I am having problems exporting GIFs of the Graphical View
The software/installer won't launch in Mac OSX
I am having trouble installing GenePalette on my Unix or Linux System
I submit my registration information, and the browser gives me an error
How big of a sequence can the program load?
How should I cite GenePalette?
How can I help?
I am having problems exporting GIFs of the Graphical View
We are aware of this problem. Often, if an image is too big, the GIF export function runs out of memory. We have tried many different options for GIF export, and we always see this problem. The solution is to either decrease the size of your image (trim it, or increase the bases/pixel ratio), or use the PostScript output option that is new to Version 1.1.
The software/installer won't launch in Mac OSX
There are a couple of things that can go wrong with the Mac OSX installer:
First, it may be your extraction software. Stuffit 8.0 has a problem that removes Unix executable permissions from the installer. Stuffit version 7.0 or the 8.0.1 update will extract this archive just fine. Also, we notice that the ZipIt program does note extract the installer executable properly.
If you are running OSX version 10.3.9, there may be a couple of problems in this update with Java. First, 10.3.9 has known issues with java that are fixed by an update. Here are the details from apple.
Second, QuickTime 7.0.4 causes a conflict with some Java launchers. You can downgrade to QT 7.0.1 here.
Although we don't really know why this happens, it seems to sometimes help to restart your computer if the installer will not launch.
I am having trouble installing GenePalette on my Unix or Linux System
All of the GenePalette installers are created with InstallAnywhere5.5(Now!). For the Linux and Unix installer, the file you extract comes as a shell script that you run on your computer (./GP1_1UNX). Try both versions of the script: With a Java Virtual Machine (JVM) and without a JVM. If these don't work you may have to install your own JVM (it must be version 1.3.1 or better). Once installed, it is extremely important that your new JVM is at a higher point in your path than any other JVM. We have also noticed that the installer had problems on a two-monitor Linux box, but that it went away when the installer was launched in single monitor mode. Please send us an email if you have any problems with the installers so that we can better troubleshoot installation for others in the future
I submit my registration information, and the browser gives me an error. How can I download GenePalette?
This problem seems to occur because of certain firewall settings. If you experient this, please fill out this form and email it to mrebeiz@ucsd.edu. You will be directed to a page that will let you download the program.
How big of a sequence can the program load?
It varies from computer to computer, but on my machine (Dual Processor G4, MacOSX) it will handle about 1 Megabase with no sweat. Once you get much larger than that, things really slow down. If the need arises (and enough people complain), we might add support for larger sequences.
How should I cite GenePalette?
If you used GenePalette in your work, please reference our paper describing the tool:
GenePalette: a universal software tool for genome sequence visualization and analysis.
Rebeiz M, Posakony JW. Dev Biol. 2004 Jul 15;271(2):431-438.
How can I help?
There are a lot of ways that we could benefit from the help of our users. First, we can always use bug reports, and user comments to improvement of the program. Many of our favorite features were suggested by a user. Another way to help is to put a link to our program on your website. Every link counts in our battle to get to the top of someone's Google search. The final way to help the GenePalette cause is to cite our paper if you used the program in your research:
GenePalette: a universal software tool for genome sequence visualization and analysis.
Rebeiz M, Posakony JW. Dev Biol. 2004 Jul 15;271(2):431-438.
[link to PubMed]