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A Web Tool for Generating High Quality Machine-readable Biological Pathways
Published on: February 8, 2017
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Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.
Briefings in Bioinformatics
|October 11, 2015
Summary
Pathway Tools software has been significantly enhanced over the last five years, adding new bioinformatics capabilities for metabolic modeling, pathway analysis, and data integration. This advanced software environment supports the creation of numerous Pathway/Genome Databases worldwide.
Area of Science:
- Bioinformatics
- Computational Biology
- Systems Biology
Background:
- Pathway Tools is a comprehensive bioinformatics software environment.
- It offers a wide range of genome, metabolic, and regulatory informatics tools.
Purpose of the Study:
- To outline the key advancements in Pathway Tools over the past five years.
- To highlight new features and their impact on biological data analysis and database creation.
Main Methods:
- Review of software development and feature additions in Pathway Tools.
- Description of new components for metabolic modeling, pathway analysis, and data management.
- Integration of Python and web services for enhanced programmability.
Main Results:
- Significant additions include metabolic modeling, route search, atom mapping, and Gibbs free energy calculations.
- New editors for signaling pathways, genome sequences, and cellular architecture were introduced.
- Enhanced data storage for gene essentiality and phenotype data, alongside improved pathway visualization.
Conclusions:
- Pathway Tools has expanded its capabilities in metabolic and regulatory informatics.
- The software facilitates the creation and curation of over 9800 Pathway/Genome Databases.
- Recent updates enhance its utility for diverse biological research applications.
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