geWorkbench - User contributions [en]

File:Columbia Logo.jpg

2022-03-04T18:40:57Z

Floratos:

File:Geworkbench banner.png

2022-03-03T22:27:55Z

Floratos: Floratos uploaded a new version of File:Geworkbench banner.png

MediaWiki:Common.css

2022-03-02T22:16:11Z

Floratos:

/** CSS placed here will be applied to all skins **/

/**
* remove Toolbox
#p-tb { display:none !important; }
**/

/** Collapsible tables *********************************************************
*
* Description: Allows tables to be collapsed, showing only the header. See
* http://www.mediawiki.org/wiki/Manual:Collapsible_tables.
* Maintainers: [[en:User:R. Koot]]
*/

table.collapsed tr.collapsible {
display: none;
}

.collapseButton { /* 'show'/'hide' buttons created dynamically by the */
float: right; /* CollapsibleTables JavaScript in [[MediaWiki:Common.js]] */
font-weight: normal; /* are styled here so they can be customised. */
text-align: right;
width: auto;
}

/* The following line hides the title of the Home page - NOT WORKING WITH ERUDITE?*/
body.page-Home h1.firstHeading { display:none; }
/*
body.page-Home.action-view h1.firstHeading, body.page-Home.action-submit h1.firstHeading { display: none; }
*/

MediaWiki:Erudite.css

2022-03-02T22:13:36Z

Floratos: Blanked the page

MediaWiki:Erudite.css

2022-03-02T22:13:03Z

Floratos: Created page with "/* The following line hides the title of the Home page */ body.page-Home h1.firstHeading { display:none; } body.page-Home.action-view h1.firstHeading, body.page-Home.action-su..."

/* The following line hides the title of the Home page */
body.page-Home h1.firstHeading { display:none; }
body.page-Home.action-view h1.firstHeading, body.page-Home.action-submit h1.firstHeading { display: none; }

MediaWiki:Common.css

2022-03-02T21:59:42Z

Floratos:

/** CSS placed here will be applied to all skins **/

/**
* remove Toolbox
#p-tb { display:none !important; }
**/

/** Collapsible tables *********************************************************
*
* Description: Allows tables to be collapsed, showing only the header. See
* http://www.mediawiki.org/wiki/Manual:Collapsible_tables.
* Maintainers: [[en:User:R. Koot]]
*/

table.collapsed tr.collapsible {
display: none;
}

.collapseButton { /* 'show'/'hide' buttons created dynamically by the */
float: right; /* CollapsibleTables JavaScript in [[MediaWiki:Common.js]] */
font-weight: normal; /* are styled here so they can be customised. */
text-align: right;
width: auto;
}

/* The following line hides the title of the Home page */
body.page-Home h1.firstHeading { display:none; }
body.rootpage-Home.action-view h1.firstHeading, body.rootpage-Home.action-submit h1.firstHeading { display: none; }

MediaWiki:Common.css

2022-03-02T21:53:09Z

Floratos:

/** CSS placed here will be applied to all skins **/

/**
* remove Toolbox
#p-tb { display:none !important; }
**/

/** Collapsible tables *********************************************************
*
* Description: Allows tables to be collapsed, showing only the header. See
* http://www.mediawiki.org/wiki/Manual:Collapsible_tables.
* Maintainers: [[en:User:R. Koot]]
*/

table.collapsed tr.collapsible {
display: none;
}

.collapseButton { /* 'show'/'hide' buttons created dynamically by the */
float: right; /* CollapsibleTables JavaScript in [[MediaWiki:Common.js]] */
font-weight: normal; /* are styled here so they can be customised. */
text-align: right;
width: auto;
}

/* The following line hides the title of the Home page */
body.page-Home h1.firstHeading { display:none; }
body.page-Home.action-view h1.firstHeading, body.page-Home.action-submit h1.firstHeading { display: none; }

MediaWiki:Common.css

2022-03-02T21:51:53Z

Floratos:

/** CSS placed here will be applied to all skins **/

/**
* remove Toolbox
#p-tb { display:none !important; }
**/

/** Collapsible tables *********************************************************
*
* Description: Allows tables to be collapsed, showing only the header. See
* http://www.mediawiki.org/wiki/Manual:Collapsible_tables.
* Maintainers: [[en:User:R. Koot]]
*/

table.collapsed tr.collapsible {
display: none;
}

.collapseButton { /* 'show'/'hide' buttons created dynamically by the */
float: right; /* CollapsibleTables JavaScript in [[MediaWiki:Common.js]] */
font-weight: normal; /* are styled here so they can be customised. */
text-align: right;
width: auto;
}

/* The following line hides the title of the Home page */
body.page-Home h1.firstHeading { display:none; }
body.page-Home.action-view h1.firstHeading, body.page-Main_Page.action-submit h1.firstHeading { display: none; }

Home

2022-03-02T21:47:24Z

Floratos:

__NOTOC__


[[Image:geworkbench_banner.png]]

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.6.0.3) was released on December 21, 2016.
* [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.6.0|See changes included in latest release]].
* [[Release_Descriptions|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].

|-
|style="background-color: #D8FAFA;" colspan="2"|
<h2>Web-enabled Version</h2>
[[GeWorkbench-web/Overview|'''geWorkbench-web''']] provides installation-free access to the geWorkbench plug-ins through a pure browser interface. You can create and account and access the application at: http://geworkbench.c2b2.columbia.edu/geworkbench/.
|}

MediaWiki:Tagline

2022-03-02T21:41:29Z

Floratos: Created page with ""

Home

2022-03-02T18:18:46Z

Floratos:

__NOTOC__


[[Image:geworkbench_banner.png]]

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.6.0.3) was released on December 21, 2016.
* [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.6.0|See changes included in latest release]].
* [[Release_Descriptions|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].

|-
|style="background-color: #D8FAFA;" colspan="2"|
''<h4><center><font color="red">New web-enabled version available</font></center></h4>''
[[GeWorkbench-web/Overview|'''geWorkbench-web''']] provides installation-free access to the geWorkbench plug-ins through a pure browser interface. You can create and account and access the application at: http://geworkbench.c2b2.columbia.edu/geworkbench/.
|}

