[BBF Standards] Representing parts

[Raik Gruenberg]

Hi Deepak,

it looks like we should have a dedicated section about the simulation of 
biobrick networks. There is obviously a large interest here. IMO your format is 
perhaps more suited for the exchange of device models rather than for the nuts 
and bolts specifications of a biobrick. Models *are* an interesting problem, 
although right now, I am a bit more concerned about getting the basics sorted 
out A.S.A.P because we otherwise may end up not having any real biobricks to 
model :-/. IMO, the model exchange needs more research and practice before we 
can nail down standards -- this is not really my area but here are some hints in 
that direction:

Reaction models (also SBML) have a fundamental flaw -- they cannot cope with the 
combinatorial complexity that is common to signaling. For example, picture a 
hexameric protein receptor built from 3 different monomers a, b and c with 
shifting abundance and different affinities for each other. This could yield 729 
possible receptor-subtypes (aabbcc, aaabbb, ababac, ...) each with different 
specificities or affinities to it's ligand(s). Now try to write down the 
reaction model of that system! And this is only the beginning of a perfectly 
normal signaling pathway... This may be a problem you don't have with true PoPs 
devices but it certainly comes up for protein devices.

An alternative to reaction models are rule-based models. Please have a look at 
this paper:
Hlavacek WS et al. (2006) Rules for modeling signal-transduction systems.
PMID: 16849649
I think we should rather exchange rules than complete models. Biobrick 'a' would 
only need an 'interaction+affinity' link to biobrick 'b' and 'c' and the 
hexameric receptor could be described as device assembled from 6 times a, b or 
c. The large reaction model can then be built fully automatically and additional 
information can be incorporated as it arrives.

Another advantage, those kind of rules can be expressed by simple relations 
between biobricks (and devices). There would be no need for a new language and 
we can start collecting these basic rules (interaction-, activity data) already now.

Also I have some reservations about creating a completely new format / language 
because it tends to seal off a community rather than opening it up. But there is 
also the opposite school of thought and new problems are perhaps sometimes 
indeed best tackled with new languages...

Greetings,
Raik

Deepak Chandran wrote:
> I had written some time back about implementing a simple file format to 
> represent biological parts. I apologize for taking so long to get back 
> to that. Anyway, the following pdf has a description of what I (we) am 
> proposing:
> 
> http://www.washington.edu/staff/deepakc/PartSyntax.pdf
> 
> This is just a working idea. Hence, I welcome any criticisms, 
> complements, complaints, etc.etc. In order to test the language, I wrote 
> a small scripting program that can "connect" models together and 
> simulate them. The link in given at the end of the pdf.
> 
> _______________________________________________
> Standards mailing list
> Standards at biobricks.org
> http://biobricks.org/mailman/listinfo/standards_biobricks.org
> 
> 

-- 
________________________________

Dr. Raik Gruenberg
http://www.raiks.de/contact.html
________________________________