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Please cite ballaxy in any research that uses or extends ballaxy.
ballaxy is based on the BALL project (http://www.ball-project.org), i.e. the Biochemical Algorithm Library BALL.
Information on how to cite the BALL project can be found here:
http://ball-trac.bioinf.uni-sb.de/wiki/FAQ#a2.1.CitingBALL
Information on how to cite Galaxy can be found here:
http://wiki.g2.bx.psu.edu/Support