{"id":1972,"date":"2018-01-11T21:09:16","date_gmt":"2018-01-11T21:09:16","guid":{"rendered":"http:\/\/www.simbhq.org\/annual\/?page_id=1972"},"modified":"2022-07-26T17:41:30","modified_gmt":"2022-07-26T17:41:30","slug":"biocycwebportal-workshop","status":"publish","type":"page","link":"https:\/\/www.simbhq.org\/annual\/biocycwebportal-workshop\/","title":{"rendered":"The BioCyc.org Microbial Genome Web Portal"},"content":{"rendered":"

The BioCyc.org Microbial Genome Web Portal<\/span><\/h2>\n<\/div>
<\/div>
<\/div><\/div>
<\/div>

BioCyc.org combines sequenced genomes with computational inferences, data imported from other databases, and a unique collection of information curated from the life-science literature. BioCyc data includes metabolic reconstructions, regulatory networks, protein features, orthologs, gene essentiality, and atom mappings. This tutorial will introduce attendees to the BioCyc data content and to its extensive array of easy to use bioinformatics tools.<\/span><\/p>\n<\/div>

Tutorial topics:<\/span><\/h3>\n

Basic concepts and operation<\/strong><\/span>

    \n
  • <\/i><\/span>
    BioCyc data content<\/div><\/li>\n
  • <\/i><\/span>
    Database selection and search<\/div><\/li>\n
  • <\/i><\/span>
    Gene, metabolite, reaction, and pathway information pages<\/div><\/li>\n<\/ul><\/p>\n

    Genome informatics<\/strong><\/span>

      \n
    • <\/i><\/span>
      BLAST search, sequence pattern search, extracting sequences<\/div><\/li>\n
    • <\/i><\/span>
      BioCyc genome browser<\/div><\/li>\n
    • <\/i><\/span>
      Regulation in BioCyc<\/div><\/li>\n<\/ul><\/p>\n

      Pathway informatics<\/strong><\/span>

        \n
      • <\/i><\/span>
        Zoomable metabolic network diagram<\/div><\/li>\n
      • <\/i><\/span>
        Metabolic network explorer<\/div><\/li>\n
      • <\/i><\/span>
        Atom mappings<\/div><\/li>\n
      • <\/i><\/span>
        Metabolic route search<\/div><\/li>\n<\/ul><\/p>\n

        Transcriptomics and Metabolomics data analysis<\/strong><\/span>

          \n
        • <\/i><\/span>
          Displaying high-throughput data on individual pathways and metabolic network diagrams<\/div><\/li>\n
        • <\/i><\/span>
          Pathway activation scores<\/div><\/li>\n
        • <\/i><\/span>
          Omics Dashboard<\/div><\/li>\n
        • <\/i><\/span>
          Pathway collages<\/div><\/li>\n
        • <\/i><\/span>
          Enrichment analysis<\/div><\/li>\n<\/ul><\/p>\n

          SmartTables and comparative analysis<\/strong><\/span>

            \n
          • <\/i><\/span>
            Using SmartTables to store, share, and analyze lists of genes and metabolites<\/div><\/li>\n
          • <\/i><\/span>
            Multi-organism search tools<\/div><\/li>\n
          • <\/i><\/span>
            Orthologs in BioCyc<\/div><\/li>\n
          • <\/i><\/span>
            Comparative analysis tools<\/div><\/li>\n<\/ul><\/p>\n<\/div>
            <\/div><\/div><\/div>

            Sunday, August 7, 2022<\/h2>\n

            8:00 am \u2013 3:30 pm<\/h3>\n<\/div>
            <\/div>
            <\/div><\/div>
            <\/div>

            Location<\/h3>\n

            Hyatt Regency San Francisco
            \nSan Francisco, CA<\/p>\n<\/div>

            <\/div>
            <\/div><\/div>
            <\/div>

            Fees<\/h3>\n

            $325<\/strong> – SIMB Member
            \n$500<\/strong> – Non-member
            \n$225<\/strong> – Student<\/p>\n

            Onsite Fees (after 7\/13)<\/h3>\n

            $375<\/strong> – SIMB Member
            \n$550<\/strong> – Non-member
            \n$225<\/strong> – Student<\/p>\n<\/div>

            <\/div>
            <\/div><\/div>
            <\/div>

            Limit: 30 attendees<\/h3>\n<\/div>
            <\/div>
            <\/div><\/div>
            <\/div>

            Presenters<\/h3>\n

            Peter D. Karp<\/strong>
            \nPeter D. Karp is the director of the Bioinformatics Research Group within the Artificial Intelligence Center at SRI International. Dr. Karp has authored 180 publications in bioinformatics and computer science in areas including metabolic pathway bioinformatics, computational genomics, scientific visualization, and biological databases. Dr. Karp has developed novel algorithms for predicting the metabolic pathway complement of an organism from its genome, for predicting which genes in an organism code for enzymes missing from its metabolic pathways, and for visualizing metabolic pathways. Karp developed the Pathway Tools software, the EcoCyc and MetaCyc databases, and the BioCyc database collection. He is a Fellow of the American Association for the Advancement of Science and of the International Society for Computational Biology. He received the Ph.D. degree in Computer Science from Stanford University in 1989, and was a postdoctoral fellow at the NIH National Center for Biotechnology Information.<\/p>\n<\/div>

            <\/div><\/div><\/div><\/div><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"100-width.php","meta":{"footnotes":""},"class_list":["post-1972","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/pages\/1972","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/comments?post=1972"}],"version-history":[{"count":26,"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/pages\/1972\/revisions"}],"predecessor-version":[{"id":7802,"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/pages\/1972\/revisions\/7802"}],"wp:attachment":[{"href":"https:\/\/www.simbhq.org\/annual\/wp-json\/wp\/v2\/media?parent=1972"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}