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.
Key Features
- 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:
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- Pattern Discovery.
- Pudge – protein structure modeling.
- SkyBase – database of molecular models.
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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: github.com/floratos-lab/geworkbench-core
Support:
Developer: Columbia University, First Genetic Trust National Cancer Institute
License: BSD-like
geWorkbench is written in Java. Learn Java with our recommended free books and free tutorials.
Related Software
| Bioinformatics Tools | |
|---|---|
| Bioconductor | Analysis and comprehension of high-throughput genomic data |
| Biopython | Tools for biological computation written in Python |
| UGENE | Set of integrated bioinformatics software |
| BioPerl | Perl tools for computational molecular biology |
| GROMACS | Versatile package to perform molecular dynamics |
| IGV | High-performance visualization genome browser tool |
| GATK | Genomic analysis toolkit focused on variant discovery |
| BioJava | Provides Java tools for processing biological data |
| InterMine | Integrate biological data sources |
| bedtools | Powerful toolset for genome arithmetic |
| EMBOSS | The European Molecular Biology Open Software Suite |
| BLAST | Algorithm for comparing primary biological sequence information |
| Galaxy | Web-based platform for data-intensive computational research |
| minimap2 | Versatile sequence alignment program |
| Scanpy | Scalable analysis of single-cell gene expression data |
| Jalview | Multiple sequence alignment editing, visualisation and analysis |
| SeqKit | Fast toolkit for manipulating FASTA and FASTQ sequence files |
| samtools | Manipulate next-generation sequencing data |
| MultiQC | Aggregates results from multiple bioinformatics analyses |
| BCFtools | Variant calling and manipulating files in the Variant Call Format |
| Foldseek | Fast searching and comparison of large protein structure datasets |
| FastQC | Quality control tool for high throughput sequence data |
| SPAdes | Versatile toolkit for assembling and analysing sequencing data |
| GenomeTools | Collection of bioinformatics tools |
| AliView | Alignment viewer and editor |
| mothur | Analyze microbial communities |
| Bandage | Visualising de novo assembly graphs |
| cramino | BAM/CRAM quality evaluation |
| abPOA | Adaptive banded Partial Order Alignment |
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