RnallViewer User Guide

RnallViewer: An RNA analysis visualization tool

Table of Contents |
Setup
| Tutorial | Functionality Overview | Customization Overview

Setting up RnallViewer

List of Files Included in the Package

The latest build of RnallViewer_Installer.jar should include:
  • BioJava
    • biojava-1.4.jar
    • bytecode-0.92.jar
    • commons-cli.jar
    • commons-collections-2.1.jar
    • commons-dbcp-1.1.jar
    • commons-pool-1.1.jar
  • Tools
  • Installations
    • Java3D: java3d-1_3_1-windows-i586-directx-rt.exe
    • Java 1.5: jre-1_5_0_05-windows-i586-p.exe
  • Sample Data
  • Preferences/NaviewPlotPrefs

Installation

To install, download the RnallViewer_Installer.jar from our website. You need to install Java 1.5 or later version (download site) and Java3D (download site) in order to run RnallViewer installer. Then RnallViewer_Installer.jar will guide you through the installation process. Sun releases periodic updates which you can look for here; the included installers may not be the latest. Periodic updates of RnallViewer and these third-party software packages may require you to download more recent versions. Links have been provided above.

Attention: During the download, you should save it as a jar file. Many computers automatically save it as a zip file. Be aware and avoid this.

Basic Setup

Once you have RnallViewer installed, you will need to do some initial customization if you do not like the default preference setting. First select General Preferences from the Preferences Menu:

You'll be greeted by a preference screen, shown on the right as it appears under OS X. We'll come back to most of the functionality here later when we discuss main display customization in the customization chapter. For now, we just need to set the locations for Rnall, Naview, a plot preferences file (more on this under 3D customization), plt22ps, and ghostscript. All of these are described later with the functionality overview.

Click the "Browse for Rnall" button to the right of the "Rnall Location" label. Search to where you installed RnallViewer and look inside the "Tools" folder. Open the folder corresponding to your system and select the Rnall executable. Repeat this procedure for the others. Naview should be inside "Tools" under the appropriate operating system folder. The plot preference file is located under the "Preferences" folder of RnallViewer. plt22ps should be in the same folder as naview. Ghostscript should also be in "Tools" under the appropriate operating system folder.

You're done with setting up RnallViewer! Feel free to check out the tutorial for a whirlwind tour of its capabilities.

Table of Contents | Setup | Tutorial | Functionality Overview | Customization Overview