[BBF Standards] Representing parts

[Raik Gruenberg]

Hi Deepak,
Let me answer the easy one first.

Deepak Chandran wrote:
> apply to multimers. However, even with a system of rules, isn't the 
> final model still in terms of reactions, although the model itself would 
> not contain all the combinations?

Absolutely. In the end you'll have a set of reactions anyway. It's just that 
your simulation program can autogenerate the complete reaction system from the 
simple rules. But the rules are the more general and could also be useful for 
other purposes -- like structure modeling for example. Like high-level 
source-code that is compiled for different architectures and much easier to 
read, change, and exchange than binary machine code.

Greetings,
Raik

> --Deepak
> 
> Raik Gruenberg wrote:
>> 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
________________________________