[BBF Standards] SB4 workshops on standards

[Mackenzie Cowell]

Howdy Everyone,

Over the last week and a half there has been a discussion of interesting
workshop topics off-list.  I am going to summarize the topics people
explicitly expressed interest in organizing with the hope that it will help
everyone collaborate before the deadline this Wednesday.  This is definitely
not an official list of any kind.

* PoBoL, a Provisional BioBrick Language (http://pobol.org) - Mac Cowell,
Jason Morrision, Raik Gruenburg, ?

* Experimental Measurement Standards - Kim de Mora, Ingrid Swanson, Jason
Kelly, ?

* Software Tools for Genetic Network Construction - Deepak Chandran, Sean
Sleight, Herbert Sauro


Additionally, here are the other workshop topics the thread thought were
interesting but that did not become explicitly attached to an organizer.  I
think it would be just great if all of these were explored at SB4.0.   If
you are an expert in any of these areas and not already presenting, I
encourage you to organize a workshop.

* General overview of Synthetic Biology standards (construction & sharing) /
Standards 101

* Physical construction standards - BBa, BB++, BB extreme, BB etc.

* Sharing BioBrick data (i.e. PoBoL, MIT Registry XML ouptut / DAS, BioJade
architecture, Registry of Models)

* Promoter Standardization

* Vector Standardization

* The current (and upcoming) ecology of Registries

* How to build an effective physical repository (i.e. storing & shipping
hundreds of thousands of biobricks)

* SB CAD tools

* SB publishing - IET SB, JBE, and Synthetic Biology

* DIYbio / "gargista" synthetic biology (diybio.org)


Mac Cowell
Bricklet.org

p.s. Based on my reading of the SB4.0 website, there are going to be three
rooms per day hosting four workshops each for three days, or *36 workshop
sessions total* - is this correct?  Or is there only one day for workshops?

p.p.s CCed to the original contributors to the thread


On Fri, May 2, 2008 at 8:49 PM, Deepak Chandran <deepakc at u.washington.edu>
wrote:

> Drew and rest,
>
> When I was naming the workshops, I was just listing general examples
> that came to mind. A third workshop can be related to the registry,
> although that could be integrated in the computational standards
> workshop depending on what perspective people want to take.
>
> At the standards workshop in Seattle, several languages were presented
> that can potentially be used to represent synthetic biology devices
> (from the functional perspective). It would be nice to have a few test
> cases (past iGEM project, perhaps?) that each language can try to
> represent. Then the community can assess what features they like and
> don't like. Since there is already a computational tools page on OWW,
> this can just expand upon that.
>
> As for another workshop before October, I think it is a good idea to
> have these topics being discussed frequently, especially for those who
> are active in the field. Travel would probably be the limiting factor.
>
> --Deepak
>
> Drew Endy wrote:
> > Deepak,
> >
> > I think that this is a great idea.  You wrote "two of three"
> > workshops, but then only list experimental and computational.  Did you
> > have a third topic in mind already?
> >
> > Or, more generally for everybody, what standards topics should we hope
> > to discuss at SB4?
> >
> > On a related note, we should also consider if folks would like to have
> > a standards workshop somewhere (Europe?) before SB4, which is not
> > until October?
> >
> > Cheers,
> > Drew
> >
> >
> > On May 2, 2008, at 8:31 PM, Deepak Chandran wrote:
> >
> >> We (Sauro group at Seattle) had been thinking about having two of three
> >> workshops at the SB4 that would address different aspects of the
> >> standardization process, such as experimental standards, computational
> >> standards, etc. Ideally, these workshops should not be held in parallel,
> >> so that people can partake in all of them. If there are enough people
> >> interested, we can plan this together. I can organize a computational
> >> standards workshop -- would anyone like to present at this one?
> >>
> >> --Deepak
> >>
> >>
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> >
>
>
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