Java applet based visualizers no longer function in any browser

Posted on Thursday, March 16, 2017 at 12:47PM by Barbara Hill

This post serves as a final update to all previous FAQs and blog posts regarding the state of Java applet visualizers in any browser.

As of March 2017, all browers have ceased support for the plugins that are needed to run a Java applet visualizer (such as MultiplotStudio) in a browser.

See this article for more information: https://www.infoq.com/news/2017/02/oracle-java-browser-applet

We are very much aware that being able to visualize your data is a big part of why you use GenePattern. To that end, we are working to rewrite our existing Java applet visualizers in JavaScript.

As of March 2017 we have released the following in JavaScript:

CLSFileCreator
HierarchicalClusteringViewer
ComparativeMarkerSelectionViewer
HeatMapViewer
ConstellationMap
*IGV.js - note that this is an alpha (ie early release) version made available for convenience

The following are currently deprecated:

CaArray2ImportViewer
CytoscapeViewer
FeatureSummaryViewer
FLAMEViewer
GeneListSignificanceViewer
GSEALeadingEdgeViewer
JavaTreeView
MAGEMLImportViewer
MAGETABImportViewer
MINCYViewer
Multiplot - Note that this module is for archival only and has been replaced, by the author, with MultiplotStudio
MultiplotStudio
PCAViewer
*PredictionResultsViewer (JavaScript version in alpha - due out in beta in March 2017)
SnpViewer - for archival purposes only, we now recommend the use of IGV for viewing snp data
SOMClusterViewer
VennDiagram

 

A footnote:

We are working on an alternative for launching legacy Java applet visualizers from the command line, in order to allow users to run visualizers, which are no longer supported but may be needed for reproducibility. The code can be found on GitHub (https://github.com/genepattern/VisualizerLauncher) but is not yet ready for use due to a recent change from http to https. 

 

Please contact us with any questions you may have, and follow us to get updates on our release process.

    

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