File:Geworkbench banner.png

2022-03-02T18:14:46Z

Floratos:

Home

2022-03-02T16:17:57Z

Floratos:

__NOTOC__


{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.6.0.3) was released on December 21, 2016.
* [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.6.0|See changes included in latest release]].
* [[Release_Descriptions|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].

|-
|style="background-color: #D8FAFA;" colspan="2"|
''<h4><center><font color="red">New web-enabled version available</font></center></h4>''
[[GeWorkbench-web/Overview|'''geWorkbench-web''']] provides installation-free access to the geWorkbench plug-ins through a pure browser interface. You can create and account and access the application at: http://geworkbench.c2b2.columbia.edu/geworkbench/.
|}

GeWorkbench-web/Tutorials

2016-09-22T14:35:29Z

Floratos: /* Relevant Desktop Version Tutorials */

{{Template:GeWorkbench-webTutorialsTopNav}}

==Overview==

The web-version of geWorkbench (geWorkbench-web) has its own set of tutorial pages. However, for some topics, a link to the desktop page is provided until an appropriate geWorkbench-web version is created.

==List of geWorkbench-web Tutorials==
* [[GeWorkbench-web/Overview|Overview]] - Introduction to geWorkbench-web and its Workspace.
* [[GeWorkbench-web/File_Formats|File Formats]] - List of data types and file formats supported by geWorkbench-web.
* [[GeWorkbench-web/Set_View |Set-View]] - As with the desktop version of geWorkbench, working with sets of arrays and markers is central to using the application.
* [[GeWorkbench-web/ANOVA| ANOVA]] - Analysis of Variance
* [[GeWorkbench-web/Cellular_Networks_KnowledgeBase | Cellular_Networks_KnowledgeBase]] - Query a wide selection of molecular and regulatory interaction databases.
* [[GeWorkbench-web/Hierarchical_Clustering| Hierarchical_Clustering]] - Run hierarchical clustering to find groups of markers or arrays with similar expression profiles.
* [[GeWorkbench-web/T-Test|T-Test]] - Test whether a significant difference in expression exists between two groups of microarrays.

==Relevant Desktop Version Tutorials==


* [[MarkUs | MarkUs ]] - Functional analysis of protein structures.

GeWorkbench-web/Tutorials

2016-09-22T14:35:01Z

Floratos: /* List of geWorkbench-web Tutorials */

{{Template:GeWorkbench-webTutorialsTopNav}}

==Overview==

The web-version of geWorkbench (geWorkbench-web) has its own set of tutorial pages. However, for some topics, a link to the desktop page is provided until an appropriate geWorkbench-web version is created.

==List of geWorkbench-web Tutorials==
* [[GeWorkbench-web/Overview|Overview]] - Introduction to geWorkbench-web and its Workspace.
* [[GeWorkbench-web/File_Formats|File Formats]] - List of data types and file formats supported by geWorkbench-web.
* [[GeWorkbench-web/Set_View |Set-View]] - As with the desktop version of geWorkbench, working with sets of arrays and markers is central to using the application.
* [[GeWorkbench-web/ANOVA| ANOVA]] - Analysis of Variance
* [[GeWorkbench-web/Cellular_Networks_KnowledgeBase | Cellular_Networks_KnowledgeBase]] - Query a wide selection of molecular and regulatory interaction databases.
* [[GeWorkbench-web/Hierarchical_Clustering| Hierarchical_Clustering]] - Run hierarchical clustering to find groups of markers or arrays with similar expression profiles.
* [[GeWorkbench-web/T-Test|T-Test]] - Test whether a significant difference in expression exists between two groups of microarrays.

==Relevant Desktop Version Tutorials==

* [[File_Formats | File Formats]] - Several file types described for the desktop version are also used in geWorkbench-web, including the tab-delimited, "Affymetrix (.exp)", and adjacency matrix formats.
* [[MarkUs | MarkUs ]] - Functional analysis of protein structures.

Home

2016-09-22T14:32:18Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
MarkUs_home_gallery.PNG
Dendrogram_home_gallery.PNG
Volcano_plot_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Motif_discovery_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.6.0.2) was released on February 20th, 2015.
* [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.6.0|See changes included in latest release]].
* [[Release_Descriptions|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].

|-
|style="background-color: #D8FAFA;" colspan="2"|
''<h4><center><font color="red">New web-enabled version available</font></center></h4>''
[[GeWorkbench-web/Overview|'''geWorkbench-web''']] provides installation-free access to the geWorkbench plug-ins through a pure browser interface. You can create and account and access the application at: http://geworkbench.c2b2.columbia.edu/geworkbench/.
|}

GeWorkbench-web/File Formats

2016-09-22T14:31:25Z

Floratos:

geWorkbench-web supports two types of data:
* Macromolecular structure data in the [http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html PDB file format].
* Gene expression data in either of the following two formats:
** [[File_Formats#Affymetrix_File_Matrix_Format_.28geWorkbench_.22.exp.22_format.29 | Affymetrix File Matrix format]].
** [[File_Formats#Tab-delimited_format | Tab-delimited format]].

Template:GeWorkbench-webTutorialsTopNav

2016-09-22T14:22:32Z

Floratos:

{| class = "wikitable" border="1" cellpadding="5" width="700px"
|
[[geWorkbench-web/Tutorials | Home]] |
[[geWorkbench-web/Overview | Overview]] |
[[geWorkbench-web/Set_View | Set View]] |
[[geWorkbench-web/File_Formats | File Formats]] |
[[Tutorials | Desktop Tutorials ]]
||
[[geWorkbench-web/ANOVA| ANOVA]] |
[[geWorkbench-web/ARACNe| ARACNe]] |
[[geWorkbench-web/Cellular_Networks_KnowledgeBase | Cellular Networks KnowledgeBase]] |
[[geWorkbench-web/Gene_Ontology| Gene Ontology]] |
[[geWorkbench-web/Hierarchical_Clustering|Hierarchical Clustering]] |
[[geWorkbench-web/MarkUs | MarkUs ]] |
[[geWorkbench-web/msViper| msViper]] |
[[geWorkbench-web/T-Test|T-Test]]
|}
<br/>

GeWorkbench-web/File Formats

2016-09-22T14:21:30Z

Floratos:

geWorkbench-Web supports two types of data:
* Macromolecular structure data in the [http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html PDB file format].
* Gene expression data in either of the following two formats:
** [[File_Formats#Affymetrix_File_Matrix_Format_.28geWorkbench_.22.exp.22_format.29 | Affymetrix File Matrix format]].
** [[File_Formats#Tab-delimited_format | Tab-delimited format]].

