OligoWiz 1.0 Server

This server performs intelligent design of oligonucleotides for DNA microarrays.

OligoWiz is implemented as a client-server solution, which consist of an easy to use Graphical User Interface (the client - written in Java) which delegates the computationally intensive operations to a server (which by default is hosted at CBS on a powerfull Multi-CPU SGI UNIX server). All the user needs to do is to download and start the GUI.

The client is written in Java 1.3.1 with portability in mind. It is tested on MacOS X, Linux and Windows, but should work on any platform with Java 1.3.1 or better. The client communicates with server using the HTTP protocol.

Running OligoWiz

If Java is allready installed, starting the OligoWiz client is as easy as double-clicking the file (Windows and MacOS X), or typing java -jar OligoWiz.jar at the command prompt (Unix).

Out of Memory! If you run large sets of sequences on OligoWiz you may experience memory problems. In most cases this can be fixed by executing OligoWiz in the following way (in a prompt): java -jar -Xmx300m OligoWiz.jar Where "300m" is the maximum amount of memory allocated by OligoWiz.jar (300 megabytes)

HTTP proxy: In order to set up OligoWiz to access our server through a proxy, the proxy parameters need to be parsed to the JVM on the command prompt: java -jar -Dhttp.proxyHost=proxyhost -Dhttp.proxyPort=portNumber OligoWiz.jar (Put in you relevant proxyhost/port number).

Java: A suitable version of Java (choose J2SE version 1.3.1 or newer) can be downloaded here:

• java.sun.com/j2se/downloads.html for Windows, Linux and Solaris.
• an up-to-date version of Java for IRIX can be found at the SGI freeware site: freeware.sgi.com.
  

The OligoWiz client can be used free of charge for both academic and commercial use, in combination with the OligoWiz server hosted at CBS. However, please see the access policies of the CBS server.