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GrinnWeb

GrinnWeb is a bioinformatics platform contains a graph database, an R package and web application for metabolomics studies. It aims to broaden metabolomics studies by allowing mapping of omics data such as genomics, transcriptomics, proteomics and metabolomics for a systems level exploration.

Features

  • There are three main functions. See each page for more information
    1) SEARCH - query for metabolites, proteins, genes and metabolic pathways
    2) BUILD - connect given metabolites based on several kinds of relationships
    3) PAIR - generate an integrated network of metabolites, proteins, genes and pathways
  • Use KEGG as a main resource to derive connections between the molecular components.
  • Generate two types of networks: a network of connected metabolites and an integrated network of metabolites, proteins, genes and pathways.
  • Link metabolites with four relationship types: biochemical reaction, enzyme catalysis, encoding gene and metabolic pathway.
  • Connect metabolites to three element types:protein, gene and pathway.
  • Provide interactive network visualization and easily export results and style for Cytoscape.

Online usage

  • For online usage under UC Davis network, click here

Local running

  • For local usage, install grinnWeb R package from github

    • 
               install.packages("devtools")
               library(devtools)
               install_github("kwanjeeraw/grinnWeb")
  • Follow the guidelines to install OpenCPU server locally.
  • Require Neo4j 2.1.5 for the grinn internal database (local version), please send us an email for the grinn database files, currently available: Human database.
    • Download and then unzip Neo4j server
    • Extract and move the grinn database files to the Neo4j server directory
    • Start the Neo4j server, for windows: Double-click on %NEO4J_HOME%\bin\Neo4j.bat, for linux: ./bin/neo4j start for more details see here
  • After installation, use the following code is to run grinnWeb locally.
    • 
                library(grinnWeb)
                library(opencpu)
                opencpu$browse("library/grinnWeb/www")

References

Metabolomics and transcriptomics data used in our examples are taken from the following publication:

  • April W, et al. Metabolomics in psoriatic disease: pilot study reveals metabolite differences in psoriasis and psoriatic arthritis. F1000Res. 2014;3:248.
  • Rosenberg A, et al. Divergent gene activation in peripheral blood and tissues of patients with rheumatoid arthritis, psoriatic arthritis and psoriasis following infliximab therapy. PLoS One. 2014;9(10).