License
BioRAT is distributed for non-commercial use.
Proxy servers
To specify the address of a proxy server, either change the command line, or edit the "bioratsettings.xml" file. The former method is the standard Java approach to specifying proxy servers. For example:
java -Xmx1000m -DproxySet=true -Dhttp.proxyHost=my.company.proxy -Dhttp.proxyPort=my.company.port -Dhttp.proxyUser=the InternetUser -Dhttp.proxyPassword=theInternetPassword frontend.Application1
Alternatively, the bioratOptions.bat program can be use to edit the bioratSettings.xml file, to include lines like these:PROXY_HOST=my.company.proxy
PROXY_PORT=my.company.port
This is more limited, but may be more convenient in some cases.
Firewall acess
When accessing the web through the GUI, the user will be prompted for their username and password if required. For command line use, the "-u" option allows the username and password to be specified on the command line. NOTE: no encryption of the password is used, so this may not be a secure method.
PDF to text conversion
The template-processing part of BioRAT can only read plain text, but many papers are distributed in PDF format. Therefore, whenever BioRAT downloads a PDF paper, it attempts to convert this into plain text.
Old version
It does this using an external script stored by default in the biorat/scripts directory. If GhostScript is installed, then the script dc_ps2ascii.bat may be edited and used. Under Unix, ps2ascii may already be available, in which case the ps2ascii.sh script in the biorat scripts directory may be used. Or you could write your own script: it should take two string parameters, the first is a PDF filename, and the second is the plain text filename. The script can be chosen using the biorat_setup.bat program.
New version Version 1.7 of BioRAT (December 2004) incorporates the JPedal PDF-to-text conversion system, and so no longer requires an external conversion tool. I.e. the dc_ps2ascii.bat script (and similar) are no longer used by BioRAT. Instead, several new library .jar files are included in biorat/lib, such as jpedal.jar. These are distributed with BioRAT, although more recent versions may be obtainable from the JPedal website.
| BioRAT home | David Corney home | Bioinformatics home |