geWorkbench – software platform for integrated genomic data analysis

geWorkbench (genomics Workbench) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications.

At present there are more than 70 available plug-ins supporting the visualization and analysis of gene expression and sequence data.

geWorkbench is the Bioinformatics platform of MAGNet, the National Center for the Multi-scale Analysis of Genomic and Cellular Networks, one of the 8 National Centers for Biomedical Computing.

Features include:

  • Computational analysis tools such as t-test, hierarchical clustering, self-organizing maps, regulatory network reconstruction, BLAST searches, pattern-motif discovery, protein structure prediction, structure-based protein annotation, etc.
  • Visualization of gene expression (heatmaps, volcano plot), molecular interaction networks (through Cytoscape), protein sequence and protein structure data (e.g., MarkUs).
  • Integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
  • Component integration through platform management of inputs and outputs. Among data that can be shared between components are expression datasets, interaction networks, sample and marker (gene) sets and sequences.
  • Dataset history tracking – complete record of data sets used and input settings.
  • Integration with 3rd party tools such as Genepattern, Cytoscape, and Genomespace.
  • Provides an environment which supports moving from one data type to another in a seamless fashion, e.g. from gene expression to sequences to patterns.
  • Provides access to a variety of external data sources, including:
    • Microarray gene expression repositories (caArray).
    • BLAST (NCBI).
    • Gene annotation pages (via bioDBNet).
    • Protein and DNA sequence retrieval (UC Santa Cruz and EBI).
    • Pathway diagrams (BioCarta).
  •  Provides a gateway to several computational services currently hosted on Columbia servers and clusters, including:
      • Pattern Discovery.
    • Pudge – protein structure modeling.
    • SkyBase – database of molecular models.

Specific types of data supported include:

  • Microarray Gene Expression:
    • GEO Soft: Series, Series Matrix, and Annotated Matrix (GDS).
    • MAGE-TAB data matrix.
    • Affymetrix GCOS/MAS5.
    • Matrix format (geWorkbench).
    • Tab-delimited (e.g. RMAExpress).
    • GenePix.
  • Microarray Gene Expression Annotation file support:
    • Affymetrix 3′ Expression.
    • Affymetrix WT Gene/Exon ST (transcript-level) including Gene Array 1.0/2.0 ST and Exon 1.0 ST.
  • DNA and Protein Sequences:
    • FASTA.
  • Pathways:
    • BioCarta.
  • Molecular structure – prediction, annotation and display.
  • Sequence Patterns:
    • Regular Expressions.
  • Gene Ontology.
  • Regulatory Networks.

Website: wiki.c2b2.columbia.edu/workbench
Support: Documentation, QuickStart
Developer: Columbia University, First Genetic Trust National Cancer Institute
License: BSD-like

geWorkbench

geWorkbench is written in Java. Learn Java with our recommended free books and free tutorials.

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