BioCyc Omics Analysis Service

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BioCyc Omics Analysis Service Peter E. Midford ecocyc.org SRI International biocyc.org metacyc.org

BioCyc Omics Data Analysis Service BioCyc Strengths Visualization Putting Gene Expression and Metabolite concentrations in context Challenge: From raw expression data to Analysis using Pathway Tools Dashboard Smart Tables Cellular Overview

Proposed Solution SRI will provide an analysis service from raw transcriptomics data to cleaned, analyzed results Results will be presented using both BioCyc and other tools (e.g., R/Bioconductor) This is not a service for power users, focus is towards wet lab users that want to get data into BioCyc tools.

Initial Analysis Proposal Initially offer analysis of RNA-seq expression data Re-format provided data, translate to appropriate identifiers Data normalization, cleaning, significance calculations using open source tools E.g. Salmon (or alignment if necessary), DeSeq2, edgeR etc. Will check for common problems (e.g., batch effects) Filtered data visualized with appropriate Pathway Tools components: SmartTable(s) containing expression data Analyze using Dashboard, Cellular Overview, table of expressed pathways, enrichment analysis Final report outlining significant results

How can we make this useful to you? Tools for processing metabolite data Other gene expression technologies Other ways of packaging archiving results Example: save all data and analysis as a (Docker) container Contribute to your outputs (e.g., publications)