The BioBricks Foundation:Standards/Technical/Synthetic Biology Graphical Notation

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Developmental information for a Synthetic Biology Graphical Notation:

contributors

please add your OWW username to List:RFC4 to join the RFC4 mailing list. You will need an OWW account first.

  • Mac Cowell - mac at diybio.org
  • Antonia Mayer - mayera ... alumni.reed.edu
  • Herbert Sauro - hsauro at u.washington.edu
  • you... add yourself!

Differences with Systems Biology

I would like to make a comment on what I think are potential differences between the aims of the SBGN community and what we might push for in the synthetic biology community. The SBGN standard serves to describe biology, quite literally most of the time (i.e it displays all phosphorylation sites, protein forms etc) whereas a standard in synthetic biology would not only describe the biology but also allow abstraction, preferably at multiple levels. Like most engineering fields, synthetic biology is both a design and implementation discipline and as such I think any notation used in synthetic biology should address both modes of thinking. At one level an implementer might concern themselves with sequences, assembly methods, host organisms, energy supplies etc, whereas at design, particularly if the design is complex, what most concerns them is function and performance rather than implementation details, hence the need I believe for higher level descriptions in addition to literal biological notation. One can imagine higher level functions such as logic, control operators such as integration or differentiation, computational operators such as differences, summation, multiplication or even frequency filters. All of these can be constructed, at least in theory, using biological networks.

Another difference with systems biology is that synthetic biologists love metadata, that is information that is useful both at design and implementation levels but that may not necessarily be displayed, or at least only displayed when the view is changed.

SBGN would be a useful standard to examine but I do not believe it could be, for example, a drop in standard for synthetic biology.

--Hsauro 17:07, 10 November 2008 (EST)

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