http://wiki.c2b2.columbia.edu/workbench/api.php?action=feedcontributions&feedformat=atom&user=Hall 2026-04-30T17:04:13Z User contributions MediaWiki 1.27.7 http://wiki.c2b2.columbia.edu/workbench/index.php?title=Properties&diff=3821 2006-11-28T17:41:19Z

<p>Hall: </p> <hr /> <div>Components often want to store and retrieve configuration settings between invocations. An API is provided for this purpose.<br /> <br /> Configuration is handled by the setting and getting of properties using the [{{SERVER}}/workbench/api/org/geworkbench/engine/properties/PropertiesManager.html &lt;tt&gt;org.geworkbench.engine.properties.PropertiesManager&lt;/tt&gt;] class. A singleton instance is available to process requests.<br /> <br /> The two important methods of this class are:<br /> &lt;pre&gt;<br /> public void setProperty(Class componentClass, String key, String value) throws IOException;<br /> &lt;/pre&gt;<br /> and<br /> &lt;pre&gt;<br /> public String getProperty(Class componentClass, String key, String defaultValue) throws IOException;<br /> &lt;/pre&gt;<br /> <br /> The first parameter to both methods can be the &lt;code&gt;Class&lt;/code&gt; object of any class in your component. This is used to determine where the configuration will be stored. This class is mapped back to the component that it is associated with. The &lt;code&gt;defaultValue&lt;/code&gt; parameter of &lt;code&gt;getProperty&lt;/code&gt; will be the returned result if there is no known value for the specified key.<br /> <br /> Here is an example use of the properties manager:<br /> <br /> &lt;pre&gt;<br /> PropertiesManager.getInstance().setProperty(getClass(), &quot;test&quot;, &quot;value&quot;);<br /> &lt;/pre&gt;<br /> <br /> and later...<br /> <br /> &lt;pre&gt;<br /> String value = PropertiesManager.getInstance().getProperty(getClass(), &quot;test&quot;, &quot;Default Value&quot;);<br /> &lt;/pre&gt;<br /> <br /> Setting the property will automatically cause the value to be saved to disk. The configuration file is an XML file stored in a &lt;code&gt;conf&lt;/code&gt; subdirectory of the component's working directory.</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Plugins&diff=3287 2006-07-07T17:41:41Z

<p>Hall: /* Normalizers */</p> <hr /> <div>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.<br /> <br /> <br /> <br /> __TOC__<br /> <br /> ==Microarray Visualization==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).<br /> |-<br /> |-<br /> <br /> |width=&quot;150&quot;|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).<br /> |- <br /> |-<br /> |width=&quot;150&quot;|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.<br /> |-<br /> |-<br /> <br /> |width=&quot;150&quot;|Microarray Viewer||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).<br /> |- <br /> |-<br /> <br /> |width=&quot;150&quot;|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).<br /> |- <br /> |-<br /> <br /> |width=&quot;150&quot;|SOM Clusters Viewer ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). <br /> |- <br /> |-<br /> <br /> |width=&quot;150&quot;|Tabular Microarray Viewer|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:Tabular.png|screenshot]]).<br /> |-<br /> |}<br /> <br /> ==Data Management==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |- <br /> |-<br /> |width=&quot;150&quot;|Marker Component ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.<br /> |- <br /> |-<br /> |width=&quot;150&quot;|Phenotype/Array Component ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.<br /> |-<br /> |-<br /> |}<br /> <br /> ==Normalizers==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Missing Value Calculation||Replacement of missing values with consensus values.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.<br /> |-<br /> |width=&quot;150&quot;|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.<br /> |-<br /> |}<br /> <br /> == Filters==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Affy Detection Call||(''Affymetrix data only)'' Filtering of measurements based on the value of their &quot;detection call&quot; attribute.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Deviation|| Filtering of markers with low dynamic range.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Expression Threshold|| Elimination of measurements that fall outside a range of explression values.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|2-channel Threshold||(''Genepix data only)'' Same as &quot;Expression Threshold&quot; filter but different threshold ranges can be specified for each channel.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Genepix Flag Filter|| ''(Genepix data only)'' Filtering of measurements based on the value of their &quot;Flags&quot; attribute.<br /> |-<br /> |}<br /> <br /> <br /> ==Annotation==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|Dataset History||Log of data transformations induced by data-modifying operations.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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 &quot;lab notebook&quot;.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).<br /> |-<br /> |width=&quot;150&quot;|Gene Ontology||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]).<br /> |-<br /> |-<br /> |}<br /> <br /> ==Network Generation==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|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]]).<br /> |-<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]).<br /> |-<br /> |}<br /> <br /> ==Analysis==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Self Organizing Map (SOM)|| Clustering of markers using self organizing maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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]]).<br /> |-<br /> <br /> |}<br /> <br /> == Sequence Analysis &amp; Visualization ==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Sequence Alignment||Server-based versions of BLAST and Smith-Waterman alignment ([[media:Synteny Blastresults.png|screenshot]]). <br /> |-<br /> |-<br /> |width=&quot;150&quot;|Synteny|| Comparison of sequence similarity between two genomic regions. The comparison results are represented as a dot matrix augmented with detailed annotation for both regions ([[media:Synteny Dotmatrix.png|screenshot]]).<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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.]<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Pattern Discovery|| Discovery of sequence motifs in sets of DNA and protein sequences.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Position Histogram || Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match ([[media:Histogram.png|screenshot]]). <br /> |-<br /> |-<br /> |width=&quot;150&quot;|Sequence Panel || Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.<br /> |-<br /> |}</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Plugins&diff=3285 2006-07-07T17:22:17Z

