geWorkbench - User contributions [en]

Collaborative Development

2006-02-21T15:40:32Z

Califano:

{{DevelopersTopNav}}

We encourage developers of geWorkbench plugins to use our CVS server infrastructure. Our source code tree comprises 2 separate CVS modules named ''geWorkbench'' and ''components'' which corespond to the core and plugin code portions outlined in the "[[Developers]]" section.

Collaborative development takes place under the components module. The module contains a number of subdirectories, each corresponding to one geWorkbench plugin. Each subdirectory has the same basic structure:
* A '''src''' directory containing the plugin code.
* An optional '''lib''' directory containing jar files required by the plugin.

The application ant build script (which is made available to collaborative developers) will also create a '''classes''' directory which will contain the executable code. To create a new plugin called "example" a new directory with the same name will be created under the components module and CVS accounts will be issued to the members of the component development team. All developers in that team will become members of a new Unix group which will own the subdirectory (the rest of the world will have read-only rights).

A full development environment can be then obtained by checking out the 2 project CVS modules, "geWorkbench" and "components". In this development space the plugin development team will be able to change the code of their plugin as they please, check it in and out of CVS, use all the available build scripts, etc. However, they will only have read rights to the core "geWorkbench" module.

Plugins

2006-02-09T05:42:15Z

Califano: /* Sequence Analysis & Visualization */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters Viewer ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.||?
|-
|-
|Self Organizing Map (SOM)|| Clustering of markers using self organizing maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.||?
|-
|-
|T Test||Identification of markers with statistically significant differential expression between sets of microarrays. T-testing is used for the determination of significance ([[media:Volcanoplot.png|screenshot]]).||?
|-

|}

== Sequence Analysis & Visualization ==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Sequence Alignment||Server-based versions of BLAST and Smith-Waterman alignment.||?
|-
|-
|Synteny|| Comparison of sequence similarity between two genomic regions. The comparison results are visalized through a dot matrix augmented with detailed annotation for both regions.-||?
|-
|-
|Promoter Analysis||Identification of putative transcription factor binding sites in DNA sequences ([[media:Promoterpanel.png|screenshot]]). The analysis use the profiles in the [http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl JASPAR Transcription Factor Binding Profile Database.]||?

|-

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T23:15:33Z

Califano: /* Sequence Analysis & Visualization */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters Viewer ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.||?
|-
|-
|Self Organizing Map (SOM)|| Clustering of markers using self organizing maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.||?
|-
|-
|T Test||Identification of markers with statistically significant differential expression between sets of microarrays. T-testing is used for the determination of significance ([[media:Volcanoplot.png|screenshot]]).||?
|-

|}

== Sequence Analysis & Visualization ==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Sequence Alignment||Server-based versions of BLAST and Smith-Waterman alignment.||?
|-
|-
|Synteny|| Comparison of sequence similarity between two genomic regions. The comparison results are visalized through a dot matrix augmented with detailed annotation for both regions.-||?
|-
|-
|Promoter Analysis||Identification of putative transcription factor binding sites in upstream regions in DNA sequences ([[media:Promoterpanel.png|screenshot]]). The analysis use the profiles in the [http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl JASPAR Transcription Factor Binding Profile Database].||?

|-

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T23:14:28Z

Califano:

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters Viewer ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.||?
|-
|-
|Self Organizing Map (SOM)|| Clustering of markers using self organizing maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.||?
|-
|-
|T Test||Identification of markers with statistically significant differential expression between sets of microarrays. T-testing is used for the determination of significance ([[media:Volcanoplot.png|screenshot]]).||?
|-

|}

== Sequence Analysis & Visualization ==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Sequence Alignment||Server-based versions of BLAST and Smith-Waterman alignment.||?
|-
|-
|Synteny|| Comparison of sequence similarity between two genomic regions. The comparison results are visalized through a dot matrix augmented with detailed annotation for both regions.-||?
|-
|-
|Promoter Analysis||Identification of putative transcription factor binding sites in upstream regions in DNA sequences ([[media:Promoterpanel.png|screenshot]]). The analysis use the profiles in the JASPAR Transcription Factor Binding Profile Database, http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl).||?

|-

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T22:17:56Z

Califano: /* Analysis */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters Viewer ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.||?
|-
|-
|Self Organizing Map (SOM)|| Clustering of markers using self organizing maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.||?
|-
|-
|T Test||Identification of markers with statistically significant differential expression between sets of microarrays. T-testing is used for the determination of significance.||?
|-

|}

== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T22:08:24Z

Califano: /* Microarray Visualization */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters Viewer ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.||?
|-
|-
|Self Organizing Map (SOM)|| Clustering of markers using the dimensionality-reduction approach of self organizing maps. The resulting clusters can be visualized in the .||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}

== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T22:07:27Z

Califano: /* Analysis */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.||?
|-
|-
|Self Organizing Map (SOM)|| Clustering of markers using the dimensionality-reduction approach of self organizing maps. The resulting clusters can be visualized in the .||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}

== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T21:15:18Z

Califano: /* Network Generation */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analysis of large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
|-
|-
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}
== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T21:13:48Z

Califano: /* Network Generation */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
|-
|-
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}
== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T21:12:47Z