GeWorkbench-web/File Formats

2016-09-22T14:21:08Z

Floratos:

GeWorkbench-web/File Formats

2016-09-21T16:35:09Z

Floratos: Created page with "geWorkbench-web supports the upload of macromolecular structure data, in the [http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html PDB file format], as well as gene e..."

geWorkbench-web supports the upload of macromolecular structure data, in the [http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html PDB file format], as well as gene expression data conforming to either of the following two formats:
* [[File_Formats#Affymetrix_File_Matrix_Format_.28geWorkbench_.22.exp.22_format.29 | Affymetrix File Matrix format]].
* [[File_Formats#Tab-delimited_format | Tab-delimited format]].

Home

2015-11-09T15:01:28Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
MarkUs_home_gallery.PNG
Dendrogram_home_gallery.PNG
Volcano_plot_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Motif_discovery_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.6.0.2) was released on February 20th, 2015.
* [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.6.0|See changes included in latest release]].
* [[Release_Descriptions|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].

|-
|style="background-color: #D8FAFA;" colspan="2"|
''<h4><center><font color="red">New web-enabled version available</font></center></h4>''
[[GeWorkbench-web/Overview|'''geWorkbench-Web''']] provides installation-free access to the geWorkbench plug-ins through a pure browser interface. You can create and account and access the application at: http://geworkbench.c2b2.columbia.edu/geworkbench/.
|}

Project Documentation

2015-07-10T04:01:15Z

Floratos:

* '''Tutorials''': The most current source of documentation is provided by the [[GeWorkbench_Tutorials | geWorkbench tutorials]]. The tutorials explain how to perform a number of common tasks using geWorkbench, and form a complete online user manual.

GeWorkbench Tutorials

2015-06-16T18:42:14Z

Floratos: Created page with "* Desktop version. * Web version."

* [[Tutorials | Desktop version]].
* [[GeWorkbench-web/Tutorials | Web version]].

MediaWiki:Sidebar

2015-06-16T18:41:04Z

Floratos:

Template:GeWorkbench-webTutorialsTopNav

2015-06-16T18:39:21Z

Floratos:

{| class = "wikitable" border="1" cellpadding="5" width="700px"
|
[[geWorkbench-web/Tutorials | Home]] |
[[geWorkbench-web/Overview|Overview]] |
[[geWorkbench-web/Set_View |Set View]] |
[[File_Formats | File Formats (desktop)]]
||
[[geWorkbench-web/ANOVA| ANOVA]] |
[[geWorkbench-web/Cellular_Networks_KnowledgeBase | Cellular Networks KnowledgeBase]] |
[[geWorkbench-web/Hierarchical_Clustering|Hierarchical Clustering]] |
[[MarkUs | MarkUs (desktop)]] |
[[geWorkbench-web/T-Test|T-Test]]
|}
<br/>

Home

2014-10-22T03:51:51Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
MarkUs_home_gallery.PNG
Dendrogram_home_gallery.PNG
Volcano_plot_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Motif_discovery_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.5.1) was released on November 1st, 2013.
* [[Release_Descriptions#Brief_overview_of_changes_in_geWorkbench_release_2.5.1|See changes included in latest release]].
* [[Release_Descriptions|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].
|-
|style="background-color: #D8FAFA;" colspan="2"|
''<h4><center><font color="red">New web-enabled version available</font></center></h4>''
'''geWorkbench-Web''' provides installation-free access to the geWorkbench plug-ins through a pure browser interface. A beta release is available for testing at: http://geworkbench.c2b2.columbia.edu/geworkbench/.
|}

GeWorkbench License

2014-06-15T21:40:48Z

Floratos:

{{DownloadTopNav}}

<center>
'''geWORKBENCH SOFTWARE LICENSE AGREEMENT'''

''Copyright 2004-{{CURRENTYEAR}} COLUMBIA University''
</center>

This software was developed by Columbia University in conjunction with First Genetic Trust and the National Cancer Institute, and so to the extent government employees are co-authors, any rights in such works shall be subject to Title 17 of the United States Code, section 105.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

2. The end-user documentation included with the redistribution, if any, must include the following acknowledgment:

"This product includes software developed by the Columbia University, First Genetic Trust and the National Cancer Institute."

If no such end-user documentation is to be included, this acknowledgment shall appear in the software itself, wherever such third-party acknowledgments normally appear.


3. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE DISCLAIMED. IN NO EVENT SHALL THE COLUMBIA UNVIERSITY OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

All other product names mentioned herein and throughout the entire project are trademarks of their respective owners.

CNKB Data

2013-11-07T17:40:42Z

Floratos:

The Cellular Networks Knowledge Base (CNKB) component in geWorkbench 2.0.0 lists the following interactomes for query. However, some data has not yet be released and is password protected, and other data sets are not yet ready for query.

Data that is currently available for query is shown in light green.

