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Computational Biology - Applications - ProteinMusic

ProteinMusic

What is it?
ProteinMusic is a Java program converting DNA sequences into music. The original idea for this project came from R. D. King here at the University of Wales, Aberystwyth and C. G Angus from the Shamen (King, R.D. & Angus, C.G. (1996)). They developed a program written in C on an Apple Mac together with a MIDI connection to a synthesizer in 1996. This program here is a complete re-write of the original program in Java. by A. Karwath.
Contact: R. D. King or A. Karwath

Software Requirements
The program is written in Java and uses the latest features of Java 2. Therefore it is necessary to have at least either the Java Run-Time-Environment (JRE) 1.3 or the full Java Standard Edition (SDK) 1.3 installed. Either version can be downloaded for nearly any system from SUN's Java pages .

Hardware Requirements
The requirements depend of what kind of operating system is used. We found that for Sparc Solaris an Ultra 1 is just sufficient. For Windows machines it depends on the version. We tested ProteinMusic on an AMD K-2 450 with Windows 98, which had enough perfomance to run the program.
 

WINDOWS:In general, every machine will need a soundcard with the corresponding drivers and enough harddrive space to install Java 2 (either the SDK or the JRE). The program itself is relativly small and occupies only 250 Kbyte.
 

LINUX:The program has now been tested on a Linux machine (thanks to Dave P.) with the following specifications: Linux kernel 2.4.0-test9 with low-latency patch; ALSA 0.5.9d driver for SBLive soundcard; Blackbox window manager; Sun JDK 1.3 for Linux; PIII 550 w. 256 MB RAM.
 

APLLE MAC:The program has now been tested on an Apple Mac running MAC OS X 10.1 (thanks to David H. K.) Specs: 2001 iBook;500 MHz G3, 256 MB RAM. He also send me a nice screenshot.

License
This software can be copied and used freely providing it is not resold in any form and its use is acknowledged. This software is provided by "as is" and any express or implied warranties, including, but not limited to, the implied warranties of merchantability and fitness for a particular purpose are disclaimed. In no event shall the regents or contributors be liable for any direct, indirect, incidental, special, exemplary, or consequential damages (including, but not limited to, procurement of substitute goods or services; loss of use, data, or profits; or business interruption) however caused and on any theory of liability, whether in contract, strict liability, or tort (including negligence or otherwise) arising in any way out of the use of this software, even if advised of the possibility of such damage.

Download
You can download the program including documentation and example sequences directly from SourceForge

Installation Instructions:
Just unzip the file. It should create a file called ProteinMusic.jar and two sub directories (docs and sequences) in a directory called pm. To start the program simply start it with the command line java -jar ProteinMusic.jar. For Windows users: open a MS-DOS command line window by pressing the Start button and select Programs and then MS-DOS Prompt. Go to the sub-directory where the ProteinMusic.jar file is located and then type java -jar ProteinMusic.jar

Screen shot

Known Issues:
The programs tends to get very slow in converting the DNA to MIDI as well as displaying the seqeunce while playing, if DNA sequences with more than 600 to 700 bps are used.

References:
King, R.D. & Angus, C.G. (1996) PM: Protein Music. CABIOS. 12, pages 251-252

Links to related sites/programs
Rockefeller links collection to the theme of DNA and protein music.

Algorithmic Arts, a company selling a DNA to MIDI converter.

Music of the Human Genome by Brent D. Hugh at mp3.com.

Moelcular Music by Dr. Linda Long (Patent Nr: GB2350469 filed)

Links from around the world reporting on ProteinMusic
The New York Times (12/09/01)

The algorithm explained, The New York Times (31/03/02)

slashdot.org

www.aber.ac.uk

www.newswales.co.uk

www.idgworld.it

www.klik.hr

www1.linkclub.or.jp

www.plastic.com

Newpaper articles:
From the Western Mail:

From the The Times: