User Manual

GPViz User Manual

Getting started / Quick tour

Changelog

GPViz change log (text file)

System requirements

GPViz is written in Java 7 and will require Java 7 or newer installed on your computer. To download Java, please visit http://www.java.com/en/download/

File formats

Gene(ral) Transfer Format (GTF)
BED format
Mutation Annotation Format (MAF)
Variant Call Format (VCF)
Mutation format (MUT)
SNP file format
Conserved Domain Database
Pfam

FAQ

I'm running out of memory. What do I do?

On Windows, open the GeneProteinViz.l4j.ini file in a text editor and change the line that says "-Xmx1024m" to reflect the amount of memory you want to give to GPViz, for example "-Xmx1536m" for 1.5GB. Note that on a 32Bit operating system like Windows XP the amount of memory you can possibly provide is limited. That limit varies, but it is usually somewhere in the range of 1.5GB-2GB. If you get an error message after changing the memory settings, try reducing it until you are able to start GPViz.

Another way to work around the memory issue is to simply load smaller files. Galaxy, for example, is a very useful tool that can help you to filter your GTF input file to reduce the size and memory requirements.

If you have enough memory to load your GTF file, but not subsequent files, try filtering and unloading genes using the "Filter" menu in GPViz. The GPViz manual can provide you with more information on how to do that.

Why doesn't GPViz accept my input files?

Please check the manual on whether your input files really contain all the necessary data, and whether it conforms the format description. A typical mistake is when tab delimited files are instead delimited by spaces or commas.
If you feel GPViz should be able to read the file, but there's an error, please just send us that file (or a snippet of it) and we'll gladly have a look and see if you we can make GPViz more compatible to suit your needs!

Where do I send bug reports or suggestions?

The easiest and fastest way is through our support forums, but you can also write directly to rene.snajder@i-med.ac.at.