Califano: /* Network Generation */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks ([[media:Reverseengineering.png|screenshot]]).||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0] ([[media:Cytoscape.png|screenshot]]). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
|-
|-
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}
== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T21:04:04Z

Califano: /* Network Generation */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks.||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]. ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
|-
|-
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}
== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T21:03:06Z

Califano: /* Normalizers */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks.||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 2.0 (http://www.cytoscape.org/). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
|-
|-
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}
== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T20:54:40Z

Califano: /* Data Management */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that expression value distribution is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Measurements are divided by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks.||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 2.0 (http://www.cytoscape.org/). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
|-
|-
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}
== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}

Plugins

2006-02-08T20:53:31Z

Califano: /* Microarray Visualization */

__TOC__

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:

==Microarray Visualization==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).||Verified to work on 3.0
|-
|-

|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).||TBD
|-
|-
|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).||TBD
|-
|-
|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.||TBD
|-
|-

|Microarray Panel||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).|| TBD
|-
|-

|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).||TBD
|-
|-

|SOM Clusters ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). ||TBD
|-
|-

|Tabular Microarray Panel|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:TBD Tabular.png|screenshot]]).||
|-
|}

==Data Management==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Gene Panel ||Definition of data views consisting of marker subgroups. The views control how much data is displayed by only using values for markers in the defined groups.||TBD
|-
|-
|Phenotype Panel ||Definition of data views consisting of microarray subgroups. The views control how much data is displayed by only using values for microarrays in the defined groups.||TBD
|-
|-
|}

==Normalizers==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.||TBD
|-
|-
|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.||TBD
|-
|-
|Mean-Variance Normalizer||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.
||TBD
|-
|-
|Missing Value Calculation||Replacement of missing values with consensus values.
||TBD
|-
|-
|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.||TBD
|-
|Quantile || Expression measurements in each microarray are adjusted so that expression value distribution is the same across all microarrays in an experiment.||TBD
|-
|-
|Housekeeping || Measurements are divided by the average expression value of a (user defined) set of housekeeping genes.||TBD
|-

|}

==Annotation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Dataset History||Log of data transformations induced by data-modifying operations.||?
|-
|-
|Dataset Annotation||Free text format box used to annotate data, images and results. Such annotations persist application invocations and can be used as an online "lab notebook".||?
|-
|-
|Experiment Information||Microarray machine parameters used in an experiment run. If available, high-level experiment information (e.g., purpose of of experiment) are also displayed||?
|-
|-
|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.||TBD
|-
|-
|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).||TBD
|-
|Go Terms||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]). ||TBD
|-
|-
|}

==Network Generation==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|ARACNE Reverse Engineering|| Analyzes a large amount of microarray data (typically 100-500 microarrays) to reverse engineer underlying gene regulatory networks.||?
|-
|-
|-
|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using Cytoscape 2.0 (http://www.cytoscape.org/). ||?
|-
|}

==Analysis==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|Hierarchical Clustering||Hierarchical clustering groups markers into clusters on the basis of similarities in their expression profiles to form a hierarchical tree that can be viewed in the Dendrogram View window.||?
|-
|-
|Self Organizing Map (SOM)|| An algorithm to perform clustering of real vectors defined on an instance space of dimensionality.||?
|-
|-
|T Test||The t-test determines if for each marker there is a significant difference between two groups.The T-test analysis implementation is based on code from the Multi Experiment Viewer (MEV) platform (http://www.tm4.org/mev.html).||?
|-

|}
== Sequence Analysis==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Synteny|| A utility for comparison of extended genomic regions.-||?

|-
|}

== Pattern Discovery==
{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Promoter Panel||This visualization panel uses the JASPAR Transcription Factor Binding Profile Database (http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl ). The promoter panel can be used to visualize transcription factor binding sites (TFBS).||?

|-
|-

|Sequence Alignment||--.||?
|-

|-
|Sequence Panel||Displays result from the Sequence Discovery Component where each sequence in the selected dataset is displayed as a thin red line proportional to the sequence length.||?

|-
|-
|Position Histogram||Displays results from the Sequence Discovery analysis plotting the positions of SPLASH motifs as a Position Histogram.||?
|-
|-
|Dot Matrix ||Displays the syteny analysis results as a comparison of two genomic regions with detailed annotation for both regions. ||tbd
|-
|}
== Filters==

{|style="border: 1px solid lightGray"
!Plugin||Description||Compatibility
|-
|-
|Affy Detection Call||(''Affymetrix data only)'' Sets all measurements whose detection status is any user-defined combination of A, P or M as missing. ||TBD
|-
|-
|Deviation|| Sets all markers whose measurements deviate below a given value across all microarrays as missing.||?
|-
|-
|Expression Threshold|| Sets all markers whose measurements are inside (or outside) a user-defined range as missing.||?
|-
|-
|Genepix Flag Filter|| ''(Genepix data only)''Designate as “missing” measurements whose Flags column assume specific user selected values.||?
|-

|-
|Missing Values||Discards all markers that have “missing” measurements in a user-defined range of microarrays. Another filter must first be applied however, in order to generate the missing values upon which this filter can operate. ||TBD
|-
|-
|2-channel Threshold||(''Genepix data only)'' Defines applicable ranges for each channel, and sets all values for which either channel intensity is inside (or outside) the defined range as missing. ||TBD
|-
|}