BioRAT Documentation
Installing BioRAT
System requirements: The exact requirements depend on how the software is to be used. For example, analysing long documents using large gazetteers and/or complex templates will require large amounts of memory. I recommend at least 0.5 Gb of RAM, and preferably 1Gb. The system has been developed and tested under both MS Windows (2000) and Unix (Solaris), and it should work on any suitable Java platform, although some minor modification to some of the settings files may be required.
- Download and install the latest version of GATE from Sheffield University. I suggest you use the "platform-specific installer", unless you are very familiar with installing and using Java software. If you don’t already have Java installed, then select the "include VM" option on the download screen. You will have to register before downloading the software. Note the directory the software is installed in.
- If you choose to install Java separately, then download a Java run-time environment (JRE) from the Sun website. NOTE: GATE requires Java v. 1.4 or later, and at least some versions are not compatible with Java 1.5. So I suggest using the J2SE v 1.4.2_06 JRE.
- Download the full installation version of BioRAT from here. This is a single zip file. Unzip it, keeping the folder names, e.g. into c:\program files\biorat. A description of these folders is given below. Under some operating systems (e.g. Unix) you may need to change the file permissions to allow some programs to be executed. See "operating systems" note below.
- Go to the BioRAT directory (where you just unzipped the BioRAT files). You will see a file called "biorat_setup.bat". Run this file, e.g. by double-clicking on it (or type 'java -jar lib/bioratoptions.jar' at the command prompt.). You can set many options here; however most of the default values should be sufficient for now. You will need to change the "GATE home directory" option. Click the "..." button to the right of this option, browse to the directory where GATE is installed (E.g. "C:\Program Files\Gate\gate-3.0-BIN"), and click "select". NOTE: this is the top-level directory of the installation. It will contain subdirectories such as "bin" and "lib", but select their parent directory.
- Click the "Go!" button beside "(Re)-create startup scripts".
- Click the "Go!" button beside "Store these settings".
- Click the "Go!" button beside "Exit setup" to leave this program.
- Although not essential, you may also want to select a PDF viewer, such as Adobe Acrobat Reader.
- After completing this set up, to launch BioRAT go to the BioRAT directory, and start the "biorat_windows.bat" program or "biorat_unix.sh" depending on your platform.
The unzipped installation requires around 10Mb of disk space. This will tend to increase as the system is used, papers are downloaded, and results produced. By default, the directory structure will look something like this:
| Directory |
Description |
| biorat\ |
top-level directory; includes initialisation file and execution scripts |
| biorat\lib\ | library directory: contains Java archives |
| biorat\etc\ | Various system files |
| biorat\data\templates | Template project files (*.xml) and template subdirectories |
| biorat\data\gazetteer\ | Set of gazetteer files (*.lst) with index (e.g. lists.def) |
| biorat\scripts\ | Various scripts and rule files |
When the system is used, further directories will be created, such as biorat\tmp, used while downloading papers; biorat\data\papers, used to store papers after downloading; biorat\data\results, used to store results of template analysis. During execution, BioRAT will write to certain directories (etc, data\results, data\papers), which must therefore be writable. Furthermore, users may wish to edit or create files in data\gazetteers and data\templates. The files in biorat\tmp are only used during web-access, and can safely be deleted afterwards.
The default directories described above can be changed by editing the settings file, which is called bioratSettings.xml by default. The biorat_setup.bat program provides a simple way to edit this file. Some can also be changed from the command line.
A note on operating systems
Being written in Java, BioRAT should work under any operating system, and has been developed and testing using MS Windows, Linux and Solaris. However, the various supporting files may need to be modified to work correctly under various OS's. For example, the biorat*.bat and biorat*.sh files, which are used to start the application, specify the paths of the library files, and different OS's used different formats to specify paths. The examples included with the distribution should be enough to show you how to get things working on your system. If you want to share your solutions or ask for further advice, please contact me.
File permissions: certain files need to be executed directly, such as the various scripts to launch BioRAT. Under Unix, you may need to specify this directly. E.g. in the main BioRAT directory, you may need to run a command such as: chmod a+x *.sh. Similarly for the scripts in the biorat\scripts directory.
Although I have not tested it directly, I believe the software works under MacOS, using the "UNIX-style" settings above.
Testing the installation
A "walkthrough" showing the basic features (with screenshots!) is available here.
Updating existing installations
To save download time, and to simplify maintenance, the core library file can be downloaded separately from the full installation. If required, download the "biorat.jar" file and place it in the biorat\lib directory, overwriting the existing copy.
Backing up the system
Details to appear.
The main files you may want to backup are all in the biorat\data directory. This includes results from template matching, papers that have been downloaded, as well as templates and gazetteers.
Page updated: March 2005