<p>Hall: /* Normalizers */</p> <hr /> <div>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.<br /> <br /> <br /> <br /> __TOC__<br /> <br /> ==Microarray Visualization==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Color Mosaic||Heat maps for microarray expression data, organized by phenotypic or gene groupings ([[media:Color-mosaic.png|screenshot]]).<br /> |-<br /> |-<br /> <br /> |width=&quot;150&quot;|Dendrogram||Tree-structured diagrams reflecting the results of hierarchical clustering analysis ([[media:Dendrogram.png|screenshot]]).<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Expression Profiles||Line graph of genes expression profiles across several arrays/ hybridizations ([[media:Expression-profile.png|screenshot]]).<br /> |- <br /> |-<br /> |width=&quot;150&quot;|Expression Value Distribution||Distribution plot of marker expression values across one or more microarrays.<br /> |-<br /> |-<br /> <br /> |width=&quot;150&quot;|Microarray Viewer||Color-gradient representation of gene expression values ([[media:Microarray-panel.png|screenshot]]).<br /> |- <br /> |-<br /> <br /> |width=&quot;150&quot;|Scatter Plot || Pairwise (array vs. array and marker vs. marker) comparison and plotting of expression values ([[media:Scatterplot.png|screenshot]]).<br /> |- <br /> |-<br /> <br /> |width=&quot;150&quot;|SOM Clusters Viewer ||Visualization of gene clusters produced by the self-organizing maps analysis ([[media:Somcluster.png|screenshot]]). <br /> |- <br /> |-<br /> <br /> |width=&quot;150&quot;|Tabular Microarray Viewer|| Spreadsheet view of all expression measurement in an experiment, one row per individual marker/probe and one column per microarray ([[media:Tabular.png|screenshot]]).<br /> |-<br /> |}<br /> <br /> ==Data Management==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |- <br /> |-<br /> |width=&quot;150&quot;|Marker Component ||Definition of data views consisting of marker subgroups. The views control the amount of data displayed.<br /> |- <br /> |-<br /> |width=&quot;150&quot;|Phenotype/Array Component ||Definition of data views consisting of microarray subgroups. The views control the amount of data displayed.<br /> |-<br /> |-<br /> |}<br /> <br /> ==Normalizers==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|Array-Based Centering||Subtraction of the mean or median measurement of a microarray from every measurement in that microarray.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Marker-Based Centering||Subtraction of the mean or median measurement of a marker profile from every measurement in the profile.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Missing Value Calculation||Replacement of missing values with consensus values.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Threshold Normalizer ||Adjustment of values that fall outside a user-specified threshold.<br /> |-<br /> |width=&quot;150&quot;|Quantile || Expression measurements in each microarray are adjusted so that the distribution of values is the same across all microarrays in an experiment.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Housekeeping || Normalization of all measurements in a microarray through division by the average expression value of a (user defined) set of housekeeping genes.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|GCRMA via R || Uses R to perform GCRMA on CEL files. See [[Instructions for R Integration]].<br /> |-<br /> <br /> |}<br /> <br /> == Filters==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Affy Detection Call||(''Affymetrix data only)'' Filtering of measurements based on the value of their &quot;detection call&quot; attribute.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Deviation|| Filtering of markers with low dynamic range.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Expression Threshold|| Elimination of measurements that fall outside a range of explression values.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|2-channel Threshold||(''Genepix data only)'' Same as &quot;Expression Threshold&quot; filter but different threshold ranges can be specified for each channel.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Genepix Flag Filter|| ''(Genepix data only)'' Filtering of measurements based on the value of their &quot;Flags&quot; attribute.<br /> |-<br /> |}<br /> <br /> <br /> ==Annotation==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|Dataset History||Log of data transformations induced by data-modifying operations.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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 &quot;lab notebook&quot;.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Marker Annotations||Retrieval of gene and pathway information for markers on a microarray.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|caBIO Pathway Listing||Visualization of BioCarta pathway diagrams ([[media:Cabiopathway.png|screenshot]]).<br /> |-<br /> |width=&quot;150&quot;|Gene Ontology||Enrichment analysis of selected groups of genes against Gene Ontology (http://www.geneontology.org) annotations ([[media:Go_Terms_Panel.png|screenshot]]).