis of gene-expression datasets.
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The EcoCyc Database: Reflecting New Knowledge About Escherichia Coli K-12
New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc.
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The BioCyc collection of microbial genomes and metabolic pathways
BioCyc.org is a microbial genome Web portal that combines thousands of genomes with additional information inferred by computer programs, imported from other databases and curated from the biomedical literature by…