1 SRI International Bioinformatics BioCyc Tutorial Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International [email protected] BioCyc.org EcoCyc.org,

1 SRI International Bioinformatics

BioCyc Tutorial

Peter D. Karp, Ph.D.Bioinformatics Research Group

SRI International

[email protected]

BioCyc.org

EcoCyc.org, MetaCyc.org, HumanCyc.org

http://www.ai.sri.com/pkarp/talks/biocyc-tutorial.ppt


A Roadmap to BioCyc

BioCyc Content

BioCyc Web site Object pages Genome browser Overviews and omics viewers Comparative analyses

Desktop BioCyc

How to learn more


What is BioCyc?

A rich information source that connects genomes and metabolic pathways

Couples curated data with computational predictions

Supports analysis of omics dataProvides comparative analysis tools

Microbial emphasis. Exceptions: Human PGDB Non-SRI PGDBs outside BioCyc


BioCyc Content


BioCyc Collection of Pathway/Genome Databases

Pathway/Genome Database (PGDB) – combines information about Pathways, reactions, substrates Enzymes, transporters Genes, replicons Transcription factors/sites, promoters, operons

Tier 1: Literature-Derived PGDBs MetaCyc: Experimentally elucidated metabolic pathways and enzymes EcoCyc: Model organism database for Escherichia coli K-12

Tier 2: Computationally-derived DBs, Some Curation -- 20 PGDBs From SRI: HumanCyc, Mycobacterium tuberculosis From other groups:

Tier 3: Computationally-derived DBs, No Curation -- 349 PGDBs


BioCyc Tiers

Tiers 1-2 Experimental data, curated from the literature Rich, extensive, accurate Contain types of data that can’t be predicted computationally

Tier 3 DBs created by subjecting annotated genomes to PathoLogic computational processing pipeline:

Pathway prediction Pathway Hole Filling Operon prediction (bacteria) Transport Inference Parser

349 PGDBs Source: CMR database

Tier 3 will be regenerated and expanded on a regular basis


Hundreds of Other PGDBs AvailableOutside BioCyc

In all domains of lifeTiers 2-3See BioCyc.org for exhaustive listTheir Web sites also powered by Pathway Tools

Examples include Yeast, Candida albicans, Dictyostelium Mouse Arabidopsis, Solanaceae, Medicago, Gramene


Curate Your Own PGDB

We encourage other groups to establish curation efforts

Adopt a BioCyc PGDBBuild your own PGDB with Pathway Tools

Pathway Tools is the software used to create, update, query, and visualize BioCyc DBs

Contact: [email protected]


Pathway/Genome Database

ChromosomesPlasmids

Genes

ProteinsRNAs

Reactions

Pathways

Compounds

CELL

OperonsPromoters

DNA Binding SitesRegulatory Interactions

Sequence Features


BioCyc Web Site


BioCyc Object Pages

Genes Genome browser Transcription units Proteins

Enzymes, transporters, transcription factors, others Extensive comments and citations Monomers and multimers are represented, and in different chemical states

RNAs Reactions Pathways Compounds

Searches are organized around the object types!


BioCyc Searches

Basic search http://biocyc.org/server.html


BioCyc Searches

Advanced search http://biocyc.org/query.html


Genome Browser


Comparative Analysis


Pathway Tools Overviews and Omics Viewers

Diagrams designed to avoid the hairball effectGenerated automatically from PGDBZoom, interrogateOmics viewers paint omics data onto overview diagrams

Provide different perspectives on the same dataset

Animation can be used for multiple time points or conditions

Can paint any data that associates numbers with genes, proteins, reactions, or metabolites

Overviews provide genome-scale visualizations of cellular networksHarness the power of the human visual system to interpret patterns in biological contexts


Desktop BioCyc


Desktop BioCyc

Linux/PC, Windows/PC, Macintosh (in March)

Why install locally?

Runs faster Significantly more functionality

More searches Regulatory Overview, Genome Overview, Metabolite Tracing

Write programs using APIs Access BioCyc when you can’t access the Internet

See: http://biocyc.org/download.shtml


Metabolite Tracing


BioCyc and Pathway Tools Availability

WWW BioCyc freely available to all BioCyc.org

BioCyc DBs freely available to non-profits Flatfile downloads in multiple formats from BioCyc.org

Pathway Tools freely available to non-profits PC/Windows, PC/Linux, SUN


How to Learn More


Learn More

BioCyc Web Seminars (Webinars) http://biocyc.org/webinars.shtml

BioCyc Publications http://biocyc.org/publications.shtml


Acknowledgements

SRI Suzanne Paley, Ron Caspi,

Ingrid Keseler, Carol Fulcher, Markus Krummenacker, Alex Shearer

EcoCyc Collaborators Julio Collado-Vides, Robert

Gunsalus, Ian Paulsen

MetaCyc Collaborators Sue Rhee, Peifen Zhang, Kate

Dreher Lukas Mueller, Anuradha Pujar

Funding sources: NIH National Center for

Research Resources NIH National Institute of

General Medical Sciences NIH National Human

Genome Research Institute

BioCyc.org

Learn more from BioCyc webinars: biocyc.org/webinar.shtml

Documents

1 SRI International Bioinformatics BioCyc Tutorial Peter D. Karp, Ph.D. Bioinformatics Research Group SRI International [email protected] BioCyc.org EcoCyc.org,