<br /> |-<br /> |-<br /> |}<br /> <br /> ==Network Generation==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|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]]).<br /> |-<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Cytoscape||Visualization of gene regulatory network created in Reverse Engineering using [http://www.cytoscape.org/ Cytoscape 2.0]([[media:Cytoscape.png|screenshot]]).<br /> |-<br /> |}<br /> <br /> ==Analysis==<br /> <br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |width=&quot;150&quot;|Hierarchical Clustering||Clustering of markers and microarrays into hierarchical binary trees. The resulting structures can be visualized in the Dendrogram plugin.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Self Organizing Map (SOM)|| Clustering of markers using self organizing maps. The resulting clusters can be visualized in the SOM Clusters Viewer plugin.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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]]).<br /> |-<br /> <br /> |}<br /> <br /> == Sequence Analysis &amp; Visualization ==<br /> {|style=&quot;border: 1px solid lightGray&quot;<br /> !Plugin||Description<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Sequence Alignment||Server-based versions of BLAST and Smith-Waterman alignment ([[media:Synteny Blastresults.png|screenshot]]). <br /> |-<br /> |-<br /> |width=&quot;150&quot;|Synteny|| Comparison of sequence similarity between two genomic regions. The comparison results are represented as a dot matrix augmented with detailed annotation for both regions ([[media:Synteny Dotmatrix.png|screenshot]]).<br /> |-<br /> |-<br /> |width=&quot;150&quot;|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.]<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Pattern Discovery|| Discovery of sequence motifs in sets of DNA and protein sequences.<br /> |-<br /> |-<br /> |width=&quot;150&quot;|Position Histogram || Visualization of results from the Pattern Discovery plugin. Motif/pattern support is plotted against relative sequence position of the motif match ([[media:Histogram.png|screenshot]]). <br /> |-<br /> |-<br /> |width=&quot;150&quot;|Sequence Panel || Visualization of results from the Pattern Discovery plugin, displaying the motif match location over each sequence from the input data set.<br /> |-<br /> |}</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=3281 2006-06-26T16:10:17Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> <br /> <br /> [[image:microarray-panel.png]]<br /> ----<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> <br /> <br /> [[Image:color-mosaic.png]]<br /> ----<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> <br /> <br /> [[Image:expression-profile.png]]<br /> ----<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> <br /> <br /> [[Image:dendrogram.png]]<br /> ----<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> <br /> <br /> [[Image:somcluster.png]]<br /> ----<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> <br /> <br /> [[Image:scatterplot.png]]<br /> ----<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> <br /> <br /> [[Image:volcanoplot.png]]<br /> ----<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> <br /> <br /> [[Image:cabiopathway.png]]<br /> ----<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> <br /> <br /> [[Image:reverseengineering.png]]<br /> ----<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> <br /> <br /> [[Image:cytoscape.png]]<br /> ----<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> <br /> <br /> [[Image:patterndiscovery.png]]<br /> ----<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> <br /> <br /> [[Image:promoterpanel.png]]<br /> ----<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> <br /> <br /> [[Image:blastresults.png]]<br /> ----</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Magnet_components&diff=3163 2006-06-06T19:16:31Z

<p>Hall: </p> <hr /> <div>==List of MAGNet Components==<br /> Coming soon.</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Magnet_components&diff=3161 2006-06-06T19:16:05Z

<p>Hall: /* List of MAGNet Components */</p> <hr /> <div>==List of MAGNet Components==<br /> Coming soon.<br /> <br /> [[Genomics Workbook]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1767 2006-02-02T18:01:05Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> <br /> <br /> [[image:microarray-panel.png]]<br /> ----<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> <br /> <br /> [[Image:color-mosaic.png]]<br /> ----<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> <br /> <br /> [[image:tabular.png]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> <br /> <br /> [[Image:expression-profile.png]]<br /> ----<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> <br /> <br /> [[Image:dendrogram.png]]<br /> ----<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> <br /> <br /> [[Image:somcluster.png]]<br /> ----<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> <br /> <br /> [[Image:scatterplot.png]]<br /> ----<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> <br /> <br /> [[Image:volcanoplot.png]]<br /> ----<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> <br /> <br /> [[Image:cabiopathway.png]]<br /> ----<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> <br /> <br /> [[Image:reverseengineering.png]]<br /> ----<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> <br /> <br /> [[Image:cytoscape.png]]<br /> ----<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> <br /> <br /> [[Image:patterndiscovery.png]]<br /> ----<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> <br /> <br /> [[Image:promoterpanel.png]]<br /> ----<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> <br /> <br /> [[Image:blastresults.png]]<br /> ----</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1766 2006-02-02T18:00:03Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> <br /> <br /> [[image:microarray-panel.png]]<br /> ----<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> <br /> <br /> [[Image:color-mosaic.png]]<br /> ----<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> <br /> <br /> [[image:tabular.png]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> <br /> <br /> [[Image:expression-profile.png]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> <br /> <br /> [[Image:dendrogram.png]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> <br /> <br /> [[Image:somcluster.png]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> <br /> <br /> [[Image:scatterplot.png]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> <br /> <br /> [[Image:volcanoplot.png]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> <br /> <br /> [[Image:cabiopathway.png]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> <br /> <br /> [[Image:reverseengineering.png]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> <br /> <br /> [[Image:cytoscape.png]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> <br /> <br /> [[Image:patterndiscovery.png]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> <br /> <br /> [[Image:promoterpanel.png]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> <br /> <br /> [[Image:blastresults.png]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1765 2006-02-02T17:59:30Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> <br /> <br /> [[image:microarray-panel.png]]<br /> ---<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> <br /> <br /> [[Image:color-mosaic.png]]<br /> ---<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> <br /> <br /> [[image:tabular.png]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> <br /> <br /> [[Image:expression-profile.png]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> <br /> <br /> [[Image:dendrogram.png]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> <br /> <br /> [[Image:somcluster.png]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> <br /> <br /> [[Image:scatterplot.png]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> <br /> <br /> [[Image:volcanoplot.png]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> <br /> <br /> [[Image:cabiopathway.png]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> <br /> <br /> [[Image:reverseengineering.png]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> <br /> <br /> [[Image:cytoscape.png]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> <br /> <br /> [[Image:patterndiscovery.png]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> <br /> <br /> [[Image:promoterpanel.png]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> <br /> <br /> [[Image:blastresults.png]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1764 2006-02-02T17:59:15Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> <br /> <br /> [[image:microarray-panel.png]]<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> <br /> <br /> [[Image:color-mosaic.png]]<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> <br /> <br /> [[image:tabular.png]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> <br /> <br /> [[Image:expression-profile.png]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> <br /> <br /> [[Image:dendrogram.png]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> <br /> <br /> [[Image:somcluster.png]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> <br /> <br /> [[Image:scatterplot.png]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> <br /> <br /> [[Image:volcanoplot.png]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> <br /> <br /> [[Image:cabiopathway.png]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> <br /> <br /> [[Image:reverseengineering.png]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> <br /> <br /> [[Image:cytoscape.png]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> <br /> <br /> [[Image:patterndiscovery.png]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> <br /> <br /> [[Image:promoterpanel.png]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> <br /> <br /> [[Image:blastresults.png]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1763 2006-02-02T17:58:49Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> <br /> <br /> [[image:microarray-panel.png]]<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> <br /> [[Image:color-mosaic.png]]<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> <br /> [[image:tabular.png]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> <br /> [[Image:expression-profile.png]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> [[Image:dendrogram.png]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> [[Image:somcluster.png]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> [[Image:scatterplot.png]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> [[Image:volcanoplot.png]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> [[Image:cabiopathway.png]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> [[Image:reverseengineering.png]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> [[Image:cytoscape.png]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> [[Image:patterndiscovery.png]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> [[Image:promoterpanel.png]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> [[Image:blastresults.png]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1762 2006-02-02T17:58:34Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> <br /> [[image:microarray-panel.png]]<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> <br /> [[Image:color-mosaic.png]]<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> <br /> [[image:tabular.png]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> <br /> [[Image:expression-profile.png]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> [[Image:dendrogram.png]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> [[Image:somcluster.png]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> [[Image:scatterplot.png]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> [[Image:volcanoplot.png]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> [[Image:cabiopathway.png]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> [[Image:reverseengineering.png]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> [[Image:cytoscape.png]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> [[Image:patterndiscovery.png]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> [[Image:promoterpanel.png]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> [[Image:blastresults.png]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1761 2006-02-02T17:56:07Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> [[image:microarray-panel.png]]<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> [[Image:color-mosaic.png]]<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> [[image:tabular.png]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> [[Image:expression-profile.png]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> [[Image:dendrogram.png]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> [[Image:somcluster.png]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> [[Image:scatterplot.png]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> [[Image:volcanoplot.png]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> [[Image:cabiopathway.png]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> [[Image:reverseengineering.png]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> [[Image:cytoscape.png]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> [[Image:patterndiscovery.png]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> [[Image:promoterpanel.png]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> [[Image:blastresults.png]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1760 2006-02-02T17:55:17Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> [[image:microarray-panel.png]]<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> [[Image:color-mosaic.png]]<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> [[image:tabular.png|frame]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> [[Image:expression-profile.png|frame]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> [[Image:dendrogram.png|frame]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> [[Image:somcluster.png|frame]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> [[Image:scatterplot.png|frame]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> [[Image:volcanoplot.png|frame]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> [[Image:cabiopathway.png|frame]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> [[Image:reverseengineering.png|frame]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> [[Image:cytoscape.png|frame]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> [[Image:patterndiscovery.png|frame]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> [[Image:promoterpanel.png|frame]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> [[Image:blastresults.png|frame]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1759 2006-02-02T17:54:32Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> [[image:microarray-panel.png|frame]]<br /> <br /> === Color Mosaic ===<br /> The Color Mosaic component displaying selected arrays, group designation and marker names.<br /> [[Image:color-mosaic.png|frame]]<br /> <br /> === Tabular Microarray Panel ===<br /> The Tabular Microarray Panel displays the raw values loaded from the data file.<br /> [[image:tabular.png|frame]]<br /> <br /> === Expression Profile ===<br /> Expression Profile plotting values for selected markers and arrays.<br /> [[Image:expression-profile.png|frame]]<br /> <br /> === Hierarchical Clustering ===<br /> A Dendrogram displays the results of the Hierarchical clustering analysis.<br /> [[Image:dendrogram.png|frame]]<br /> <br /> === SOM Clustering ===<br /> Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.<br /> [[Image:somcluster.png|frame]]<br /> <br /> === Scatter Plot ===<br /> Compare multiple markers or arrays with the standard Scatter Plot analysis.<br /> [[Image:scatterplot.png|frame]]<br /> <br /> === Volcano Plot ===<br /> The Volcano Plot shows the results of a T Test analysis.<br /> [[Image:volcanoplot.png|frame]]<br /> <br /> === caBIO Pathway ===<br /> Using a connection to caBIO, pathway diagrams can be retrieved and displayed.<br /> [[Image:cabiopathway.png|frame]]<br /> <br /> === Reverse Engineering ===<br /> Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.<br /> [[Image:reverseengineering.png|frame]]<br /> <br /> === Cytoscape ===<br /> Use the Cytoscape network visualization to view the reverse engineered regulatory network.<br /> [[Image:cytoscape.png|frame]]<br /> <br /> === Pattern Discovery ===<br /> Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.<br /> [[Image:patterndiscovery.png|frame]]<br /> <br /> === Promoter Panel ===<br /> The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.<br /> [[Image:promoterpanel.png|frame]]<br /> <br /> === BLAST Queries ===<br /> The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.<br /> [[Image:blastresults.png|frame]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1757 2006-02-02T17:53:06Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> The Microarray Panel displaying marker values for selected array.<br /> [[image:microarray-panel.png|frame]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]<br /> <br /> === caBIO Pathway ===<br /> [[Image:cabiopathway.png|frame|Using a connection to caBIO, pathway diagrams can be retrieved and displayed.]]<br /> <br /> === Reverse Engineering ===<br /> [[Image:reverseengineering.png|frame|Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.]]<br /> <br /> === Cytoscape ===<br /> [[Image:cytoscape.png|frame|Use the Cytoscape network visualization to view the reverse engineered regulatory network.]]<br /> <br /> === Pattern Discovery ===<br /> [[Image:patterndiscovery.png|frame|Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.]]<br /> <br /> === Promoter Panel ===<br /> [[Image:promoterpanel.png|frame|The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.]]<br /> <br /> === BLAST Queries ===<br /> [[Image:blastresults.png|frame|The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1756 2006-02-02T17:51:11Z