==CNKB Data Summary==

{| border="1" cellpadding="5" cellspacing="0" style="margin:10px;font-size:75%;width:800px"
|-style="color:black;background-color:#AAFFAA;"
!Name
!Version
!Interaction Types
!Availability
!Date of release
!Number of interactions
!Data source

|-style="color:black;background-color:#CCFFCC;"
|BCi
|1.0
|"protein-dna", "protein-protein", "TF-modulator"
|open
|01/2008
|41,727; 22,554; 1,912
|Califano lab

|-style="color:black;background-color:#CCFFCC;"
|[http://thebiogrid.org/ BioGRID]
|2.0.61
|"protein-protein"
|open
|align="center"|—
|178,546
|align="center"|—

|-style="color:black;background-color:#FFFFFF;"
|[http://dip.doe-mbi.ucla.edu DIP]
|2.4
|"physical interaction","direct interaction","physical association","covalent binding","association","deacetylation reaction","acetylation reaction","phosphorylation reaction","dephosphorylation reaction"
|not ready
|align="center"|—
|39,412
|align="center"|—

|-style="color:black;background-color:#CCFFCC;"
|Geneways
|6.0
|"protein-protein"
|open
|align="center"|—
|26,931
|Rzhetsky lab

|-style="color:black;background-color:#CCFFCC;"
|HGi_Phillips
|1.0
|"protein-dna"
|open
|12/15/2009
|118,114
|Califano lab

|-style="color:black;background-color:#FFFFFF;"
|HGi_Sun
|1.0
|"protein-dna"
|pending publication
|12/15/2009
|54,595
|Califano lab

|-style="color:black;background-color:#CCFFCC;"
|HGi_TCGA
|1.0
|"protein-dna", "mRNA-miRNA"
|open
|12/15/2009
|46,227; 5,156
|Califano lab

|-style="color:black;background-color:#FFFFFF;"
|HGi_TCGA
|2.0
|"TF-modulator"
|pending publication
|03/15/2010
|15,071
|Califano lab

|-style="color:black;background-color:#CCFFCC;"
|[http://www.hprd.org/ HPRD]
|8.0
|"protein-protein"
|open
|align="center"|—
|44,428
|align="center"|—

|-style="color:black;background-color:#FFFFFF;"
|[http://www.ebi.ac.uk/intact IntAct]
|2.0.0
|"protein-protein"
|not ready
|align="center"|—
|202,052
|align="center"|—

|-style="color:black;background-color:#CCFFCC;"
|[http://www.reactome.org/ Reactome]
|31
|"neighboring_reaction","reaction","direct_complex","indirect_complex"
|open
|align="center"|—
|172,295
|align="center"|—

|-style="color:black;background-color:#FFFFFF;"
|[http://mint.bio.uniroma2.it MINT]
|2.6
|"physical association","colocalization","phosphorylation reaction","direct interaction","sumoylation reaction","dephosphorylation reaction","association","methylation reaction","ubiquitination reaction","covalent binding","deacetylation reaction","physical interaction","cleavage reaction","enzymatic reaction","disulfide bond","glycosylation reaction","acetylation reaction","neddylation reaction","hydroxylation reaction","deneddylation reaction"
|not ready
|align="center"|—
|18,634
|align="center"|—

|-style="color:black;background-color:#CCFFCC;"
|align="center"|—
|align="center"|—
|align="center"|—
|align="center"|—
|align="center"|—
|align="center"|—
|align="center"|—
|}

==Local abbreviations used==

* '''BCi''' - B-Cell interactome, produced by an ARACNe run on B-Cell microarray data from the lab of Dr. Ricardo Dalla-Favera.
* '''HGi''' - Human High-Grade Glioma interactome, produced by analysis of microarray data from several sources:
** '''Phillips''' - data published by Phillips et al. ...
** '''Sun''' - data published by Sun et al. ...
** '''TCGA''' - data obtained from The Cancer Genome Atlas project (NCI).

==Notes==

* '''HGi version 1.0''' - interactome derived from ARACNe runs (transcriptional).
* '''HGi version 2.0''' - interactome derived from a MINDy run (TCGA data only) (post-translational).

Home

2013-09-16T04:29:10Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
MarkUs_home_gallery.PNG
Dendrogram_home_gallery.PNG
Volcano_plot_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Motif_discovery_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.4.1) was released on October 26th, 2012.
* [[Previous_Releases#Brief_overview_of_changes_in_geWorkbench_release_2.4.1|See changes included in latest release]].
* [[Previous_Releases|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].
|}

Home

2013-09-16T04:28:46Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
MarkUs_home_gallery.PNG
Dendrogram_home_gallery.PNG
Volcano_plot_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Motif_discovery_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production version of geWorkbench (v2.4.1) was released October 26th, 2012.
* [[Previous_Releases#Brief_overview_of_changes_in_geWorkbench_release_2.4.1|See changes included in latest release]].
* [[Previous_Releases|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].
|}

Template:DevelopersTopNav

2013-08-18T13:03:27Z

Floratos:

{| class = "wikitable" border="1" cellpadding="5" width="700px"
|
[[Developers | Developers Home]] |
[[A Simple Plugin]] |
[[.GEAR_files | geWorkbench Archive Files]] |
[[Collaborative Development]] |
[[Design Documentation]] |
[{{SERVER}}/workbench/api/index.html Javadocs] |
[http://gforge.nci.nih.gov/projects/geworkbench gForge Page] |
[[Report Defects]]
|}
<br/>

Template:TutorialsTopNav

2013-08-18T13:02:40Z

Floratos:

