[BBF Standards] Model System

[Drew Endy]

The repressilator is a work of art, it's not made from standard  
biological parts.  This is not a criticism of the repressilator,  
rather an observation.  Nobody has yet made a ring oscillator for  
standard biological parts.  Lots to do to make this happen.

In any case, there has actually been a tremendous response to the  
issues raised by your questions.

Specifically, one could model "simple" gene expression devices.  (see  
Jason Kelly's video from today introducing how to standardize  
measurement around such parts).

Also, there is great data for BBa_F2620, a cell-cell communication  
receiver device built from different standard biological parts.

And, as you note, iGEM is a great opportunity too (although the  
characterization data around iGEM tends to be ad hoc and  
qualitative).  There are many people from iGEM on this list, including  
the organizers.


On Feb 27, 2008, at 9:01 PM, Ralph Santos wrote:

>
> You make an excellent point, and I was hoping to see more response to
> it.  Unfortunately I can't do any wet bench work myself, but if there
> aren't any available resources to physically construct a model  
> system to
> focus discussion, perhaps we need to consider alternatives.
>
> One place to look that's right beneath our noses is iGEM competition.
> How many iGEM people follow the standards discussion?
>
> Alternatively, there's a few papers in the scientific literature which
> might be worth citing or posting on the wiki for reference as
> exemplars.  One of my pet papers along these lines is the Elowitz
> repressilator paper.  It's short, describes a compact little system  
> with
> interesting behavior.  I believe the pieces are already registered
> parts.  Unfortunately, I can't think of what other papers might be
> appropriate along those lines.
>
> Are there other papers worth including?  Are the other sources of
> practical model systems?
>
> ---ralf
>
>
>
>
> Julius B. Lucks wrote:
>> Hello List,
>>
>> It seems to me that many of these abstract discussions would benefit
>> immensely from a concrete model system around which to discuss.  It
>> looks like from the character of the discussion that there is not
>> enough discussion about the practical laboratory details and users
>> that will ultimately defined the needs and the user community for  
>> such
>> Biobrick abstractions.  I would like to pose the following question  
>> to
>> the list:
>>
>> Is there a simple and practical model system that can be constructed
>> and characterized in the lab around which to focus and coordinate
>> discussion?
>>
>> If this is the case, or one exists already, then it could really  
>> focus
>> the discussion, and give it a much needed practical slant.  In
>> particular, I am imagining a system with at most 3 parts that can be
>> made, individually characterized, and characterized in all
>> combinations, so that:
>>
>> 1.) People on the laboratory side can get involved in the discussion:
>> Ideally someone would volunteer to make the 3 parts, someone would
>> volunteer to characterize them, and someone would volunteer to
>> characterize combinations.  (I realize this could be a lot to ask  
>> with
>> people's busy schedules, but hopefully 3 parts would not take too  
>> much
>> time).
>>
>> 2.) People on the information science side could have an actual  
>> system
>> on which to test ideas:  There has been lots of abstract discussion,
>> but until it is actually applied, I'm not sure that the ideas being
>> posited can be truly developed and vetted.
>>
>> This system could very well already exist, in which case the list
>> should decide to focus the discussion around it.  The one standards
>> process that I am familiar with is the RSS 1.0 -> RSS 2.0 -> Atom
>> standards process in which each step benefitted greatly from having
>> lots of hands-on experience using the previous versions in a concrete
>> way.  I'm advocating something like that here.
>>
>> In the end, whatever standards are developed have to be immediately
>> practical and useful for the laboratory scientists who will  
>> eventually
>> make parts, characterize them, and use whatever standard format to
>> express the ideas behind these parts.  Focusing on a real world
>> example system would help achieve that goal.
>>
>> Cheers,
>>
>> Julius
>>
>> ---------------------------------------------------------------------------------------
>> Please Reply to My Permanent Address: julius at younglucks.com
>> <mailto:julius at younglucks.com>
>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
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