FAQ

Why are the fonts fuzzy in tools when using Mac OS Mojave?

Refer to this page (thanks to Jalview).

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Why do I get an “Unsupported/Corrupt file format” error when I try to import GenBank file to one of the tools?

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

It’s possible that your system or network’s firewall configuration is blocking access. To test this try accessing the VBRC Vocs tools from another computer on another network.

If you can access the tools on a different computer, outside of your usual network, it is likely your work firewall is blocking the necessary ports.

To test this further, try checking if ports 4440, 7798 and 7900 are accessible on 4virology.net using a port checker such as https://www.yougetsignal.com/tools/open-ports/. To access the VBRC tools, you will need to talk to your system administrator to ask for access to the following hosts and ports: 4virology.net, ports 4440, 7798, and 7900

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What’s Java Web Start doing?

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.

Java Web Start Warning

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.

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.

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Do I need to have an account to use VBRC tools?

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
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How do I run VBRC tools?

All VBRC tools require Java to run and are launched using Java Web Start. To run any of our applications you must have Java 1.6 or higher (Java 1.8 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.

NOTE: Java 9 and 10 work, but will show deprecation warnings. Ignore these warnings. Starting with Java 11, Java Web Start will no longer work.

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Why am I not receiving the confirmation email for my VBRC account?

Confirmation emails from WordPress sites such as this one can sometimes be picked up by spam filters. This may be a particular problem for university email addresses. We recommend checking your spam folder for the email. If that doesn’t work, try signing up with an email address from a major provider such as Gmail or Hotmail.

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