What standards are needed in computational systems biology? The results of a survey on this topic have been recently summarized by Edda Klipp and colleagues (Klipp et al, 2007, Nat Biotech 4:390). Even if it is somewhat unclear how representative the sample of respondents were with respect to the larger systems biology community, some of the top priorities identified are interesting (I list only the three first):
Respondents expressed most strongly the need for standardization in the following fields: first, graphical representation of biochemical networks; second, experimental procedures; third, model encoding and model exchange;…
How to encourage standards in biological graphical notations? One way would be to provide tools that facilitate the use of standardized notations by a wide range of users, beyond the circle of modelers. I was wondering whether a visual wiki could not help in this regard. An idea would be to have an open-source plugin for a common wiki software that would allow embedding of editable diagrams and would be specially tailored to draw biological diagrams, for example as Kitano’s process diagrams or Kohn’s interaction maps.
Would it be possible or easy to customize such software to specialize it for drawing biological diagrams? What are the existing solutions for visual wikis? Would a visual encyclopedia of biological processes be something that may drive biologists to use standardized notations?