Author: Peter Karp
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Crowd-sourcing and author submission as alternatives to professional curation
This perspective considers the significant experience accumulated by the bioinformatics community with these two alternatives to professional curation in the last 20 years…
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How the strengths of Lisp-family languages facilitate building complex and flexible bioinformatics applications
We present a rationale for expanding the presence of the Lisp family of programming languages in bioinformatics and computational biology research.
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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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Metabolic Pathways for the Whole Community
Here we adopt the MetaPathways annotation and analysis pipeline and Pathway Tools to construct environmental pathway/genome databases that describe microbial community metabolism using MetaCyc.
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Optimal Metabolic Route Search Based on Atom Mappings
We present the algorithm used in the new RouteSearch tool within the Pathway Tools software.
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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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Curation Accuracy of Model Organism Databases
We assessed the accuracy of EcoCyc and CGD by manually selecting curated assertions within randomly chosen EcoCyc and CGD gene pages and by then validating that the data found in the referenced publications supported those assertions.
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A Framework for Application of Metabolic Modeling in Yeast to Predict the Effects of Nssnv in Human Orthologs
Here we present the next step in the workflow toward using yeast metabolic modeling to predict human metabolic behavior resulting from nsSNV.
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A Genome-Scale Metabolic Flux Model of Escherichia coli K-12 Derived from the EcoCyc Database
We present EcoCyc–18.0–GEM, a genome-scale model of the E. coli K–12 MG1655 metabolic network.
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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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PortEco: A Resource for Exploring Bacterial Biology through High-Throughput Data and Analysis Tools
PortEco ( http://porteco.org) aims to collect, curate and provide data and analysis tools to support basic biological research in Escherichia coli.