A Glossary for Computational Biology

This glossary represents my current best understanding of these notions, and consolidates definitions from my own publications and working notes. Since others have found it useful in several different contexts, I now post it. Many of these definitions are not novel, though I have attempted to clarify the formal mathematical and computational definitions for nonmathematical readers. Similarly, I have defined a few key biochemical ideas for those less biologically inclined. When a published definition has been used as the root of the one given here, I have indicated this by the phrase “Derived from X”. A list of symbols used in the glossary will be found in Section 3. Because the ideas are drawn from so many different fields — and because it is useful to combine these ideas when discussing the formal and computational aspects of biology — I have exercised care in my choice of symbols. In many cases, I have had to switch fonts to avoid ambiguities in a symbol’s meaning: for example, switching the usual G for graph in mathematics to G so that I can retain G for the Gibb’s free energy of physical chemistry. I believe I have managed to preserve the type of letter for each variable, but at the price of using many different fonts. This raises a caveat: if your PostScript viewer or printer doesn’t have all the required fonts, you may have difficulty reading the glossary.