Assemble: a graphical tool to construct and study RNA architectures

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Requirements

To use Assemble efficiently, you need:

a Java environment installed on your computer. Assemble can run with Java 1.5 and 1.6
an internet connection (Assemble uses several Web Services)
an OpenGL compliant graphic card
a 3-buttons mouse (several features need the wheel button)

Installation and start of Assemble

Please note that you have to install Assemble in a location where you have the rights to create new files. Assemble creates several temporary files in its tmp subdirectory.

	For Windows Assemble has been installed and tested successfully on Windows 7 and Windows XP with Java 6 (Windows Vista should be compatible also). You have to follow these steps: if you don't have it, download and install the last version of Java download the last version of Assemble unzip the zip file by double-clicking on it inside the Assemble directory, edit the launch_Assemble_for_Windows.bat file with your favorite text editor to precise the location of your Java environment. In the following line: set JAVA_HOME="C:\Program Files (x86)\Java\jdk1.6.0_18\" Change the path between the double quotes to fit your Java installation. Once the modification saved, doucle-click on the launch_Assemble_for_Windows.bat file. This file allows you also to modify the amount of memory allocated to Assemble (500M are allocated by default). The first launch of Assemble takes a while due to the initialization of the embedded structural library (a.k.a. the MyPDB library).
	For MacOSX Assemble has been installed and tested successfully on MacOSX Tiger, Leopard and Snow Leopard (Intel and PowerPC architectures) and Java 5 or 6. The MacOSX environment already includes a Java environment. You have to follow these steps: download the last version of Assemble unzip the zip file by double-clicking on it inside the Assemble directory, double-click on the launch_Assemble_for_MacOSX.command file. You can edit this file with your favorite text editor to modify the amount of memory allocated to Assemble (500M are allocated by default). The first launch of Assemble takes a while due to the initialization of the embedded structural library (a.k.a. the MyPDB library).
	For Linux Assemble has been installed and tested successfully on Ubuntu 9.x and 10.x with Java 6. You have to follow these steps: to check if you have a Java environment installed or if your Java environment is the official one from Sun (non official versions of Java (gcj, cacao, kaffe,...) are not suitable for Assemble), open a terminal (Applications -> Accessories -> Terminal), and type "java -version": If the java command is not found, you have to install a Java environment. if you don't have it, download and install the Java environment from Sun using the Synaptic Package Manager of Ubuntu (in System -> Administration). Choose the sun-java6-jre package and follow the instructions: download the last version of Assemble unzip the zip file by double-clicking on it inside the Assemble directory, double-click on the launch_Assemble_for_Linux.sh file. You can edit this file with your favorite text editor to modify the amount of memory allocated to Assemble (500M are allocated by default). The first launch of Assemble takes a while due to the initialization of the embedded structural library (a.k.a. the MyPDB library).