<p>Hall: Reverted edit of Floratos, changed back to last version by Hall</p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]<br /> <br /> === caBIO Pathway ===<br /> [[Image:cabiopathway.png|frame|Using a connection to caBIO, pathway diagrams can be retrieved and displayed.]]<br /> <br /> === Reverse Engineering ===<br /> [[Image:reverseengineering.png|frame|Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.]]<br /> <br /> === Cytoscape ===<br /> [[Image:cytoscape.png|frame|Use the Cytoscape network visualization to view the reverse engineered regulatory network.]]<br /> <br /> === Pattern Discovery ===<br /> [[Image:patterndiscovery.png|frame|Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.]]<br /> <br /> === Promoter Panel ===<br /> [[Image:promoterpanel.png|frame|The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.]]<br /> <br /> === BLAST Queries ===<br /> [[Image:blastresults.png|frame|The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1603 2006-01-25T20:36:49Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]<br /> <br /> === caBIO Pathway ===<br /> [[Image:cabiopathway.png|frame|Using a connection to caBIO, pathway diagrams can be retrieved and displayed.]]<br /> <br /> === Reverse Engineering ===<br /> [[Image:reverseengineering.png|frame|Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.]]<br /> <br /> === Cytoscape ===<br /> [[Image:cytoscape.png|frame|Use the Cytoscape network visualization to view the reverse engineered regulatory network.]]<br /> <br /> === Pattern Discovery ===<br /> [[Image:patterndiscovery.png|frame|Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.]]<br /> <br /> === Promoter Panel ===<br /> [[Image:promoterpanel.png|frame|The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.]]<br /> <br /> === BLAST Queries ===<br /> [[Image:blastresults.png|frame|The BLAST panel runs queries against the Paracel Blast machine running at the Columbia Genome Center.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Blastresults.png&diff=1602 2006-01-25T20:34:21Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1601 2006-01-25T20:24:49Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]<br /> <br /> === caBIO Pathway ===<br /> [[Image:cabiopathway.png|frame|Using a connection to caBIO, pathway diagrams can be retrieved and displayed.]]<br /> <br /> === Reverse Engineering ===<br /> [[Image:reverseengineering.png|frame|Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.]]<br /> <br /> === Cytoscape ===<br /> [[Image:cytoscape.png|frame|Use the Cytoscape network visualization to view the reverse engineered regulatory network.]]<br /> <br /> === Pattern Discovery ===<br /> [[Image:patterndiscovery.png|frame|Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.]]<br /> <br /> === Promoter Panel ===<br /> [[Image:promoterpanel.png|frame|The Promoter Panel uses the JASPAR Transcription Factor Binding Profile Database to search for promoter regions in the loaded sequence.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Promoterpanel.png&diff=1600 2006-01-25T20:22:44Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1599 2006-01-25T19:53:22Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]<br /> <br /> === caBIO Pathway ===<br /> [[Image:cabiopathway.png|frame|Using a connection to caBIO, pathway diagrams can be retrieved and displayed.]]<br /> <br /> === Reverse Engineering ===<br /> [[Image:reverseengineering.png|frame|Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.]]<br /> <br /> === Cytoscape ===<br /> [[Image:cytoscape.png|frame|Use the Cytoscape network visualization to view the reverse engineered regulatory network.]]<br /> <br /> === Pattern Discovery ===<br /> [[Image:patterndiscovery.png|frame|Use the SPLASH algorithm to discover sparse amino or nucleic acid patterns in a loaded sequence.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Patterndiscovery.png&diff=1598 2006-01-25T19:52:04Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1597 2006-01-25T19:43:03Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]<br /> <br /> === caBIO Pathway ===<br /> [[Image:cabiopathway.png|frame|Using a connection to caBIO, pathway diagrams can be retrieved and displayed.]]<br /> <br /> === Reverse Engineering ===<br /> [[Image:reverseengineering.png|frame|Use the ARACNE algorithm to reverse engineer the underlying gene regulatory network.]]<br /> <br /> === Cytoscape ===<br /> [[Image:cytoscape.png|frame|Use the Cytoscape network visualization to view the reverse engineered regulatory network.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Cytoscape.png&diff=1596 2006-01-25T19:41:18Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Reverseengineering.png&diff=1595 2006-01-25T19:41:12Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1594 2006-01-25T19:31:05Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]<br /> <br /> === caBIO Pathway ===<br /> [[Image:cabiopathway.png|frame|Using a connection to caBIO, pathway diagrams can be retrieved and displayed.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Cabiopathway.png&diff=1593 2006-01-25T19:30:28Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1592 2006-01-25T19:26:40Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]<br /> <br /> === Volcano Plot ===<br /> [[Image:volcanoplot.png|frame|The Volcano Plot shows the results of a T Test analysis.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Volcanoplot.png&diff=1591 2006-01-25T19:25:58Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1590 2006-01-25T19:24:06Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]<br /> <br /> === Scatter Plot ===<br /> [[Image:scatterplot.png|frame|Compare multiple markers or arrays with the standard Scatter Plot analysis.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Scatterplot.png&diff=1589 2006-01-25T19:23:28Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1588 2006-01-25T19:21:46Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:somcluster.