From SnOwy - Ed's Wiki Notebook
20100614.135754 Pre-working session
- With all the work that presently exists, it would be silly to reinvent the wheel-- especially since our wheel isn't guaranteed to be any more functional than anyone else's.
- We should look for a niche that hasn't yet been filled.
- Biochemical ← Biobrick and Device ← Biocschematics
- -- what exactly are 'standards'? -- Should look into that-- (language semantics (IEEE-like) vs language syntax (ANSI-like))?
- Michael Pederson's thesis -- notes
- Usable for both systems biology and synthetic biology (recognize one as inverse function of the other)
- Contribution: Language for Biochemical Systems (LBS) -- based on Calculus of Biochemical Systems
- Contribution: a language for Genetic Engineering of Cells (GEC) -- GEC programs translate to biobricks with a constraint satisfaction engine
20100614.135544 Log
- From Matthew's letter below, previous works...
- Biochemical level: SBML, SBW
- Biobrick and Device level: GenoCAD, Eugene
- Bioschematics level: Spectacles, SBOL-V
- Standards: Eugene, SBOL-V (used by Spectacles)
Hi all,
I just added some notes on previous software projects to the BioCompiler wiki page.
It basically comes down to SBML and SBW being the standards for biochemical-level
simulation and information exchange. At the BioBrick/Device-level layer of
abstraction, there are a few projects which work as grammar checkers (GenoCAD,
Eugene) and there are some that handle the visualization of bioschematics
(Spectacles, SBOL-V). Eugene and SBOL-V are both attempts at standards (and, in
fact, Spectacles uses SBOL-V).
I'm hoping the dependency list on the wiki page will help in the construction of
the previous work flowchart, but we still need to add previous work on the
academic-theoretical side of things. If anyone is looking for things to do, I also
added some action items to the BioCompiler page as well.
Matt
20100608 Log
- I have obtained pertinent papers, will document what's been read and what was learned soon.
References - Links to UWiGEM BioCompiler
20100107 Log
- Biocompiler is a promising tool so far
- Need to flesh in details and provide cultural context
- My tasks
- Assist with description of Background and Abstract
- Describe tasks and how they chain together using a flowchart (the work of other groups)
