What is PARADISE?

I observed from discussions i had with S2S or Assemble users, or by reading publications citing these tools, that there is a confusion with the name PARADISE. I will try to explain it with this post. S2S and Assemble are two graphical tools constructed above a common layer. This layer is mainly composed of two parts:
- the implementation of the biological concepts manipulated through the graphical tools (tertiary and secondary structures, structural alignments, atoms, helices, nucleotides,...)
- the implementation of a communication protocol to allow the graphical tools to interact with each other (this aspect will be improved with the next releases) and with external elements (like the RNA Web Services).

This layer is PARADISE. Why did I gave an explicit name to this part of my framework? Because it is possible to use PARADISE without the graphical tools. If you're looking in the "lib" folder of your S2S or Assemble, you will see a paradise.jar file. Inside this "lib" folder, you can type in a terminal:

java -jar paradise.jar

to start a scripting console. This console allows you to write scripts using all the biological objects and the communication protocols developed so far. These scripts have to be written with the Groovy language (also used to write your own S2S/Assemble plugins). I'm using this console to do some batch processing.



Now you should understand better what PARADISE is. It's not S2S, not Assemble, it's a part of them.

PS: for those interested in the technical details, the communication protocol is based on a multi-agent framework implemented using the JADE library