Frequently Asked Questions (FAQ)


  1. How do I run VBRC tools?
  2. What’s the advantage of using the Java tools?
  3. Do I need to have an account to use VBRC tools?
  4. What’s Java Web Start doing?
  5. Why won’t VOCs etc work on old Java?
  6. Why won’t VOCs etc work after I have updated Java (Mac OSX only)?
  7. Why can’t I access the databases in VOCs (or another tool)?
  8. When I try to import GenBank file to one of the tools, I get the error “Unsupported/Corrupt file format”.

 

How do I run VBRC tools? Top of page

All VBRC tools require Java to run and are launched using Java Web Start. To run any of our applications you must have Java 1.4 or higher (Java 1.6 recommended) installed. You can install Java from the Java site.

When you click on the link for any of our applications, it will download a .jnlp file onto your computer. If Java Web Start is configured to run in your browser, the application will automatically launch after it has been downloaded. Otherwise, you can click on the .jnlp file to launch the application. If a dialog appears with “Open using application…”, select the javaws application, located at <JAVA_HOME>/javaws.

 

What’s the advantage of using the Java tools? Top of page

Java is a programming language that runs software inside a virtual machine on your computer. This machine can be created on all the common computer systems, so the bottom line is that the VBRC software should run on your computer! That is providing it’s reasonably up to date and has Java 1.4 or higher (up to Java 1.6) installed.

Java tools also usually have more functionality than software that can be incorporated into a web browser.

 

Do I need to have an account to use VBRC tools? Top of page

Yes. We have implemented this to help us keep track of our user-base. When you set up an account you become part of the VBRC community and the advantages are:

  • You can comment on blog posts
  • You can set up a profile and publicize your work/lab/papers
  • You will be notified of new tools and help tutorials by (very) occasional mail-outs.
  • You can participate in our community forums to discuss a wide range of topics

 

What’s Java Web Start doing? Top of page

Java Web Start launches full-featured applications with a single click on a web page link. If the application is not present on the local system (i.e. if the application is launched for the first time) Java Web Start automatically downloads all necessary files required to run the application. It stores the files on your local computer so the application is ready to be relaunched anytime, either from the web link or from the Java Web Start application. When relaunching a Java Web Start application Java Web Start will download modified resources so that you always have the most current version.

Applications launched by Java Web Start, by default, run in a restricted environment (a “sandbox”) with limited access to files and network. Since the VBRC Java Web Start applications may need access to files on the local system, a printer in the local network, or the content of the clipboard, an alert window is displayed asking if permission can be granted to do so.

A Java Web Start application can also request unrestricted access to the local system. These applications have what is called a digital signature, which is intended to be an indication of the application’s trustworthiness. In this case, Java Web Start will show a Security Advisory dialog when the application is launched for the first time. The security warning will show information from the signature about the origin of the application, i.e. the vendor who developed it.

Java Web Start Warning

To accept this application’s request, click “Start”. To see more details on the request and Dr. Chris Upton’s Java Certificate, click “Details”. If you wish not to accept the request, click “Exit”. Choosing “Exit” will cause the program to close.

Once the Workbench Application has downloaded, it is like any other program that you might run on your local system, therefore it needs access to the system to function properly.

 

Why won’t VOCs etc. work on old Java? Top of page

Some of the VBRC tools need at least version 1.4 of Java, others require 1.5. It’s best to be running the latest version of Java that your system recommends. The bottom line is that you need a fairly recent computer/system to get the best out of any software, including bioinformatics tools!

 

Why won’t VOCs etc work after I have updated Java (Mac OS X only)? Top of page

Most of the VBRC tools were designed for version 1.6 of Java, and may not work properly with newer versions. If, after installing the latest Java update, you find that certain VBRC tools are not working correctly, follow these steps to re-enable the Apple-provided Java SE 6 web plug-in and Web Start functionality.

Note: You must be logged in as an administrator. If prompted for your administrator password after a command, enter it and then press the Return or Enter key.

  1. Open Terminal, located in the Utilities folder.
  2. Enter this command, then press the Return or Enter key:
    sudo mkdir -p /Library/Internet\ Plug-Ins/disabled
  3. Enter this command, then press the Return or Enter key:
    sudo mv /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin /Library/Internet\ Plug-Ins/disabled
  4. Enter this command, then press the Return or Enter key:
    sudo ln -sf /System/Library/Java/Support/Deploy.bundle/Contents/Resources/JavaPlugin2_NPAPI.plugin 
     /Library/Internet\ Plug-Ins/JavaAppletPlugin.plugin
  5. To re-enable Java SE 6 Web Start, enter this command, then press the Return or Enter key:
    sudo ln -sf /System/Library/Frameworks/JavaVM.framework/Commands/javaws /usr/bin/javaws

If, during this procedure you receive the error “The directory is not empty”, do the following:

  1. Go to the “Applications” directory
  2. Search for “JavaAppletPlugin.plugin”.
  3. If there are 2 (or more) files found delete the older file(s).
  4. Continue the procedure from where you were before you received the error.

(Source: http://support.apple.com/kb/HT5559)

 

Why can’t I access the databases in VOCs (or another tool)? Top of page

It’s possible that your system’s firewall configuration is blocking access. To test this:

  1. Try accessing the VBRC Vocs tools from another computer on another network. That is, if you’re at work right now, try it from home tonight.
  2. To check immediately to see whether you can get through:
    1. Open a console window and type “telnet athena.bioc.uvic.ca 4500″
    2. If you are able to connect, you’ll see the following output:
      • (chaos:~) telnet athena.bioc.uvic.ca 4500
        Trying 142.104.33.184…
        Connected to athena.bioc.uvic.ca.
        Escape character is ‘^]’.
      • type control-square bracket and then quit to exit
      • you’ll need to check the following server and port combinations as well:
        1. athena.bioc.uvic.ca 4440
        2. leto.bioc.uvic.ca 7798
        3. leto.bioc.uvic.ca 7800
    3. If you got no response from the telnet command, you may be blocked by your firewall configuration
      1. If you’ve talked to someone from VBRC recently and you’re reasonably sure that the systems are up and running:
      2. You’ll need to talk to your system administrator to ask for access to the following hosts and ports: athena.bioc.uvic.ca, ports 4500 and 4440 and leto.bioc.uvic.ca ports 7798 and 7800

 

When I try to import GenBank file to one of the tools, I get the error “Unsupported/Corrupt file format”. Top of page

This error can be reported when the sequence length specified in the header of the GenBank file is smaller than the true length of the sequence contained in the file.

Try changing the sequence length specified in the header to the actual length of the sequence at the bottom of the file.

 

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