Pathway Tools version 24.0: Integrated Software for Pathway/Genome Informatics and Systems Biology Peter D. Karp∗, Suzanne M. Paley, Peter E. Midford, Markus Krummenacker, Richard Billington, Anamika Kothari, Wai Kit Ong, Pallavi Subhraveti, Ingrid M. Keseler, and Ron Caspi Bioinformatics Research Group, SRI International 333 Ravenswood Ave, Menlo Park, CA 94025
[email protected] ∗To whom correspondence should be addressed. arXiv:1510.03964v4 [q-bio.GN] 12 Nov 2020 1 Abstract 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 align- ments, a genome-variant analyzer, and comparative-genomics operations. It offers metabolic- informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, pre- diction 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 reg- ulatory 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 35,000 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. Biographical Note Dr. Peter Karp is the Director of the Bioinformatics Research Group at SRI International. He received the PhD degree in Computer Science from Stanford University.