geWorkbench

Revision as of 11:23, 26 February 2010

The geWorkbench platform employs a component repository infrastructure to manage a large collection of pluggable components that can be used to customize the application's graphical user interface. This (ever growing) list of plug-in components covers a wide range of fucntionality for a number of different genomic data modalities.

The Status of the pluggable components below is defined as:

Status	Comment
(a) Release	This plugin is part of the latest geWorkbench version.
(b) Development	This plugin is currently actively being developed.
(c) Suspension	This plugin is currently not actively being developed.
(d) Discontinued	This plugin is not part of geWorkbench anymore.

Analysis

Plugin	Status	Description
ANOVA	Release	Analysis of Variance - detection of significant differences in expression between more than two groups. (Screenshot)
Evidence Integration	Development	A sequence and structure-based approach for functional annotation and protein-protein interaction analysis.
Hierarchical Clustering	Release	Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin. (Screenshot)
KNN	Release	k-Nearest Neighbors analysis (a GenePattern component).
Mark-Us	Release	Assesses the biochemical function for a given protein structure. (Screenshot)
MatrixReduce	Release	Transcription Factor binding motifs. (Screenshot)
MEDUSA	Development	The Motif Element Detection Using Sequence Agglomeration is an integrative method for learning motif models of transcription factor binding sites by incorporating promoter sequence and gene expression data (Leslie Lab, MSKCC).
MRA	Release	The Master Regulator Analysis combines regulatory information from interaction networks with differential expression analysis. (Screenshot)
PCA	Release	Principal Component Analysis (a GenePattern component).
Pudge	Release	Computational protein structure prediction using sequence homology. It integrates tools used at different stages of the structural prediction process. (Screenshot Parameters, Screenshot Result)
SkyBase	Development	Database of protein structure models produced by SkyLine based on structures solved by the NESG structural genomics consortium.
SkyLine	Development	Automated high-throughput pipeline for reverse homology-based comparative protein structure modeling based on the input template structure.
SOM	Release	Clustering of markers using Self Organizing Maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin. (Screenshot)
SVM 3.0	Release	The Support Vector Machine is a supervised classification method that computes a maximal separating hyperplane between the expression vectors of different classes or phenotypes (a GenePattern component).
T-Test	Release	Identification of markers with statistically significant differential expression between sets of microarrays. (Screenshot Plot, Screenshot Mosaic)
Weighted Voting	Release	Weighted Voting Analysis (a GenePattern component).

Annotation

Plugin	Status	Description
Dataset Annotation	Release	Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online notebook.
Dataset History	Release	Log of data transformations induced by data-modifying operations.
Experiment Information	Release	Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed.
Gene Ontology	Release	Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations. (Screenshot)
Marker Annotations	Release	Retrieval of gene and pathway information for markers on a microarray (caBIO Pathways/Cancer Gene Index); it includes visualization of BioCarta pathway diagrams. (Screenshot Table, Screenshot BioCarta, Screenshot CGI)

Data Filtering

Plugin	Status	Description
Affy Detection Call	Release	Filtering of measurements based on the value of their "detection call" attribute (Affymetrix data only) .
Deviation Filter	Release	Filtering of markers with low dynamic range.
Expression Threshold	Release	Elimination of measurements that fall outside a range of explression values.
2-channel Threshold	Release	Same as "Expression Threshold" filter but different threshold ranges can be specified for each channel (GenePix data only).
Genepix Flag Filter	Release	Filtering of measurements based on the value of their "Flags" attribute (GenePix data only).
Missing Value Filter	Release	Discards all markers that have missing measurements in more than a user specified number N of microarrays.

Data Management

Plugin	Status	Description
Arrays/Phenotypes	Release	Definition of data views consisting of microarray subgroups. The views control the amount of data displayed. (Screenshot)
Markers	Release	Definition of data views consisting of marker subgroups. The views control the amount of data displayed. (Screenshot)
Project Folders	Release	Manages projects and workspaces of the user. (Screenshot)

File Import

Plugin	Status	Description
Affymetrix CEL	Release	Loads Affymetrix probe CELl intensity files ("*.cel").
Affymetrix File Matrix	Release	Loads Affymetrix EXPperiment files ("*.exp").
Affymetrix MAS5/GCOS	Release	Loads output files from the GeneChip Operating Software formerly known as MAS5 Statistical algorithm (several different file extension).
FASTA Format	Release	Loads files that are in FASTA format (".fasta" and ".txt").
Genepix File Format	Release	Loads files in GenePix Result format ("*.gpr").
PDB Structure Format	Release	Loads files in the Protein Data Base format ("*.pdb")
Tab-delimited (RMA Express Format)	Release	Loads tab-delimited files from the Robust Multichip Analysis ("*.txt")

Menu Tools

Plugin	Status	Description
CCM	Release	The Component Configuration Manager allows users to manage plugins dynamically at any given time in the application environment. (Screenshot)
genSpace	Release	It logs information about the analysis tools used in geWorkbench in order to enable collaboration support for the geWorkbench users.
Online Help	Release	geWorkbench Online Help uses the Java help 2.0 system to provide real-time help on component questions.
Preferences	Release	Allows users to predefine a few basic visual settings and choose a Text Editor.
Version Information	Release	Provides basic information about the currently installed user version of geWorkbench.
Welcome Screen	Release	Introduction to geWorkbench during the initial opening of the application.

