Over time, this project should be a clean-up and further development of an
application originating from a master's thesis that aimed to help biochemists.
The thesis is titled "Energy Landscape Analysis for Peptides using Barrier
Trees." The original text of this README is included below.

Note that the project depends on several libraries and a nontrivial technical
environment. A setup guide and/or a more accessible application should be made
available in the coming months.

Setup guide: http://goo.gl/4EPWN
User manual: http://goo.gl/zLmPD

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This project, the master's thesis of Martin Kamp Jensen, was developed using
Eclipse [1]. The Eclipse project files are included in this distribution. This
project can also be built and run using Apache Ant [2] by using the "build.xml"
Ant build script.

This project requires a Java Runtime Environment compatible with Java SE Runtime
Environment 6 from Oracle [3].

The source code is licensed under the Apache License, Version 2.0 found in the
LICENSE file. The external libraries used by this project is released under
different licenses available in the "lib" directory. In particular, note that
the BioShell library is a closed-source package that is publicly available for
academic non-profit institutions.

[1] http://eclipse.org/
[2] http://ant.apache.org/
[3] http://www.oracle.com/technetwork/java/javase/downloads/index.html