MaGnET: Malaria Genome Exploration Tool

Free software tool for visualisation and exploration of integrated Plasmodium falciparum 3D7 functional genomics datasets

Troubleshooting

We hope that you find MaGnET intuitive and straightforward to use. MaGnET has been designed to work on most operating systems and workspace environments. However, some users may run into problems if they are using non-standard software or set-ups. Here are some pointers to solving potential problems when starting to use MaGnET.


Problem: MaGnET is not opening with Java Web Start on my computer.


How to fix:


  1. MaGnET requires a recent version of Java available from Oracle here. MaGnET has been created using Java 1.7 from Oracle and should run on any system with this or a more recent version (the current version is 1.8 update 111) installed. Check if you have Java installed or get the latest version. We strongly recommend updating your Java before running MaGnET, to avoid issues like the problem described below.
  2. If you think you have at least version 1.7 installed, please check that this is the Oracle Java version and NOT an open source version of Java such as Open JDK or IcedTea (this is more likely to be found on Linux or Mac OS computers rather than Windows). There is a problem with Java Web Start in these versions so you will need to download the Java version from Oracle in order to use MaGnET.
  3. If you have checked the above and still can't get MaGnET to open then you should check that Java is associated with the JNLP file type. On Windows, you can do this by navigating to the place where the file "magnet.jnlp" has downloaded, right click on the file and choose "Open with", and check that "Java(TM) Web Start Launcher" is the default program. If not, then you will need to either (i) select it from the list of recommended or other programs, or (ii) click "Browse" and navigate to the Java installation folder on your computer; in the "bin" directory under the latest version of Java, select the "javaws.exe" program and click "Open".

Problem: MaGnET application is blocked by Java Security.


How to fix:


  1. Java has very high security settings and has identified possible risks associated with running MaGnET because the application has been "self-signed" by the authors rather than a professional signing body. Running MaGnET poses no harm to your computer, but Java requires you to specify the MaGnET home page address in your Exception Site List to be allowed to run it.
  2. This page explains how to find the Java Control Panel and add a site to the Exception Site List.
  3. Add http://malariagenomeexplorer.org to the list.

Problem: I get an error saying something about certificate issues with Jmol (or similar).


How to fix:


  1. Some users with older Java versions have experienced Java complaining about certificate issues with Jmol, one of the libraries MaGnET uses. If this is the case for you, updating to the latest version of Java should resolve the issue (see first solution).

Problem: I cannot connect to one of the MaGnET database mirrors.


How to fix:


  1. Please note that the Edinburgh mirror is currently offline as the server is being upgraded. We hope to make it available again soon. Please use the Florida mirror in the meantime, and if you are still unable to access this database you may be suffering from the security issue described in the next point.
  2. The Java Web Start version of MaGnET runs on your computer and accesses one of the database mirrors provided for MaGnET online. Some institutions have strict security settings for their networks which means that they automatically block connections to database servers. The quickest workaround is to try to connect using a wireless or home connection. However, please note that download speeds achievable over wireless connections will not match those over ethernet connections.
  3. Therefore, in the longer term we recommend that you ask your IT department/systems administrators to add the MaGnET databases to the list of allowed connections. For details of the database servers currently in operation please send an email to the authors.

Problem: I am using a Mac computer and having problems opening gene factsheets.


How to fix:


  1. Mac users running Java 1.7 update 9 found a problem with opening gene factsheets (the problem may have occurred with other versions that we don't know about). Updating your Java should fix this.