Network Generation

Plugin	Status	Description
ARACNe	Release	The Algorithm for the Reconstruction of Accurate Cellular Networks analyses large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks. (Screenshot)
caArray	Release	Search and download of gene expression data from instances of caArray (NCI microarray database product).
Cancer GEMS	Development	Interface to the NCI Cancer Genetic Markers of Susceptibility project.
CNKB	Release	The Cellular Networks Knowledge Base queries an in-house repository of locally generated B-cell interaction network data and information from external databases in order to build a network of interactions for selected genes. (Screenshot Throttle Graph, Screenshot Network)
Cytoscape	Release	Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 1.0. (Screenshot)
MINDy	Release	The Modulator Inference by Network Dynamics algorithm extends ARACNe to include detecting the influence of modulators of transcription factor activity.
NetBoost	Development	NetBoost is a network characterization algorithm.

Normalization

Plugin	Status	Description
Array-Based Centering	Release	Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.
Housekeeping Normalizer	Release	Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.
Log2 Normalizer	Release	Applies a log2 transformation to all measurements in a microarray.
Marker-Based Centering	Release	Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.
Mean-Variance Normalizer	Release	Transformation of expression measurements to standard units: for every marker, the mean measurement of the marker profile (across all microarrays in an experiment) is subtracted from each measurement in the profile and the resulting value is divided by the standard deviation of the profile.
Missing Value Normalizer	Release	Replacement of missing values with consensus values.
Quantile Normalizer	Release	Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.
Threshold Normalizer	Release	Adjustment of values that fall outside a user-specified threshold.

Sequence Analysis & Visualization

Plugin	Status	Description
Alignment Results	Release	It parses and displays the results of sequence similarity searches which were run on the NCBI BLAST service. (Screenshot)
Pattern Discovery	Release	Discovery of sequence motifs in sets of DNA and protein sequences. (Screenshot)
Position Histogram	Release	Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match. (Screenshot)
Promoter Analysis	Release	Identification of putative transcription factor binding sites in DNA sequences. The analysis use the profiles in the JASPAR Transcription Factor Binding Profile Database. (Screenshot Logo, Screenshot Sequence 1, Screenshot Sequence 2)
Sequence Alignment	Release	Run jobs on the NCBI BLAST servers directly within geWorkbench.
Sequence Panel	Release	Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.
Sequence Retriever	Release	Retrieve sequences for annotated markers from Santa Cruz (Nucleotides) and EBI (Proteins). (Screenshot)
Synteny	Discontinued	Comparison of sequence similarity between two genomic regions. The comparison results are represented as a dot matrix augmented with detailed annotation for both regions.

Visualization

Plugin	Status	Description
Analysis Panel	Release	Framework to support numerous, individually loadable analysis methods.
ANOVA Tabular Viewer	Release	Displays the results of ANOVA analysis of gene expression data in tabular format. (Screenshot)
CEL Image Viewer	Release	Visualization of data in Affymetrix CEL files. (Screenshot)
Color Mosaic	Release	Heat maps for microarray expression data, organized by phenotypic or gene groupings. (Screenshot)
Dendrogram	Release	Tree-structured diagrams reflecting the results of hierarchical clustering analysis. (Screenshot)
Evidence Integration Viewer	Development	Displays the results of the Evidence Integration analysis.
Expression Profiles	Release	Line graph of genes expression profiles across several arrays/ hybridizations. (Screenshot)
Expression Value Distribution	Release	Distribution plot of marker expression values across one or more microarrays. (Screenshot)
GeneWays	Release	An essential component needed to display elements in Cytoscape and ARACNe.
GO Terms Viewer	Release	Displays the results of Gene Ontology Enrichment Analysis. (Screenshot)
Image Viewer	Release	Visualization of screenshots saved within geWorkbench (e.g. dendrograms).
Jmol	Release	Visualization of 3D protein structures from PDB files. (Screenshot)
Mark-Us Browser	Release	Displays the results of a Mark-Us analysis. (Screenshot)
MatrixReduce	Release	Visualization of MatrixReduce calculations using logo, chromosomal and tabular displays.
MEDUSA Viewer	Development	Displays the results of a MEDUSA analysis.
Microarray Viewer	Release	Color-gradient representation of gene expression values. (Screenshot)
MINDy Viewer	Release	The results of a MINDy calculation are presented in several different tabular displays and a heat map.
MRA Viewer	Release	Displays the results of the MRA in tablular and graphical form. (Screenshot)
NetBoost Viewer	Development	Displays a Boosting Iteration Graph, Confusion Matrix and Score Table from NetBoost Analysis.
Normalization Panel	Release	Framework to support numerous, individually loadable normalization components.
PCA Viewer	Release	Displays PCA results.
Pudge Browser	Release	Visualization of Pudge results. (Screenshot Parameters, Screenshot Result)
Scatter Plot	Release	Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values. (Screenshot Array, Screenshot Marker)
SkyBase Viewer	Development	Displays the results from the SkyBase search.
SkyLine Output All	Development	Displays all models from the Skyline modeling.
SkyLine Output Each	Development	Displays each model from the Skyline modeling.
SOM Clusters Viewer	Release	Visualization of gene clusters produced by the self-organizing maps analysis. (Screenshot)
SVM Viewer	Release	Visualizes results obtained from classifying samples based on SVMs generated using the Gene Pattern v3 SVM service.
Tabular Microarray Viewer	Release	Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray. (Screenshot)
Volcano Plot	Release	Visualize fold-change vs significance (P-value) for t-test results. (Screenshot)

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+|width="150"|ANOVA Tabular Viewer||Release||Displays the results of ANOVA analysis of gene expression  data in tabular format. ([[media:T_ANOVA_Tabular_Viewer.png|Screenshot]])
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