Free software tool for visualisation and exploration of integrated Plasmodium falciparum 3D7 functional genomics datasets
The current version of MaGnET is MaGnET 2.0. New features in version 2.0:
- Addition of a "Window Control Panel" - a navigation tool allowing easy moving between open analysis windows;
- Introduction of mirror databases, currently one in West Coast North America and one in Europe (other mirrors under development);
- Addition of 2 RNA-Seq gene expression datasets - see the Datasets page for details;
- Improved loading speed of genomic data and gene expression datasets;
- Addition of UniProt IDs and links to UniProt;
- Addition of EC numbers and reactions;
- Updated set of PDB structures.
How to download and use MaGnET
MaGnET is available to use as a Java Web Start application. Download a .jnlp file and run it directly from your desktop, accessing the database and files on one of the mirror sites. Two mirror sites are currently available, one at FfAME, Florida, USA and one in Edinburgh, Scotland, UK. Other mirror sites are under development.
Alternatively, you may download a version of the software and database to run locally (requires MySQL).
MaGnET has been developed under Windows 7 using Oracle Java 1.7. The cross-platform portability of Java means MaGnET should work on any operating system, though its appearance may differ. While MaGnET should work with all versions of Oracle Java from 1.7 upwards, better performance may be achieved with more recent versions of Java. Note, some users have experienced errors with older versions of Java, in which case updating to the latest Java version (currently version 1.8 update 111 [as of Jan 2017]) fixes the problem. See the troubleshooting page for more information.
Please note that more recent versions of Java have high security settings which now require you to add the MaGnET home page (http://malariagenomeexplorer.org) to your list of allowed sites (see here for how to do this).
Although MaGnET has undergone rigorous testing there may be things our testers have overlooked. If you find any bugs or annoying behaviour, please send an email describing the bug, any suggestions for how you would prefer it to behave, and your operating system name. Especially for the Java WebStart version, we recommend upgrading to the newest Java 1.8 update that is available for your computer and operating system.
Open MaGnET using the link below and connect to one of the database mirrors in Florida, USA or in Edinburgh, UK (other mirror sites under development).
To access the tutorial follow the links on the right.
MaGnET Java Web Start Application
For use with Java 1.7/1.8+
Download a JNLP file which contains a path to the latest version of the application and database running on our server. No need to visit this website again to run the program, just save the JNLP file.
Right click and select 'save as' to save the file to your computer (Mac users: ctrl-click).
N.B. If the JNLP file doesn't automatically open then navigate to the folder where it has been downloaded to, right-click (Mac users: ctrl-click) on the file name (magnet.jnlp) and choose Open with -> Java(TM) Web Start Launcher (Windows) or Java Web Start (Mac). Consult the Troubleshooting page for further advice.
MaGnET Downloadable Application & Database
For advanced users with technical knowledge/support, requires MySQL Community Server 5+ and Java 1.7/1.8+
To download a local version of the application and database to install locally on your computer, right click and select 'save as' to save the file to your computer (Mac users: ctrl-click).
MaGnET is provided under the GPL license.
N.B. If the MySQL connector that is provided with the download doesn't work (error connecting to the database), then try downloading the latest MySQL connector/J for your platform.