{| class = "wikitable" border="1" cellpadding="5" width="700px"
|
[[Tutorials | Home]] |
[[QuickStart | Quick Start]] |
[[Basics | Basics]] |
[[Menu_Bar | Menu Bar]] |
[[Preferences | Preferences]] |
[[Component Configuration Manager | Component Configuration Manager]] |
[[Project Folders| Project Folders]] |
[[Information_Panel | Information Panel]] |
[[Local Data Files | Local Data Files]] |
[[File_Formats | File Formats]] |
[[caArray | caArray]] |
[[Array_Sets | Array Sets]] |
[[Marker_Sets| Marker Sets]] |
[[Viewing a Microarray Dataset | Viewing a Microarray Dataset]] |
[[Filtering| Filtering]] |
[[Normalization| Normalization]] |
[[Tutorial_Data | Tutorial Data]]
||
[[Analysis Framework | Analysis Framework]] |
[[ANOVA | ANOVA]] |
[[ARACNe | ARACNe]] |
[[BLAST | BLAST]] |
[[Cellular_Networks_KnowledgeBase | Cellular Networks KnowledgeBase]] |
[[Classification | Classification]] |
[[Color_Mosaic | Color Mosaic]] |
[[Cytoscape Network Viewer | Cytoscape]] |
[[Differential Expression | Differential Expression (t-test)]] |
[[Expression Value Distribution | Expression Value Distribution]] |
[[Fold_Change| Fold-Change]] |
[[Gene_Ontology_Term_Analysis | Gene Ontology Term Analysis]] |
[[Gene_Ontology_Viewer | Gene Ontology Viewer]] |
[[genSpace | genSpace]] |
[[Grid_Services | Grid Services]] |
[[GSEA | GSEA]] |
[[Hierarchical Clustering | Hierarchical Clustering ]] |
[[IDEA | IDEA]] |
[[Jmol | Jmol]] |
[[Marker Annotations | Marker Annotations]] |
[[MarkUs | MarkUs]] |
[[Master Regulator Analysis | Master Regulator Analysis]] |
[[MRA-FET| (MRA-FET Method)]] |
[[MARINa | (MRA-MARINa Method)]] |
[[MatrixREDUCE | MatrixREDUCE]] |
[[MINDy| MINDy]] |
[[Pattern Discovery | Pattern Discovery]] |
[[Promoter Analysis | Promoter Analysis]] |
[[Pudge | Pudge]] |
[[SAM | SAM]] |
[[Sequence_Retriever | Sequence Retriever]] |
[[SkyBase | SkyBase]] |
[[SkyLine | SkyLine]] |
[[SOM | SOM]] |
[[SVM | SVM]] |
[[Volcano_Plot|Volcano Plot]]
|}
<br/>

Home

2013-08-18T13:00:27Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
MarkUs_home_gallery.PNG
Dendrogram_home_gallery.PNG
Volcano_plot_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Motif_discovery_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10" width="700px"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production release of geWorkbenc (v2.4.1) was released October 26th, 2012.
* [[Previous_Releases#Brief_overview_of_changes_in_geWorkbench_release_2.4.1|See changes included in latest release]].
* [[Previous_Releases|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].
|}

Support

2013-08-18T12:56:41Z

Floratos:

* [[Community |Access to end-user and developer forums]].
* [[FAQ |Frequently asked questions]].
* [[Known Issues |Known issues]].

Template:DevelopersTopNav

2013-08-18T12:55:13Z

Floratos:

{| class = "wikitable" border="1" cellpadding="5"
|
[[Developers | Developers Home]] |
[[A Simple Plugin]] |
[[.GEAR_files | geWorkbench Archive Files]] |
[[Collaborative Development]] |
[[Design Documentation]] |
[{{SERVER}}/workbench/api/index.html Javadocs] |
[http://gforge.nci.nih.gov/projects/geworkbench gForge Page] |
[[Report Defects]]
|}
<br/>

MediaWiki:Sidebar

2013-08-18T12:52:09Z

Floratos:

MediaWiki:Sidebar

2013-08-18T12:51:52Z

Floratos:

Support

2013-08-18T12:50:57Z

Floratos: Created page with "* Access to documentation and user/developer forums. * Frequently asked questions. * Known issues."

* [[Community |Access to documentation and user/developer forums]].
* [[FAQ |Frequently asked questions]].
* [[Known Issues |Known issues]].

Screenshots

2013-07-18T17:00:14Z

Floratos: /* Cellular Network Knowledge Base */

==Overview==



The geWorkbench graphical interface with a CNKB query result dislayed in Cytoscape.

[[Image:GeWorkbench_2.3.0_Main_Cytoscape_no_frame.png|{{ImageMaxWidth}}]]

==geWorkbench Configuration==

===Component Configuration Manager===

Individual components can be loaded as needed.

[[Image:CCM_Main.png|{{ImageMaxWidth}}]]

==Project and Data Management==

===Project Folders===

Data sets are loaded into "projects" within a workspace. Individual analysis results are stored under their parent dataset.

[[Image:T_ANOVA_Saved_Color_Mosaic_View.png]]

===Array/Phenotypes===
Sets of arrays can be defined and included or excluded from particular analyses (via checkboxes). Sets can be individually marked as belonging to case (here indicated with a red thumbtack) or control groups.

[[Image:T-test_Set_selection_BCell.png]]

===Markers===
Sets of arrays can be defined and included or excluded from particular analyses (via checkboxes).

[[Image:Marker_Sets_Example.png]]

In addition, routines such as ANOVA or t-test return lists of significant markers to the Markers component.

[[Image:ANOVA_Example_Markers.png]]

===Retrieval from caArray===

Microarray data can be retrieved directly from instances of caArray.

[[Image:Open_File_Remote_caArray_show_arrays.png|{{ImageMaxWidth}}]]

== Microarray Data Displays==

=== Microarray Viewer===
The Microarray Viewer displaying marker values for selected array.

[[Image:GeWB_Microarray_Viewer.png|{{ImageMaxWidth}}]]

----

=== Tabular Microarray Viewer===
The Tabular Microarray Viewer displays expression values in spreadsheet format.

[[Image:Tabular_Microarray_Viewer_Number.png|{{ImageMaxWidth}}]]

----

===CEL Image Viewer===

Allows viewing of Affyemtrix CEL files.

[[Image:T_CEL_viewer.png|{{ImageMaxWidth}}]]

----

=== Color Mosaic ===
The Color Mosaic component displaying selected arrays, group designation and marker names.

[[Image:GeWB_Color_Mosaic_Viewer.png|{{ImageMaxWidth}}]]

----

=== Expression Profile ===
Expression Profile plotting values for selected markers and arrays.

TP53 (31618) and PTTG2 (31631_f_at)

[[Image:GeWB_Expression_Profile_2markers.png|{{ImageMaxWidth}}]]

----

===Expression Value Distribution===

[[Image:T_EVD.png|{{ImageMaxWidth}}]]

----

=== Scatter Plot ===
Compare multiple markers or arrays with the standard Scatter Plot analysis.