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1587 2006-01-25T19:21:35Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]<br /> <br /> === SOM Clustering ===<br /> [[Image:dendrogram.png|frame|Self Ordered Map clustering results are displayed as series of expression profiles corresponding to discovered groupings.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Somcluster.png&diff=1586 2006-01-25T19:20:30Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1585 2006-01-25T19:19:32Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hierarchical clustering analysis.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1584 2006-01-25T19:18:39Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]<br /> <br /> === Hierarchical Clustering ===<br /> [[Image:dendrogram.png|frame|A Dendrogram displays the results of the Hieracrchical clustering analysis.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Dendrogram.png&diff=1583 2006-01-25T19:17:51Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1581 2006-01-25T17:39:23Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Tabular Microarray Panel ===<br /> [[image:tabular.png|frame|The Tabular Microarray Panel displays the raw values loaded from the data file.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=File:Tabular.png&diff=1580 2006-01-25T17:36:58Z

<p>Hall: </p> <hr /> <div></div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1579 2006-01-25T17:35:45Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> <br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|frame|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|frame|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1578 2006-01-25T17:35:05Z

<p>Hall: </p> <hr /> <div>== geWorkbench 3.0 screenshots ==<br /> <br /> === Microarray Panel ===<br /> <br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1577 2006-01-25T17:34:28Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> <br /> [[image:microarray-panel.png|frame|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1576 2006-01-25T17:34:10Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> [[image:microarray-panel.png|frame|Please read the FAQ.]]<br /> <br /> {| style=&quot;border:1px solid lightgray;&quot; cellpadding=&quot;2&quot; align=&quot;center&quot;<br /> |style=&quot;width:300px;padding-right:8px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |style=&quot;width:300px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |-<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;padding-right:16px;&quot;|''Opportunity's'' first panorama, taken by the navcam on Sol 1 of the mission. This 360-degree panorama is the first panorama beamed back to Earth from the Mars Exploration Rover ''Opportunity'' shortly after she touched down at Meridiani Planum, Mars. The image was captured by the rover's navigation [[camera]], and is [[grayscale]].<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;&quot;|First color panorama taken by ''Opportunity''. This color image shows the martian landscape at Meridiani Planum, where the ''Opportunity'' successfully landed at 9:05 p.m. PST on [[January 24]],[[2004]]. This is one of the first images beamed back to Earth from the rover shortly after she touched down. The image was captured by the rover's panoramic camera.<br /> |}<br /> <br /> [[Image:microarray-panel.png|thumb|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1575 2006-01-25T17:33:24Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> [[image:microarray-panel.png|thumb|left|Please read the FAQ.]]<br /> <br /> {| style=&quot;border:1px solid lightgray;&quot; cellpadding=&quot;2&quot; align=&quot;center&quot;<br /> |style=&quot;width:300px;padding-right:8px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |style=&quot;width:300px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |-<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;padding-right:16px;&quot;|''Opportunity's'' first panorama, taken by the navcam on Sol 1 of the mission. This 360-degree panorama is the first panorama beamed back to Earth from the Mars Exploration Rover ''Opportunity'' shortly after she touched down at Meridiani Planum, Mars. The image was captured by the rover's navigation [[camera]], and is [[grayscale]].<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;&quot;|First color panorama taken by ''Opportunity''. This color image shows the martian landscape at Meridiani Planum, where the ''Opportunity'' successfully landed at 9:05 p.m. PST on [[January 24]],[[2004]]. This is one of the first images beamed back to Earth from the rover shortly after she touched down. The image was captured by the rover's panoramic camera.<br /> |}<br /> <br /> [[Image:microarray-panel.png|thumb|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1574 2006-01-25T17:24:13Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> [[Image:microarray-panel.png|thumb|left|Please read the FAQ.]]<br /> <br /> {| style=&quot;border:1px solid lightgray;&quot; cellpadding=&quot;2&quot; align=&quot;center&quot;<br /> |style=&quot;width:300px;padding-right:8px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |style=&quot;width:300px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |-<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;padding-right:16px;&quot;|''Opportunity's'' first panorama, taken by the navcam on Sol 1 of the mission. This 360-degree panorama is the first panorama beamed back to Earth from the Mars Exploration Rover ''Opportunity'' shortly after she touched down at Meridiani Planum, Mars. The image was captured by the rover's navigation [[camera]], and is [[grayscale]].<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;&quot;|First color panorama taken by ''Opportunity''. This color image shows the martian landscape at Meridiani Planum, where the ''Opportunity'' successfully landed at 9:05 p.m. PST on [[January 24]],[[2004]]. This is one of the first images beamed back to Earth from the rover shortly after she touched down. The image was captured by the rover's panoramic camera.