Pathway Tools version 28.0: Integrated Software for Pathway/Genome Informatics and Systems Biology
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| Main Authors: | , , , , , , , , |
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| Format: | Preprint |
| Published: |
2015
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| _version_ | 1866914951916945408 |
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| author | Karp, Peter D. Paley, Suzanne M. Krummenacker, Markus Kothari, Anamika Midford, Peter E. Subhraveti, Pallavi Swart, Austin Moore, Lisa Caspi, Ron |
| author_facet | Karp, Peter D. Paley, Suzanne M. Krummenacker, Markus Kothari, Anamika Midford, Peter E. Subhraveti, Pallavi Swart, Austin Moore, Lisa Caspi, Ron |
| contents | Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings, and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. The software creates and manages a type of organism-specific database called a Pathway/Genome Database (PGDB), which the software enables database curators to interactively edit. It supports web publishing of PGDBs and provides a large number of query, visualization, and omics-data analysis tools. Scientists around the world have created more than 45,000 PGDBs by using Pathway Tools, many of which are curated databases for important model organisms. Those PGDBs can be exchanged using a peer-to-peer database-sharing system called the PGDB Registry. |
| format | Preprint |
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arxiv_https___arxiv_org_abs_1510_03964 |
| institution | arXiv |
| publishDate | 2015 |
| record_format | arxiv |
| spellingShingle | Pathway Tools version 28.0: Integrated Software for Pathway/Genome Informatics and Systems Biology Karp, Peter D. Paley, Suzanne M. Krummenacker, Markus Kothari, Anamika Midford, Peter E. Subhraveti, Pallavi Swart, Austin Moore, Lisa Caspi, Ron Genomics Quantitative Methods Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer, and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings, and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. The software creates and manages a type of organism-specific database called a Pathway/Genome Database (PGDB), which the software enables database curators to interactively edit. It supports web publishing of PGDBs and provides a large number of query, visualization, and omics-data analysis tools. Scientists around the world have created more than 45,000 PGDBs by using Pathway Tools, many of which are curated databases for important model organisms. Those PGDBs can be exchanged using a peer-to-peer database-sharing system called the PGDB Registry. |
| title | Pathway Tools version 28.0: Integrated Software for Pathway/Genome Informatics and Systems Biology |
| topic | Genomics Quantitative Methods |
| url | https://arxiv.org/abs/1510.03964 |