====Array vs Array====

[[Image:GeWB_Scatter_Plot_array_vs_array.png|{{ImageMaxWidth}}]]

====Marker vs Marker====

[[Image:GeWB_Scatter_Plot_marker_vs_marker.png|{{ImageMaxWidth}}]]

----

==Gene and Pathway Annotations==

===Marker Annotations===
Retrieve and display gene and pathway information from CGAP and Cancer Gene Index (CGI).

[[Image:GeWB Marker Annotations.png|{{ImageMaxWidth}}]]

----

===Marker Annotations - BioCarta Pathways===

Displays BioCarta images retrieved from caBIO.

[[Image:GeWB_Marker_Annotations_Pathway.png|{{ImageMaxWidth}}]]

----

===Marker Annotations - Cancer Gene Index===

Displays literature citations from the Cancer Gene Index project.

[[Image:GeWB_Marker_Annotations_CGI.png|{{ImageMaxWidth}}]]

----

==Statistical tests, clustering and classification==

===Gene Ontology Term Over-representation Analysis===

[[Image:T_GO_Terms_TableBrowser_Gene_Detail.png|{{ImageMaxWidth}}]]

===T Test===
====Volcano Plot====

A t-test result display on a "volcano plot": Log significance vs log fold change.

[[Image:T_t-test_volcano_BCELL_webm_qldm.png|{{ImageMaxWidth}}]]

====Color Mosaic====
The t-test result can also be displayed as a color mosaic.

(Visualization preference setting: Relative)

[[Image:T_t-test_colormosaic_BCELL_webm_qldm.png|{{ImageMaxWidth}}]]

----

===Analysis of Variance (ANOVA)===

Detects markers for which a statistically significant difference exists in a data set containing multiple classes of samples.

====Color Mosaic View====

(Visualization preference setting: Absolute)

[[Image:T_ANOVA_ColorMosaic.png|{{ImageMaxWidth}}]]

====Tabular View====

[[Image:T_ANOVA_Tabular_Viewer.png|{{ImageMaxWidth}}]]

=== Hierarchical Clustering Dendrogram ===
A Dendrogram displays the results of the Hierarchical clustering analysis.

[[Image:T_HC_Dendrogram_display.png|{{ImageMaxWidth}}]]
----

=== SOM Clustering ===
Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.

[[Image:T_SOM_result.png|{{ImageMaxWidth}}]]
----

===Classification (GenePattern)===
GenePattern components that perform classification on microarray datasets have been adapted to geWorkbench.

====K-Nearest Neighbors (KNN)====

[[Image:Tutorial-GP-KNN-parameters.png|{{ImageMaxWidth}}]]

====Weighted Voting====
[[Image:Tutorial-GP-WV-parameters.png|{{ImageMaxWidth}}]]

====Example of classifier result====

The classifiers return groups of markers to the Markers component:

[[Image:Tutorial-GP_KNN-ClassPredictions.png]]
----

==Sequence Analysis / Pattern Discovery==

===Sequence Retriever===
Retrieve genomic and protein sequences for selected markers. Retrieved sequences can be individually selected and added to the project as new data nodes.

[[Image:T_SequenceRetriever_AfterRetrieval.png|{{ImageMaxWidth}}]]

=== BLAST Queries ===
The Sequence Alignment component submits BLAST jobs to the NCBI server and displays the results such that individual hits can be used in further analysis steps.

[[Image:T_SequenceAlignment_BLAST_results.png|{{ImageMaxWidth}}]]
----

=== Pattern Discovery ===
Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.

====Motif discovery and display====
The Pattern Discovery component itself with results displayed in the sequence viewer.

[[Image:PatternDiscovery_Basic_histone_result_exact_seqs.png|{{ImageMaxWidth}}]]

====Position Histogram====

The Pattern Discovery component with results displayed as histogram of support for selected discovered motifs across the sequence data set. Support indicates what fraction of the seqeunces are matched by the motif at a within a sliding window about a given location.

[[Image:PatternDiscovery_Basic_Histones_Result_exact_3_histogram.png|{{ImageMaxWidth}}]]

----

===Promoter===
Individual motifs from the JASPAR Transcription Factor Binding Profile Database can be scanned against loaded genomic sequences.

====Motif selection and Logo display====

[[Image:T_Promoter_CDH2_AP2_2000updn_setup_logo.png|{{ImageMaxWidth}}]]

====Result of a scan against a single sequence====

[[Image:T_Promoter_CDH2_AP2_2000updn_scan.png|{{ImageMaxWidth}}]]

====Sequence-level display of match====

[[Image:T_Promoter_CDH2_AP2_2000updn_scan_fullseq.png|{{ImageMaxWidth}}]]

----

===MatrixREDUCE===

MatrixREDUCE is a tool for inferring the binding specificity and nuclear concentration of transcription factors from microarray data.

[[Image:T_MatrixREDUCE_PSAM_view.png|{{ImageMaxWidth}}]]

----

==Network Discovery and Visualization==

=== Cytoscape - ARACNe Network display ===
The adjacency matrix generated by an ARACNe network reverse engineering run displayed in Cytoscape.

[[Image:T_ARACNE_result1.png|{{ImageMaxWidth}}]]

----

===Cellular Network Knowledge Base (CNKB)===
Results of queries against the CNKB can be filtered based on confidence values using the throttle graph.

====Query results and Throttle Graph====

[[Image:CNKB_Result_Display_3types_threshold0.75_v2.2.png|{{ImageMaxWidth}}]]

====CNKB query results displayed in Cytoscape====

Display of CNKB interactions in Cytoscape.

[[Image:CNKB_Result_Cytoscape_3types_v2.2.png|{{ImageMaxWidth}}]]

----

===Master Regulator Analysis===

[[Image:MRA_viewer_GBM_FOSL2_v2.png|{{ImageMaxWidth}}]]

----

==Molecular Structure==

===JMOL Structure Viewer===

JMOL is a viewer for PDB protein structure files.

