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Thinking about license change
Biskit is published under the classic GPL "free software" license which means that Python programs based on Biskit also need to be made open source. However, most scientific open source software projects are nowadays released with less restrictive licenses. These licenses allow the mixing with closed, proprietary software.
The current Biskit license: GPL v3
Academic software should be open source. No matter what. In computational biology, source code is the ultimate documentation of a method or protocol. It still upsets me seeing computational articles with more or less elaborate descriptions of their methods, but without the actual code attached. Why any scientific journal would accept the withholding this crucial bit of evidence is beyond me. Besides, public money has paid for it so the public has the right to see (and remix) the result.