Author: Suzanne Paley
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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 biologist curators.
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Update notifications for the BioCyc collection of databases
The BioCyc update notifications service is a new mechanism to keep researchers informed of the latest developments in their areas of interest.
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Pathway collages: personalized multi-pathway diagrams
We define software for constructing personalized multi-pathway diagrams called pathway-collages using a combination of manual and automatic layouts.
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Representation and inference of cellular architecture for metabolic reconstruction and modeling
We developed a tool for inferring cellular architectures across many domains of life and extended our Cell Component Ontology to enable representation of the inferred architectures.
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The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases
The MetaCyc database (MetaCyc.org) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life.
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Computational Metabolomics Operations at Biocyc.Org
BioCyc.org is a genome and metabolic pathway web portal covering 5500 organisms, including Homo sapiens, Arabidopsis thaliana, Saccharomyces cerevisiae and Escherichia coli.
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Pathway Tools version 19.0 update: Software for Pathway/Genome Informatics and Systems Biology
The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations.
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The EcoCyc Database
This review outlines the data content of EcoCyc and of the procedures by which this content is generated.
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Addition of Escherichia coli K-12 Growth Observation and Gene Essentiality Data to the Ecocyc Database
We have integrated data on the growth or nongrowth of E. coli K-12 obtained from published observations using a variety of individual media and from high-throughput phenotype microarrays into the EcoCyc database.
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The EcoCyc Database
The long-term goal of the project is to describe the complete molecular catalog of the E. coli cell, as well as the functions of each of its molecular parts, to facilitate a system-level under-standing of E. coli.