Author: Peter Karp
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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.
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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.
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Metabolic Reconstruction Databases and Their Application to Metabolomics Research
This chapter describes the MetaCyc family of Pathway/Genome Databases (PGDBs).
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Interactive Retinal Vessel Extraction by Integrating Vessel Tracing and Graph Search
We propose an interactive approach that enables a user to efficiently obtain near perfect vessel segmentation with a few mouse clicks. Given two seed points, the approach seeks an optimal path between them by minimizing a cost function.
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Dead End Metabolites – Defining the Known Unknowns of the E. coli Metabolic Network
We have analysed the occurrence of dead end metabolites within the database – these are metabolites which lack the requisite reactions (either metabolic or transport) that would account for their production or consumption within the metabolic network.
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The COMBREX Project: Design, Methodology, and Initial Results
COMBREX is an NIH-funded enterprise that has brought computational and experimental biologists together, with the goal of greatly improving our overall understanding of microbial protein function.
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Groups: Knowledge Spreadsheets for Symbolic Biocomputing
‘Groups’ is an implementation of Knowledge Spreadsheets (KSs) within the Pathway Tools system.
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The Challenge of Constructing, Classifying, and Representing Metabolic Pathways
This review describes the criteria that need to be considered, and the rules that have been developed by MetaCyc curators as they make decisions regarding the representation and classification of metabolic pathway information in MetaCyc.
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A Systematic Comparison of the MetaCyc and Kegg Pathway Databases
We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012…
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A systematic comparison of the MetaCyc and KEGG pathway databases
We present a comparison of the compound, reaction, and pathway content of MetaCyc version 16.0 and a KEGG version downloaded on Feb-27-2012 to increase understanding of their relative sizes, their degree of overlap, and their scope.
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Groups: Knowledge Spreadsheets for symbolic biocomputing
Groups allows Pathway Tools users to define a group of objects (e.g. groups of genes or metabolites) from a Pathway/Genome Database.