Overview of the Pathway Tools Software and Pathway/Genome Databases © 2013 SRI International

SRI International An independent, nonprofit corporation Founded by Stanford University in 1946 Independent in 1970; changed name from Stanford Research Institute to SRI International in 1977 ~2,000 employees ~20 locations worldwide Silicon Valley - Headquarters Washington, D.C. Princeton, New Jersey Harrisonburg, Virginia St. Petersburg, Florida State College, Pennsylvania Arecibo, Puerto Rico Tokyo, Japan OPPORTUNITIES PROFILE INNOVATIONS CAPABILITIES PROGRAMS

Tutorial Overview Mix of lectures and lab sessions Questions encouraged at any time

MetaCyc Family of Pathway/Genome Databases 20,000+ databases from many institutions All domains of life with microbial emphasis Genomes plus predicted metabolic pathways DBs derived from MetaCyc via computational pathway prediction Common schema Common controlled vocabularies Managed using Pathway Tools software MetaCyc Family 20,000+ BioCyc.org 11,000 Archives of Toxicology 85:1015 2011

Highly Curated Pathway/Genome Databases Organism Organization Publications Curated From MetaCyc Multiorganism SRI 51,000 EcoCyc E. coli 33,000 BsubCyc B. subtilis 4,000 HumanCyc H. sapiens AraCyc A. thaliana TAIR/Carnegie Institution 4,100 YeastCyc S. cerevisiae SGD/SRI 980 MouseCyc M. musculus MGD/Jackson Laboratory http://biocyc.org/otherpgdbs.shtml

Pathway Tools Enables Multi-Use Metabolic Databases Metabolic Model Encyclopedia Queryable Database Mention that all of these five usage facets are validated. Zoomable Metabolic Map Omics Data Analysis

+ Annotated PathoLogic Genome MetaCyc Pathway/Genome Pathway/Genome Database Pathway/Genome Navigator MetaFlux Pathway/Genome Editors Briefings in Bioinformatics 11:40-79 2010 Licensed by 8,000+ Groups

Pathway/Genome Navigator Omics Viewers SmartTables Outline for Tutorial Introduction Pathway/Genome Navigator Omics Viewers SmartTables

MetaCyc: Curated Metabolic Database MetaCyc v20.1 2016 KEGG 2017 SEED 2015 Citations 51,000 Pathways 2,500 316 Modules 583 Subsystems Reactions 13,800 10,411 Metabolites 13,400 17,883 Mini-reviews (textbook pages) 7,500 MetaCyc is free and open, contains computed atom mappings “A Systematic Comparison of the MetaCyc and KEGG Pathway Databases BMC Bioinformatics 2013 14(1):112

Information Sources -- Publications Primary Pathway Tools citation: "Pathway Tools version 19.0: Integrated Software for Pathway/Genome Informatics and Systems Biology," Briefings in Bioinformatics 2015. Pathway Tools overview publication: "Pathway Tools version 19.0: Integrated Software for Pathway/Genome Informatics and Systems Biology", 2015, http://arxiv.org/abs/1510.03964 Primary BioCyc/MetaCyc citation: "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases", Nucleic Acids Res, 44:D471-80, 2016.

Information Sources BioCyc Web site: Help Menu Basic Help Search Help BioCyc Glossary Publications Website User Guide PGDB Concepts Guide to EcoCyc Guide to MetaCyc