From GenPlay, Einstein Genome Analyzer

Jump to: navigation, search

How can I cite GenPlay?

If you like GenPlay and use it for your research, please help us by citing our publication in Bioinformatics:

Bioinformatics. 2011 May 19
GenPlay, a multi-purpose genome analyzer and browser.
Lajugie J, Bouhassira E.
Department of Medicine, Albert Einstein College of Medicine, Bronx, New York 10461, USA.

PMID: 21596789

You can also add a link to GenPlay.net from your website to increase our visibility.

Thank you for your support!

Where can I find the executable of GenPlay?

GenPlay can be launched from the Downloads page of this website. You need to register in order to download GenPlay. Registering is free and takes less than a minute.

Do I need a license to use GenPlay?

GenPlay is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

Where can I download the source code of GenPlay?

The source code of GenPlay are available from the GIT repository at https://github.com/JulienLajugie/GenPlay You can check out the latest source code with a git client with the following command:

 git clone git://github.com/JulienLajugie/GenPlay.git

GenPlay feels sluggish. How can I improve the responsiveness ?

GenPlay will fill sluggish and unresponsive while it is busy updating or copying tracks.

GenPlay indicate that tracks are being copied or updated on the bottom center of the screen. While GenPlay is busy, it lets users zoom and pan but they cannot access any functions or change chromosomes. When GenPlay is busy, zooming and panning might feel sluggish.

The Java garbage collection function might also interfered with browsing or all other GenPlay activities. Memory management is automatic in Java and cannot be easily controlled by the developers. Java garbage collection (which reorganized RAM usage) launches automatically and somewhat unpredictably. During garbage collection the computer becomes completely unresponsive. This is usually not a major issue since it happens relatively rarely for a short time. However, if there is not enough RAM memory on the computer or if there are not too many other programs or background tasks running in parallel, Java might need to collect the garbage more frequently. I that is the case, GenPlay can become very unresponsive. To maximize GenPlay responsiveness, close all unnecessary tasks and applications than runs concurrently with GenPlay.

GenPlay can also become unresponsive if you load too much data at the same time. Memory usage is indicated on the lower right of the screen. This indicator change color from green to red. If it is consistently red, you are overloading your memory. Overloading the system does not necessarily crash GenPlay, because most operating systems can shift the data from the RAM to the hard drive when the RAM is full, but this will slow down GenPlay and your computer to a considerable extent.

If you are routinely using GenPlay at close to the maximum amount of memory available on your computer or if you are using multiple instances of GenPlay at the same time, you might be able to improve performance by increasing the size of your paging file but the best solution is to use a more powerful machine.

GenPlay is multi-threaded and can take advantage of multi-processors. GenPlay performance are highly dependent on the hardware. GenPlay can run on almost any machine but will only shine on a relatively modern multi-core machine with sufficient memory. If you do not have access to such a machine, GenPlay runs very fast on small machine if the data are loaded one chromosome at a time or if the analyses are performed at lower resolution.

During zooming, the item I want to zoom in on keep sliding off the edge of the display. How should I use the zoom functionality to avoid this problem?

During the conception of the software we decided to handle this problem as follow:

  • A double click on a feature centers the screen on the selected feature.
  • A mouse wheel up or down zoom in or out on the feature that is at the center of the screen. An unintended click on the mouse wheel starts the scroll mode which can be undesirable.

When I try to launch GenPlay on Mac OS I get the following message: "GenPlay is damaged and can't be opened. You should move it to the Trash". What should I do?

OS X Mountain Lion (10.8) has a new security feature called Gatekeeper. Gatekeeper is enabled by default and prevents applications distributed outside of the Mac App Store from launching.

Here is a workaround:

  • Open Gatekeeper settings located in "System Preferences > Security & Privacy"
  • Set "Allow applications downloaded from:" to "Anywhere" and confirm by pressing "Allow From Anywhere"
  • Download, unpack and run GenPlay
  • Once an application is successfully launched, it no longer goes through Gatekeeper. Thus you can restore Gatekeeper settings to the default option "Mac App Store and identified developers" after successfully launching the profiler

I am using the Java Webstart launcher, how can I make sure I am using the last version of GenPlay ?

To be sure that you are not actually using an old version of GenPlay you need to delete the Java temporary files from the Java control panel. On Windows, the Java control panel is accessible from the Windows Control Panel > Java icon.

I have a Java error when I launch GenPlay, what do I do?

What is it?

In order to run a Java application, the computer needs to use a Java Runtime Environment (JRE). Many software install their own JRE, sometimes in their own directories, sometimes in the directory the JRE is supposed to be.

That can lead the operating system to get lost when it has to run Java applications and create incoherencies.

What to do then?

The main idea is to uninstall ALL JREs you have installed on your computer and to install the newer JRE ONLY.

Here is a fix for Windows:

In the best case, you will have to do the steps 1 and 4 only.

1. Go to "Control Panel" > "Programs and Features" and find the Java installation. Run the uninstall program for all of them.

You may experience an error when uninstalling meaning that you cannot fully uninstall the JRE. Then do step 2 and 3, skip them otherwise.

2. If it is the case, then you need to delete the folders manually.

For 32bits Windows, go to the folder:

C:\Program Files\Java

For 64bits Windows, go to both folders:

C:\Program Files (x86)\Java

C:\Program Files\Java

Delete all folders starting with "jre".

3. That is not a clean uninstall. In order to avoid issues in the future (especially when installing a newer JRE), you need to clean up the registry. Use a registry cleaner (such as CCleaner, Eusing Free Registry Cleaner, Wise Registry Cleaner ...).

This cleaning step is really important before installing a newer JRE.

4. Once ALL JREs uninstalled, download the latest Java version (here) and install it.

5. If the WebStart does not still work, please change the default software for opening ".jnlp" file. The system may have kept previous JRE version paths that are obviously not working anymore.

In order to change a default program, go to "Control Panel" > "Default Programs" > "Associate a file type or protocol with a program" and find the ".jnlp" extension and click the button "Change program…".

Go to the folder where the JRE is installed, then to the folder "bin" and select the file "javaws.exe".