Assemble: a graphical tool to construct and study RNA architectures
======================================================================

Authors:
Fabrice Jossinet <f.jossinet@ibmc.u-strasbg.fr>
Eric Westhof <e.westhof@ibmc.u-strasbg.fr>

Compilation of sources
======================

You will need:

* A version 1.5+ of the Sun Java Virtual Machine (non official versions of Java (like gcj) are not suitable . The 1.6 version of Java is not supported at now).
* Apache Ant (http://jakarta.apache.org/ant/)

To compile, type:

ant

in the Assemble directory

This will create an "Assemble" subdirectory from which you can run Assemble.

Requirements to install and start Assemble
==========================================

Assemble is made of two parts: the graphical interface and a set of RNA algorithms.

The graphical interface needs:

    * a version 1.5+ of the Sun Java Virtual Machine. Non official versions of Java (like gcj) are not suitable for Assemble. The 1.6 version of Java is not supported by Assemble at now.
    * an OpenGL compliant graphic card. Assemble has been successfully tested with ATI 9200, ATI 9600, Nvidia 6800 and Nvidia 7800, but should work with any OpenGL compliant card
    * a 3-buttons mouse is also highly recommended

The RNA algorithms are provided already compiled for:

    * MacOSX (PowerPC G5 and Intel processors)
    * Linux (Intel processors)

If your computer is not listed above, you will have to compile the algorithms yourself. You can also connect your Assemble application to a remote one. At last, you can use Assemble in a "disconnected" mode. Everything is explained below.

Installation and start of Assemble for MacOS X and Linux Users
==============================================================

    * download the last version
    * unflat the tar.gz file by double-clicking on it or by typing "tar -xzvf your_file.tar.gz" in a terminal
    * inside the Assemble directory, double-click on the assemble.jar file or type "java -jar assemble.jar" using a terminal (if you need more memory, type "java -Xmx600M -Xms600M -jar assemble.jar" to get 600M of memory for example)
    * from the Assemble splash screen, connect to localhost
    * it's done!!

If you get a message saying that "Your computer's architecture is not compatible with the RNA algorithms of Assemble", you have two options:

Option 1: install the RNA algorithms yourself
---------------------------------------------

    * in a terminal, type in the lib subdirectory of Assemble: ./algorithms_installation.sh
    * if the RNA algorithms have been installed successfully, restart Assemble
    * it's done!!

If you have problems to compile the RNA algorithms, you can contact us for help.

Option 2: connect your Assemble to a remote one
-----------------------------------------------

    * start the first Assemble on a MacOSX or Linux computer and note the IP address of this machine
    * start the second Assemble on your computer
    * in the splash screen of the second Assemble, register the IP address of the first machine and connect to it
    * it's done!!

Installation and start of Assemble for Windows Users
====================================================

At now, we're not providing the RNA algorithms compiled for Windows systems. Consequently, you have to follow these steps:

    * install and start an Assemble tool on a Linux or MacOSX computer in your intranet as described above
    * on your Windows machine, download the last version of Assemble
    * unflat the tar.gz file by double-clicking on it or by typing "tar -xzvf your_file.tar.gz" in a terminal
    * inside the Assemble directory, double-click on the assemble.jar file or type "java -jar assemble.jar" using a terminal (if you need more memory, type "java -Xmx600M -Xms600M -jar assemble.jar" to get 600M of memory for example)
    * in the splash screen, register the IP address of the first machine and connect to it
    * it's done!!

What is the "disconnected mode" of Assemble?
============================================

This mode is helpful if your classical usage of Assemble is as connected to a remote one. Using this mode, you can load and manipulate a 3D model previously saved, even if your computer is not connected to a network (if you're travelling or if your network is down). The drawback is that several functionalities will be inactived.

To use this mode:

    * start Assemble
    * in the splash screen, choose "Don't connect"
    * it's done!!

Licensing and legal issues
==========================

For legal and licensing issues, please read the LICENSE file.

Feedback
========

Assemble is an on-going project. We are still working on Assemble and new versions will be distributed
as soon as available.
Your feedback as users is very important to us.
Check the website http://www.bioinformatics.org/assemble for how to report bugs and send suggestions.

More Informations
=================

Visit http://www.bioinformatics.org/assemble

Questions and bug reports to Fabrice Jossinet <f.jossinet@ibmc.u-strasbg.fr>.

Thanks for using Assemble.