[[Image:T_JMOL_Viewer.png|{{ImageMaxWidth}}]]

----

===Mark-Us - Protein Functional Annotation===

Mark-Us is a web server to assist the assessment of the biochemical function for a given protein structure. MarkUs identifies related protein structures and sequences, detects protein cavities, and calculates the surface electrostatic potentials and amino acid conservation profile.

[[Image:T_MarkUs_Web_result.png|{{ImageMaxWidth}}]]

----

===PUDGE===

Pudge is a server for the prediction of the 3D structures of proteins. While the server can be run without any user intervention, it is primarily designed to be interactive and to allow functional information to be used as a guide to the modeling.

PUDGE allows a pipeline of modeling and evaluation steps, depicted below, to be set up and run.

[[Image:T_Pudge_Parameters.png]]

Pudge has a number of output types, the following illustrates a sequence alignment:

[[Image:T_Pudge_Alignment_example.png|{{ImageMaxWidth}}]]

----

Home

2013-07-18T16:56:28Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
MarkUs_home_gallery.PNG
Dendrogram_home_gallery.PNG
Volcano_plot_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Motif_discovery_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production release of geWorkbenc (v2.4.1) was released October 26th, 2012.
* [[Previous_Releases#Brief_overview_of_changes_in_geWorkbench_release_2.4.1|See changes included in latest release]].
* [[Previous_Releases|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].
|}

Home

2013-07-17T19:06:07Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Dendrogram_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
MarkUs_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Volcano_plot_home_gallery.PNG
Motif_discovery_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Common Fund]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production release of geWorkbenc (v2.4.1) was released October 26th, 2012.
* [[Previous_Releases#Brief_overview_of_changes_in_geWorkbench_release_2.4.1|See changes included in latest release]].
* [[Previous_Releases|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].
|}

Project Documentation

2013-07-17T15:53:39Z

Floratos:

* '''Tutorials''': The most current source of documentation is provided by the [[Tutorials | geWorkbench tutorials]]. The tutorials explain how to perform a number of common tasks using geWorkbench, and form a complete online user manual.

* '''Training Slides''': A set of [{{SERVER}}/workbench/data/geWorkbench-HandsOnTraining.ppt PowerPoint training slides] has been created which covers the basics of using geWorkbench plus several of the more advanced modules, such as Network Reverse Engineering and annotation retrieval.

* '''Video demo''' of geWorkbench: [{{SERVER}}/workbench/data/geWorkbench-caBIG-demo.wmv geWorkbench Demo] (You can click on this link directly in Internet Explorer. For Firefox, please right click on the link and select "Save Link as").

User:Mhonig

2013-07-17T04:51:35Z

Floratos:

* {{#urlget: first|Sancho}}
* {{#urlget: last|Panza}}

GeWorkbench License

2013-07-16T20:02:07Z

Floratos:

{{DownloadTopNav}}

<center>
'''geWORKBENCH SOFTWARE LICENSE AGREEMENT'''

''Copyright 2004-{{CURRENTYEAR}} COLUMBIA University''
</center>

This software was developed by Columbia University in conjunction with First Genetic Trust and the National Cancer Institute, and so to the extent government employees are co-authors, any rights in such works shall be subject to Title 17 of the United States Code, section 105.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

2. The end-user documentation included with the redistribution, if any, must include the following acknowledgment:

"This product includes software developed by the Columbia University, First Genetic Trust and the National Cancer Institute."

If no such end-user documentation is to be included, this acknowledgment shall appear in the software itself, wherever such third-party acknowledgments normally appear.

3. This license does not authorize the incorporation of this software into any proprietary programs.

4. THIS SOFTWARE IS PROVIDED "AS IS," AND ANY EXPRESSED OR IMPLIED WARRANTIES, (INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE) ARE DISCLAIMED. IN NO EVENT SHALL THE COLUMBIA UNVIERSITY OR THEIR AFFILIATES BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

All other product names mentioned herein and throughout the entire project are trademarks of their respective owners.

Template:DownloadTopNav

2013-07-16T20:00:58Z

Floratos:

{| border="1" cellpadding="5"
|
[[Download and Installation | Download Instructions]] |
[[geWorkbench License | License Information]]
|}
<br/>

Community

2013-07-16T19:49:05Z

Floratos:

As of August 11 2008, geWorkbench is supported through [https://cabig-kc.nci.nih.gov/Molecular/KC/ NCI's Molecular Analysis Tools Knowledge Center]. End-user and development related queries and issues should be posted at the geWorkbench discussion forums therein: https://cabig-kc.nci.nih.gov/Molecular/forums/. '''The old [[#Discontinued_GForge-based_Mailing_Lists | Gforge-based discussion lists for geWorkbench]] are being discontinued'''.

Browsing of forum postings is open to the public. To add a posting or to reply to one, you will need an account. Please fill the [http://wikiutils.nci.nih.gov/KC_signup "Access Account Request Form"] to request that an account be created for you by the NCI personnel. After receiving your account credentials you will be able to post messages to the geWorkbench [https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=3 end-user] and [https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=12 developer] forums. You can also subscribe to a forum or to a specific topic by clicking on the "subscribe forum" or "subscribe topic" link at the bottom of the corresponding page. This will allow you to receive an email notification when new posts are made.

The geWorkbench "landing page" at caBIG is https://cabig.nci.nih.gov/tools/geWorkbench.

