Molevolve

March 11 : Version 0.1.0 released!

Download Molevolve (Release Notes & Change Log). Unpack the zip file and follow the instructions described in README to build and/or deploy.

Molevolve's project page is hosted at SourceForge.net.

What is Molevolve?

Molevolve is a Java library for running a Genetic Algorithm (GA) to model the 3-dimensional structures of peptide chains from amino-acid sequences. Client code can specify its own peptide chain model, fitness functions and GA operations.

Molevolve is implemented using J2SE 5.0 (JDK 1.5.x).

Licensing : LGPL

In keeping with CyberDemia's philosophy of openness, Molevolve is released under the open-source GNU Lesser General Public License (LGPL). This means you can download and run Molevolve for free for personal or commercial use. Furthermore, you can incorporate or bundle Molevolve into your own products as long as you abide by the conditions of the LGPL.

Features

Brief summary of existing features:

1. Supports input of amino-acid sequence from a simple comma-separated values (CSV) format or the PDB format.
2. API to develop your own custom peptide model and fitness function implementation that can be registered with Molevolve at deployment time. A simple default model/fitness function is provided as a sample.
3. API to develop your own custom Genetic Algorithm implementations that can be registered with Molevolve at deployment time. Some simple default GA steps are provided as samples.
4. API to provide your own terminating conditions that can be registered with Molevolve at deployment time. A simple termination condition is provided as an example.
5. API to register your listeners to receive notification events during various stages of the GA simulation.
6. API to generate modeled output structures (the GA population) as PDB files. These PDB files can be viewed using the open-source JMOL viewer.
7. Simple Swing GUI front-end to load amino-acid sequence, run the GA simulation and write out generated PDB files.
8. Build, deploy and execute using Apache ANT.

Screen Shots

The following is a screen shot of the Molevolve 0.1.0 Swing GUI front-end on a Mandrake 10.0 KDE desktop (Acqua-Graphite theme).

Requirements

You need to download the following programs to build and run Molevolve ( later versions of these programs might work, but there is no guarantee ) :

• JDK 1.5.x
• Jakarta Ant 1.6.2

In addition, the downloaded zip file contains various required libraries such as The Chemical Development Kit (CDK) and Vecmath. These have been integrated into the automated build process. There is no need to separately download these libraries.

External Links

Molevolve is listed on the following sites:

Molevolve is created and maintained by CyberDemia Research & Services. Please submit any bug reports, comments, suggestions or enquiries at Molevolve's SourceForge.net project page.