"I love BioCyc Pathway/Genome Database Collection"

2022-05-07 16:52:59

hide show operations OPERATIONS Tools Search Search Genes, Proteins or RNAsSearch CompoundsSearch ReactionsSearch PathwaysSearch DNA or mRNA SitesSearch Growth MediaAdvanced SearchCrossOrganismSearchBLAST Search Current Organism BLAST All BioCycSequence Pattern SearchGoogle Search of this Site Genome GenomeBrowserGenomeOverviewCircularGenomeViewerRegulatoryOverviewBrowseGeneOntologyMapSequenceCoordinatesGenerateGenomePosterSmartTables PublicSmartTables SpecialSmartTables Metabolism CellularOverviewRun Metabolic ModelDead-endMetabolitesChokepointReactions Metabolic Route Search Metabolic Network ExplorerMetaboliteTranslationServicePathwayCollagesBrowsePathwayOntologyBrowseEnzymeCommissionOntologyBrowseCompoundOntologyGenerateMetabolicMapPoster AnalysisComparativeAnalysisOmicsDataAnalysisSummaryStatisticsMetabolomicsPathwayCoverageListFunctionalGeneClusters MultipleSequenceAlignment UpdateNotifications Reports Historyofupdates Pathwayevidence(sortedbyscore) Pathwayevidence(sortedbyclass) Pathwayholes Sites BioCyc MetaCyc EcoCyc HumanCyc BsubCyc YeastCyc Algae and Cyanobacteria Helicobacter pylori Listeria monocytogenes Mycobacterium tuberculosis Peptoclostridium difficile Pseudomonas aeruginosa Salmonella enterica Shigella flexneri Vibrio cholerae Pathway Tools Information Academic Download Help Login/AccountHelpSearchingIntro to BioCycWebsiteUserGuideWebinarsGlossaryPGDBConceptsGuideGuidetoBioCycContactUs/Licensing/Support Archaea databases Bacteria databases Eukaryota databases MetaCyc Metabolic Encyclopedia ChangeCurrentDatabase Current Database: Search in Current Database: Genome Browser Metabolic Map Extensive, Highly Curated Data BioCyc integrates genome data with a comprehensive body of additional data including metabolic reconstructions, regulatory networks, protein features, orthologs, gene essentiality, and atom mappings. Learn More Genome Browser image A Vast Set of Bioinformatics Tools Browsers for genomes, metabolic networks, and regulatory networks. Transcriptomics and metabolomics data analysis, comparative analysis, and metabolic route search. Sequence search and alignment. Learn More   Explore Metabolic Maps for Thousands of Organisms The Cellular Overview enables you to browse through zoomable metabolic map diagrams that are customized to each BioCyc organism. Learn More Cellular Overview image generated by Pathway Tools. RouteSearch: Search for Paths Through the Metabolic Network Search for lowest-cost paths through the metabolic network of the selected organism. Learn More Metabolic Reconstruction from Sequenced Genomes Install SRI's Pathway Tools software (free to academics) to predict metabolic pathways for sequenced genomes, generate metabolic models. Learn More Gene Expression Data Analysis Multiple tools are available in this website for analysis of gene expression data. Learn More Cellular Overview Omics Viewer image generated by Pathway Tools. Comparative Genome Analysis Multiple comparative analysis tools are available in this website. Learn More Multi-organism Genome Browser image generated by Pathway Tools. Search Databases by Organism Properties BioCyc contains data on phenotypic properties of organisms, such as human-microbiome body site, aerobicity, and temperature range. Learn More Image by Arek Socha from Pixabay The BioCyc Database Collection Tier 1 databases such as EcoCyc are the most highly curated. BioCyc databases are computationally derived from MetaCyc. Learn More Request Addition of New Genome to BioCyc BioCyc Database Collection The Omics Dashboard: A New View of Omics Data Visualize omics data as a set of graphs hierarchically organized by functional category. Drill down for more detail in areas of interest. Learn More Cellular Dashboard image generated by Pathway Tools. 12345678910 20,005 Pathway/Genome Databases to Search BioCyc is a collection of 20,005 Pathway/Genome Databases (PGDBs) for model eukaryotes and for thousands of microbes, plus software tools for exploring them. BioCyc is an encyclopedic reference that contains curated data from 130,000 publications. The EcoCyc and MetaCyc databases are freely available, but access to the remaining BioCyc databases requires a paid subscription. Try Free BioCyc Intro The following websites are part of BioCyc. Opening these sites in your browser is a convenient way to pre-select that database for searches. What people are saying < ··· > Learning Library Webinar Series Webinar #1: Introduction to BioCyc These six sequential segments, giving