HALO - A Java framework for precise transcript half-life determination Version: 1.3 Software suite for the calculation of RNA half-lives from measurements of newly transcribed, pre-existing and total RNA. Web: http://www.bio.ifi.lmu.de/software/halo Contact: Caroline Friedel (Caroline.Friedel@bio.ifi.lmu.de) Getting started =============== After unpacking the download archive to a directory of your choice run gui.sh for the graphical user interface or cmdline.sh to start the command line tools Use gui.bat and cmdline.bat if you are on Windows. By default, the GUI and commandline tools use a maximum heap size of 1024MB. If you need more than that, you can increase the max heap size using the -XmX option in Java, e.g. : gui.sh -Xmx2000M cmdline.sh -Xmx2000M Requirements ============ HALO requires the Java 6.0 Runtime Environment or higher which is freely available at http://www.java.com For visualization (optional) the JFreeChart library is used (available under the GNU Lesser General Public License at http://www.jfree.org/jfreechart/ and distributed with the HALO release). Documentation ============= You find the documentation files in the doc/ subdirectory (start with index.html) or online at http://www.bio.ifi.lmu.de/files/Software/halo/doc/index.html Package structure ================= *.sh Shell startup scripts *.bat Windows startup scripts README.txt this file doc/ HALO documentation lib/ Compiled binaries src/ HALO source codes data/ HALO example data files (if downloaded)