<br /> |}<br /> <br /> [[Image:microarray-panel.png|thumb|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1573 2006-01-25T17:24:05Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> [[Image:microarray-panel.jpg|thumb|left|Please read the FAQ.]]<br /> <br /> {| style=&quot;border:1px solid lightgray;&quot; cellpadding=&quot;2&quot; align=&quot;center&quot;<br /> |style=&quot;width:300px;padding-right:8px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |style=&quot;width:300px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |-<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;padding-right:16px;&quot;|''Opportunity's'' first panorama, taken by the navcam on Sol 1 of the mission. This 360-degree panorama is the first panorama beamed back to Earth from the Mars Exploration Rover ''Opportunity'' shortly after she touched down at Meridiani Planum, Mars. The image was captured by the rover's navigation [[camera]], and is [[grayscale]].<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;&quot;|First color panorama taken by ''Opportunity''. This color image shows the martian landscape at Meridiani Planum, where the ''Opportunity'' successfully landed at 9:05 p.m. PST on [[January 24]],[[2004]]. This is one of the first images beamed back to Earth from the rover shortly after she touched down. The image was captured by the rover's panoramic camera.<br /> |}<br /> <br /> [[Image:microarray-panel.png|thumb|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1572 2006-01-25T17:23:03Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> [[Image:microarray-panel.jpg|thumb|left|Please read the FAQ.]]<br /> {| style=&quot;border:1px solid lightgray;&quot; cellpadding=&quot;2&quot; align=&quot;center&quot;<br /> |style=&quot;width:300px;padding-right:8px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |style=&quot;width:300px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |-<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;padding-right:16px;&quot;|''Opportunity's'' first panorama, taken by the navcam on Sol 1 of the mission. This 360-degree panorama is the first panorama beamed back to Earth from the Mars Exploration Rover ''Opportunity'' shortly after she touched down at Meridiani Planum, Mars. The image was captured by the rover's navigation [[camera]], and is [[grayscale]].<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;&quot;|First color panorama taken by ''Opportunity''. This color image shows the martian landscape at Meridiani Planum, where the ''Opportunity'' successfully landed at 9:05 p.m. PST on [[January 24]],[[2004]]. This is one of the first images beamed back to Earth from the rover shortly after she touched down. The image was captured by the rover's panoramic camera.<br /> |}<br /> <br /> [[Image:microarray-panel.png|thumb|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1571 2006-01-25T17:22:35Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> [[Image:Keyboard closeup.jpg|thumb|left|Please [[meta:MediaWiki FAQ|read the FAQ]].]]<br /> {| style=&quot;border:1px solid lightgray;&quot; cellpadding=&quot;2&quot; align=&quot;center&quot;<br /> |style=&quot;width:300px;padding-right:8px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |style=&quot;width:300px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |-<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;padding-right:16px;&quot;|''Opportunity's'' first panorama, taken by the navcam on Sol 1 of the mission. This 360-degree panorama is the first panorama beamed back to Earth from the Mars Exploration Rover ''Opportunity'' shortly after she touched down at Meridiani Planum, Mars. The image was captured by the rover's navigation [[camera]], and is [[grayscale]].<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;&quot;|First color panorama taken by ''Opportunity''. This color image shows the martian landscape at Meridiani Planum, where the ''Opportunity'' successfully landed at 9:05 p.m. PST on [[January 24]],[[2004]]. This is one of the first images beamed back to Earth from the rover shortly after she touched down. The image was captured by the rover's panoramic camera.<br /> |}<br /> <br /> [[Image:microarray-panel.png|thumb|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall http://wiki.c2b2.columbia.edu/workbench/index.php?title=Screenshots&diff=1570 2006-01-25T17:18:10Z

<p>Hall: </p> <hr /> <div>=== Microarray Panel ===<br /> {| style=&quot;border:1px solid lightgray;&quot; cellpadding=&quot;2&quot; align=&quot;center&quot;<br /> |style=&quot;width:300px;padding-right:8px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |style=&quot;width:300px;&quot;|[[Image:microarray-panel.png|300px]]<br /> |-<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;padding-right:16px;&quot;|''Opportunity's'' first panorama, taken by the navcam on Sol 1 of the mission. This 360-degree panorama is the first panorama beamed back to Earth from the Mars Exploration Rover ''Opportunity'' shortly after she touched down at Meridiani Planum, Mars. The image was captured by the rover's navigation [[camera]], and is [[grayscale]].<br /> |class=&quot;thumbcaption&quot; style=&quot;vertical-align:top;font-size:85%;&quot;|First color panorama taken by ''Opportunity''. This color image shows the martian landscape at Meridiani Planum, where the ''Opportunity'' successfully landed at 9:05 p.m. PST on [[January 24]],[[2004]]. This is one of the first images beamed back to Earth from the rover shortly after she touched down. The image was captured by the rover's panoramic camera.<br /> |}<br /> <br /> [[Image:microarray-panel.png|thumb|The Microarray Panel displaying marker values for selected array.]]<br /> <br /> === Color Mosaic ===<br /> [[Image:color-mosaic.png|The Color Mosaic component displaying selected arrays, group designation and marker names.]]<br /> <br /> === Expression Profile ===<br /> [[Image:expression-profile.png|Expression Profile plotting values for selected markers and arrays.]]</div>

Hall