[BBF Standards] Model System

Wed Mar 5 11:59:29 EST 2008

I am sure there are many iGEM teams that would love to participate in the
construction and characterization of a model system.  New teams in
particular often have a difficult time generating a project idea that is not
too ambitious and is in line with the principles of synthetic biology (which
remain opaque to some teams).

I think everyone, particularly iGEM teams searching for a meaningful
project, would benefit from a wishlist of most-wanted parts/devices and a
blueprint showing how building the parts would contribute to a larger goal.
Maybe it could be the blueprint for a model system, if we can actually
define one.   Or if not, why not one of the SynBERC testbeds?

thanks,
Mac

On Wed, Feb 27, 2008 at 9:10 PM, Drew Endy <endy at mit.edu> wrote:

> 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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> >>
> >
> >
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>
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-- 
Mac Cowell
iGEM Coordinator
igem.org
231.313.9062
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