you a guided tour of the BioCyc collection in concise bites. To download or view, just click on one of the links following each segment's name. BioCyc Overview Part 1 (7:44) [mp4 video] or [YouTube] BioCyc Overview Part 2 (4:44) [mp4 video] or[YouTube] Searching in BioCyc (17:00) [mp4 video] or [YouTube] Genome Browsing, Searching, and Alignment (15:38) [mp4 video] or [YouTube] Pathways (13:19) [mp4 video] or [YouTube] Reactions (3:37) [mp4 video] or [YouTube] Compounds (6:42) [mp4 video] or [YouTube] Webinar #2: Introduction to SmartTables The following webinar will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The webinar is broken up into parts, ranging from basic operations to more advanced uses such as gene expression analysis and metabolomics. To download or view, click one of the links below. Part 1: SmartTables Overview (4:30) [mp4 video] or [YouTube] Part 2: SmartTables Basics (12:43) [QuickTime Video] Part 3: SmartTables Transformations (8:08) [QuickTime Video] Part 4: SmartTables Import and Export (9:00) [QuickTime Video] Part 5: SmartTables Gene Expression Analysis (7:40) [QuickTime Video] Part 6: Metabolomics Analysis with SmartTables (6:45) [QuickTime Video] Webinar #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network This webinar introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms. Part 1: The Cellular Overview: Navigating metabolic networks (17:15) [mp4 video] or [QuickTime Video] or [YouTube] Part 2: Comparative Genomics (21:06) [Windows Media Video] or [QuickTime Video] Part 3: Ortholog Viewing (10:02) [Windows Media Video] or [QuickTime Video] Part 4: The Regulatory Overview -- exploring transcriptional regulatory networks (15:21) [mp4 video] or [YouTube] Webinar #4: Omics Data Analysis This webinar will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools. Transcriptomics Analysis Tools [brief tour (2:40) mp4 video or YouTube] [detailed tutorial (21:36) mp4 video or YouTube] Metabolomics Analysis Tools [brief tour (3:26) mp4 video or YouTube] [detailed tutorial (24:09) mp4 video or YouTube] Omics Dashboard Part 1 (16:35) [mp4 video], or [YouTube] Omics Dashboard Part 2 (24:29) [mp4 video], or [YouTube] Webinar #5: Pathway Collages Pathway collages are multi-pathway diagrams that you can customize by, for example, overlaying omics data, altering the relative positions of pathways, and modifying connections among pathways. Learn how to generate, customize and export high-quality pathway-collage diagrams showing collections of user-specified pathways. Pathway Collages (22:39) [mp4 video], [QuickTime Video] or [YouTube] Webinar #6: Creating a Pathway/Genome Database Learn the entire process of building a BioCyc-like Pathway/Genome Database (PGDB) for an organism with a sequenced and annotated genome. Build a PGDB for your own lab or for the whole scientific community. Part 1: Building the Database Via Automated Inference Tools (56:42) [Windows Media Video] or [QuickTime Video] or [YouTube] Part 2A: General Editing Strategies (8:00) [Windows Media Video] or [QuickTime Video] or [YouTube] Part 2B: Creating and Editing Reactions and Compounds (17:32) [Windows Media Video] or [QuickTime Video] or [YouTube] Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10) [Windows Media Video] or [QuickTime Video] or [YouTube] Part 2D: Making and Editing Pathways (9:42) [Windows Media Video] or [QuickTime Video] or [YouTube] Webinar #7: Using the Structured Advanced Query Page An introduction to the Structured Advanced Query Page, which allows complex queries and queries across one or more databases in the BioCyc collection. You'll learn about:The basic steps of setting up an advanced query; Four examples of increasingly complex queries, including how to query across multiple databases; Where to learn more about the structure of BioCyc databases. Quick Introduction (6:27): "Structured Advanced Query Page Quick Introduction" [Windows Media Video] or [mp4 video] or [YouTube] Full Webinar (42:15): "Structured Advanced Query Page" [Windows Media Video] or [mp4 video] or [YouTube] GeneralInformation IntrotoBioCyc Subscriptions Publications UpdateHistory ContactUs AboutUs DataandServices Software/DataDownloads Web Services&APIs LinkingtoBioCyc MetabolicandGenomePosters RequestNewBioCycGenome Credits HowtoCite AdvisoryBoard Contributors BioCycCredits FollowUs PathwayToolsBlog MailingList ©2022 SRI International, 333 Ravenswood Avenue, Menlo Park, CA 94025-3493 SRI International is an independent, nonprofit corporation. Privacy policy Disclaimer Specify List of Organism Databases