The home page of the Knowledge Center is at:
https://cabig-kc.nci.nih.gov/Molecular/KC/index.php/Main_Page

The various forums supported by the Molecular Analysis Tools Knowledge Center are available at:
https://cabig-kc.nci.nih.gov/Molecular/forums/

The geWorkbench-related forums are available at:
'''End-user forum''': https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=3
'''Developers forum''': https://cabig-kc.nci.nih.gov/Molecular/forums/viewforum.php?f=12

===About the Molecular Analysis Tools Knowledge Center===

The caBIG™ Molecular Analysis Tools Knowledge Center is an NCI-supported Center operated by the Columbia University Herbert Irving Comprehensive Cancer Center and The Broad Institute of MIT and Harvard. The Knowledge Center provides a centralized, authoritative repository of knowledge, information, and web-based support to facilitate the deployment and ongoing development of caBIG™ tools, standards, and infrastructure in the molecular analysis domain. Key services provided by the Knowledge Center include:

* Providing domain expertise on using the supported tools to carry out molecular analyses
* Posting up-to-date installation packages for related tools
* Maintaining technical and end-user documentation
* Fostering open source development of caBIG tools by the community
* Collecting and monitoring defect reports, feature requests, and end-user requirements

The [https://cabig-kc.nci.nih.gov/MediaWiki/index.php/Main_Page caBIG™ Knowledge Centers program] (which comprises several Centers) is a component of the caBIG™ Enterprise Support Network (ESN). The development of geWorkbnech is in part funded through the caBIG™ (cancer Biomedical Informatics Grid) initiative. Information about the caBIG™ initiative is available at https://cabig.nci.nih.gov/. Information about the caBIG™ Enterprise Support Network is available at https://cabig.nci.nih.gov/esn/.

Community

2013-07-16T19:48:40Z

Floratos:

Overview

2013-07-16T17:58:23Z

Floratos:

__NOEDITSECTION__
==Introduction==

geWorkbench is an open-source bioinformatics platform that offers a comprehensive and extensible collection of tools for the management, analysis, visualization and annotation of biomedical data. Many kinds of analysis are supported - for microarrays, there are filtering and normalization, basic statistical analyses, clustering, network reverse engineering, as well as many common visualization tools. For sequence data there are routines such as BLAST, pattern detection, transcription factor mapping, and syntenic region analysis. Furthermore, genomic sequences around markers of interest found in microarray experiments can be easily retrieved and, for example, used for promoter/transcription factor analysis.

Specific types of data supported include:

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

Most importantly, geWorkbench provides an environment which supports moving from one data type to another in a seamless fashion, e.g. from gene expression to sequences to patterns.

[[Image:slide1.gif]]

==geWorkbench as an interface to external data and computational resources==

geWorkbench provides access to a variety of external data sources, including:
*Microarray gene expression repositories (caArray)
*BLAST
*Gene annotation pages (via caBIO)
*Protein and DNA sequence retrieval
*Pathway diagrams (BioCarta)

geWorkbench also provides a gateway to several computational services currently hosted on Columbia servers and clusters, including:
*Pattern Discovery
*Pudge - protein structure modeling
*SkyBase - database of molecular models

==Basic Layout of the Graphical User Interface==

The graphical user interface for geWorkbench is divided into three major sections, for

# Projects - Data management (upper left)
# Visualization tools (upper right)
# Marker and Array/Phenotype set selection and management (lower left)

[[Image:GeWorkbench_2.3.0_Main_GUI_MicroarrayViewer.png|{{ImageMaxWidth}}]]

The Data Management area can hold one workspace, and a workspace in turn can hold one or more projects. Projects can be used as wished to group different data sets. Each opened data file or analysis result is stored in a project. A workspace and all the data it contains can be saved and returned to later.

The GUI provides a menu bar at top with a standard choice of commands. Many commands that are available in the menu bar are also available by right-clicking on data objects.

==Developing for geWorkbench==

geWorkbench has been designed using a plug-in framework which allows new modules to be developed with relative ease. A repository will be maintained for community-developed modules. Developers can take advantage of all the existing capabilities for data management and visualization, and thus concentrate development efforts on the more important, novel aspects of their project.

Home

2013-07-16T17:57:12Z

Floratos:

__NOTOC__
<sgallery width="700" showinfopane="false" timed="true" delay="4000" showcarousel="false">
ARACNe_with_t-test_home_gallery.PNG
BLAST_home_gallery.PNG
CCM_home_gallery.PNG
Dendrogram_home_gallery.PNG
Gene_Ontology_home_gallery.PNG
MarkUs_home_gallery.PNG
JMol_viewer_home_gallery.PNG
Skybase_home_gallery.PNG
TF_binding_site_prediction_home_gallery.PNG
Volcano_plot_home_gallery.PNG
Motif_discovery_home_gallery.PNG
</sgallery>

{| class="wikitable" style="background-color:#F8EDD6;" cellpadding="10"
|colspan="2"|
<h2>Overview</h2>
'''geWorkbench''' (<u>ge</u>nomics <u>Workbench</u>) is a Java-based open-source platform for integrated genomics. Using a component architecture it allows individually developed plug-ins to be configured into complex bioinformatic applications. At present there are more than 70 available [[Plugins|plug-ins]] supporting the visualization and analysis of gene expression and sequence data. Example use cases include: <toggledisplay status="hide">
* loading data from local or remote data sources.
* visualizing gene expression, molecular interaction networks, protein sequence and protein structure data in a variety of ways.
* providing access to client- and server-side computational analysis tools such as t-test analysis, hierarchical clustering, self organizing maps, regulatory neworks reconstruction, BLAST searches, pattern/motif discovery, etc.
* validating computational hypothesis through the integration of gene and pathway annotation information from curated sources as well as through Gene Ontology enrichment analysis.
<br/>
geWorkbench is the Bioinformatics platform of [http://magnet.c2b2.columbia.edu MAGNet], the '''National Center for the Multi-scale Analysis of Genomic and Cellular Networks''' (one of the [http://www.ncbcs.org 7 National Centers for Biomedial Computing] funded through the [http://nihroadmap.nih.gov/ NIH Roadmap]).

</toggledisplay>
|-
| style="width: 50%; background-color: #F2F8C7;"|
<h2>Quick Start</h2>
Please see the [[QuickStart| Quick Start]] guide to geWorkbench to see how to get started using geWorkbench right away.
| style="width: 50%; background-color: #C7F8CB;"|
<h2>Current Release</h2>
The latest production release of geWorkbenc (v2.4.1) was released October 26th, 2012.
* [[Previous_Releases#Brief_overview_of_changes_in_geWorkbench_release_2.4.1|See changes included in latest release]].
* [[Previous_Releases|See history of past releases]].
* [[Download_and_Installation|Download geWorkbench]].
|}