CoBaltDB
Introduction
CoBaltDB is a client-server application, with the server installed and staying at Biogenouest bioinformatics platform, keeping all needed pre-computed genomic data, while the CoBaltDB Client or GUI is a Java application which communicates with the server via web-services. The CoBaltDB Client needs to be downloaded on your computer.
In order to run, CoBaltDB needs Java JRE 5 (or a more recent version). If not already installed on your machine, the latter can be downloaded at the following address:
http://java.sun.com/javase/downloads/index_jdk5.jsp
Download
The application repertory can be downloaded as
CoBaltDB.zip
or
CoBaltDB.tar.gz
archive file.
Download the User Guide here.
Additional information: access the Supplementary Data here.
Access the list of tools and databases related to subcellular localization in prokaryotes.
If you use CoBaltDB in your research, we would greatly appreciate if you could cite our publication:
CoBaltDB: Complete bacterial and archaeal orfeomes subcellular localization database and associated resources.
Goudenège D, Avner S, Lucchetti-Miganeh C, Barloy-Hubler F.
BMC Microbiol. 2010 Mar 23;10:88.
Installation & Launch of the Application
Once CoBaltDB has been downloaded, unzip the CoBaltDB.zip or CoBaltDB.tar.gz file by clicking on it, or by typing under Linux:
tar -xzvf CoBaltDB.tar.gz
A CoBaltDB/ directory should appear. In order to launch CoBaltDB, no matter which platform, first go to the CoBaltDB/ directory;
- On Windows, simply double-click on file: StartCoBaltDB_Windows.bat
- On Mac OS X, double-click on file: StartCoBaltDB_MacOSX.command
- On Linux, double-click on file: StartCoBaltDB_Linux.sh or in a terminal window, type: ./StartCoBaltDB_Linux
Depending on the requests submitted, the CoBaltDB Client may require large amounts of memory. By default, this is somewhat accounted for within the files above. However, if your computer has less than 1Go available RAM, please replace the -Xmx1g option inside the above corresponding file by –Xmx128m, –Xmx256m or –Xmx512m according to your system available RAM.
Note : on Mac OS X 10.5 (Apple Leopard) systems, a Java bug has been reported which causes CoBaltDB to fail. In this case it is necessary to upgrade to Java 6 by downloading it here. You should also tell the system to use the latest version. This can be achieved by launching: Applications/Utilities/Java/Java Settings, and by positioning version 6 above the other versions in the General panel.
Contacts