[BBF Standards] outrule emergent properties
Markus Schmidt
markus.schmidt at idialog.eu
Fri Feb 1 11:59:06 EST 2008
The combinatorial power of N biobricks is actually not NxN, but
factorial: N!
with e.g. 20 biobricks you have a total of 2*10 to the power of 18
ways of possible interaction. And by that we don't talk about things
like pH and so on (which prohibits a system that modifies the pH, and
so on)
The lack of physical separation of signals, as is the case in
microelectronics, could be one of the biggest limitations to the
standardized bioparts concept.
Ways to limit the combinatorial power for testing are necessary, as
you said.
Actually this could lead to a design process where you operate e.g. on
a system level and design your nice circuit, but depending on the
circuit the design computer programme chooses one of different devices
(and finally parts) that interact in the way you like. That means that
one system can be realised by multiple devices and a device by
multiple parts. This is clearly not perfect, and not what is
envisaged, but a possible and path-dependend solution.
Markus
Am 31.01.2008 um 23:34 schrieb Josh Perfetto:
> Makes sense. Two things on plays nice:
>
> 1. While it may not be currently possible to say with
> certainty which parts will work well together through modeling, NxN
> combinatorial testing is not practical. It is therefore of great
> value to know which parts would not be expected to work together
> through the use of modeling. Information to help us do that (i.e.
> information about the small molecules used internally for starters)
> should be included in the data model of a part.
> 2. I’m not entirely sure about this, but I think we should
> consider modeling part interactions, especially when empirical data
> is involved, as separate entities than the parts themselves. We
> also need to think about how to model such interactions—is it binary
> works/doesn’t, or are there caveats that should be incorporated into
> the model? When an interaction is defined, are there conditions
> (i.e. pH range etc.) that should be attached to that interaction
> definition?
>
> -Josh
>
> From: Julius B. Lucks [mailto:julius at younglucks.com]
> Sent: Thursday, January 31, 2008 10:30 AM
> To: Raik Gruenberg
> Cc: Josh Perfetto; standards at biobricks.org
> Subject: Re: [BBF Standards] functional composition of BioBrick parts?
>
> Hi All,
>
> I agree with the separation of the task at hand:
>
>
> 1) What is the minimal data set needed to describe a biobrick?
> (including What
> is a Biobrick?)
> 2) What is the best format / technology for exchange?
>
>
> But I would rephrase #1 to say
>
> 1.) What is the data model needed to describe a biobrick?
>
> Once the data model is firmly in place, the format should follow as
> the one that best implements that data model. For example, if we
> settle on an RDF-like 'everything is a relationship triplet'
> approach, then some format that can handle these triplets would be
> most appropriate. In addition, with a model like this, there are
> XML-based and more human-readable formats that can both implement
> the model equally well.
>
> I think that tying our selves to a format too early will make us not
> have a clear model in mind, and will cause us to hack up the
> format. It is best to do model, then format.
>
> So things to think about in a model are what type of relationships
> to we want to convey?
>
> * Inheritance (where was a particular part derived from, and by who
> = link + data)
> * Characterization (something quantitative about that part by itself
> = data)
> * Plays well with others (what other parts can this one interact
> with - with possible data associated with this interaction = link +
> data)
> * ...
>
> Other ideas?
>
> Cheers,
>
> Julius
>
>
>
> It would be good if we could capture the main suggestions and
> arguments on a
> wiki page -- I would be happy to take care of that but didn't manage
> to create
> one on http://parts.mit.edu/registry. Could someone with the
> permissions please
> add some empty page to the community portal box (like the ones for
> the other RFC
> groups)?
>
> Anyway, we have started discussing 2). Suggestions were roughly:
>
> a) create a new XML format
> b) adapt existing CellML, SBML XML formats
> c) create a custom file format
> d) use Turtle/N3 notation for semantic web documents
>
> If we get a wiki page, we could put up a little section on each
> possibility and
> collect pro's and cons.
>
> Does anyone have the needed permissions to create a page on the
> registry wiki?
> Or perhaps i just overlooked the right link?
>
> Greetings,
> Raik
>
> Josh Perfetto wrote:
> My initial instinct is also that a separate ontology will be needed to
> properly describe BioBricks. However I would expect it would be both
> -Josh
>
>
> Yes definitely, there are a bunch of new ontologies coming up in
> systems
> biology and I think they will have some relevance here, though I
> suspect
> there could still be a need for something specifically related to
> synthetic biology.
>
> The existence of these ontologies makes human readable formats
> difficult
> to deal with and XML is the proper place for them. However, as humans,
> we also need a human readable face and I think there has to be some
> kind
> of two way world, or at least each software application will present
> parts and devices in their own human readable format even if the
> back-end is ultimately XML. This is the way SBML and CellML work. We
> are
>
> Herbert Sauro
>
> On Wednesday 30 January 2008, "Josh Perfetto" <josh at maulikai.com>
> wrote:
> Yes, I think ease of processing and the representational power of the
> format is more important nowadays than human readability. We need
> standard representations that can be adopted by software developers
> to build powerful processing systems for BioBricks. We can expect
> such software to present a more human-usable interface to manipulate
> the BioBricks than a file format ever could.
>
> Have you ever heard of these 'ontologies' that have jumped up?
> http://www.biomodels.net/
> http://obofoundry.org/
>
>
> --
> ________________________________
>
> Dr. Raik Gruenberg
> http://www.raiks.de/contact.html
> ________________________________
>
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*-----------------------------------------------------*
Dr. Markus Schmidt
International Dialogue and Conflict Management
Abt-Karlg. 19/21, 1180 Vienna, Austria
office: +43 1 9900811
mobile: +43 660 6856623
email: markus.schmidt at idialog.eu
www.idialog.eu
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