Virtual Chinese Genome Browser

Installation Guide

• To use the web-based applet of VCGDB, users must have a Java Runtime Environment (JRE) version 1.6.0 or upper properly installed. You may find the the newest version of Java from the official website http://www.java.com.
• You may change the PATH system variable, Please refer to the official description here.
• After installing JRE, you may have to configure the plugins for your internet browser depends on operation system and browser you are using, which we will illustrate below.
• The browser may ask for your permission when initializing the VCGBrowser applet.
• If your browser still cannot correctly display the VCGBrowser applet, we strongly recommend you using our application of VCGBrowser, and choose the version that has JRE integrated. You can download it from here.

Internet Browser Configuration

Browsers for Windows

• Internet Explorer

1. Click Tools and then Internet Options
2. Select the Security tab, and select the Custom Level button
3. Scroll down to Scripting of Java applets
4. Make sure the Enable radio button is checked
5. Click OK to save your preference

• Chrome

1. Enter about:plugins in the search field.
2. Scan for Java and check whether Java is enabled (if the Disable link appears, Java is already enabled)
3. Click on the Enable link (if available)
4. (Optional) Check the Always allowed box to stop additional Chrome warnings when running Java content

Browsers for Windows and Mac OS X

• Firefox

1. Start Mozilla Firefox browser or restart it if it is already running
2. At the top of the browser, select the Firefox button (or Tools menu in Windows XP), then Add-ons
   The Add-ons Manager tab will open.
3. In the Add-ons Manager tab, select Plugins
4. Click Java (TM) Platform plugin to select it
5. Click on the Enable button (if the button says Disable, Java is already enabled)

• Safari

1. Launch Safari browser
2. Click on Safari and select Preferences
3. Click on the Securitytab
4. Check (select) Enable Java check box
5. Close Safari Preferences window

• Opera 4.x and Up

1. Opera for Windows does not use Java, but an embedded version already inside the Opera Web browser.
2. Opera for other platforms may supports Java . Please consult your Opera platform documentation.
3. For further information, please review the following Opera Support article:
   Support for Java software in Opera

Browsers for Linux (Fedora, CentOS, Ubuntu, etc.)

• Google Chrome

1. Become the root user by running the su command and then enter the super-user password. Type:
   sudo -s
2. Create a directory called plugins if you do not have it. Type:
   mkdir -p /opt/google/chrome/plugins
3. Go to Google chrome plugins directory before you make the symbolic link. Type:
   cd /opt/google/chrome/plugins
4. Create a symbolic link. Type:
   ln -s /usr/local/java/jre1.7.0/lib/amd64/libnpjp2.so
5. Restart your browser and test Java

• Mozilla Firefox

1. Become the root user by running the su command and then enter the super-user password. Type:
   sudo -s
2. Create a directory called plugins if you do not have it. Type:
   mkdir -p /usr/lib/mozilla/plugins
3. Go to Google chrome plugins directory before you make the symbolic link. Type:
   cd /usr/lib/mozilla/plugins
4. Create a symbolic link. Type:
   ln -s /usr/local/java/jre1.7.0/lib/amd64/libnpjp2.so
5. Restart your browser and test Java

 

• If you just want to glance at VCGBrowser, you can just click "Example" and choose an item/region/gene/gwas you would like to browse.
• The Search page may help you to locate the region you are interested in, and a hyperlink to browse the region directly.
• You can use your mouse wheel to zoom in or out the region.
• Move your mouse on the map, and the progress bar will tell you the exact location of it.
• Drag your mouse on the map to zoom into the region you would like to browse.
• A simple double click on the map will center you mouse location and zoom max.
• A click on any glyph(gene, duplication, gwas, dynamic bar, indel triangle, rare variant symbol) will trigger an instant query to VCGDB and in return with detail infomation.
• You can scroll along the detail information panel, and a simple click will restore it to center.
• If you are using the application version of VCGBrower, you may maximum the window to have a bigger view of the browser, and you need to regenerate the map to synchronize the coordinates.

 

• From Java 7 Update 21 (7u21), April 2013, all Java content accessed through the browser (including Applets and Applications) will ask permission before starting to run.Reference.
• The digital certification (DC) have to be added into "Trusted Root Certification Authority" of your computer if you want to see a high security level logo when running VCGBrowser. Reference.
• The digital certification supports IE core internet browsers only, but it does not impact the performance of VCGBrowser in other browsers like Chrome, Firefox, Opera, etc.
• VCGBrowser uses servlet to search information from VCGDB that will not write data on your computer and cause any security issue.
• Once you allow security prompt, VCGBrowser will run stably with full functioning.