[BBF Standards] [standards] Hello?

[Drew Endy]

The BBF Standards list is brand new and is ramping up.  There are  
still key people signing up.  My guess is that we won't be at full  
strength for another week.

In getting started, here's some context for what's going on, why this  
list was started, how this list complements current materials on  
openwetware.org, and an ad hoc outline of short term goals / needs.

Basically, the BBF is supporting an open technical standards setting  
process for defining what BioBrick standard biological parts are.  The  
resulting standards are likely to grow and change over time, as  
technology and understanding improves.  The resulting standards  
themselves will be open, so that anybody can consider them and decide  
whether or not they want to produce new BioBrick parts, or tools for  
designing or using BioBrick parts.  We aren't trying to keep people  
from using BioBrick parts, from making new parts, or establish a  
proprietary brand.  Rather, we want to ensure that the formal  
definition(s) for BioBrick parts don't get destroyed or lost as the  
community grows.

To pull this off, we'll need to do many different things, both as a  
group and individually.

Some work will best be handled via websites such as openwetware  
(OWW).  In fact, all of the BBF webpages are currently hosted on OWW.   
For example, http://openwetware.org/wiki/The_BioBricks_Foundation

We should start new pages for technical standards under the BBF pages  
on OWW.  [Note, any BBF member should feel free to get an OWW account  
and edit the BBF pages; there are lots of things to contribute and  
improve].

Some of our work and discussion will best be handled by email.  Hence  
the purpose of this list.  We need to be able to coordinate with one  
another easily, discuss issues, and make announcements.  Sometimes an  
email list is the best way to handle this.  So, feel free to use this  
list for anything along these lines, or other messages that are needed  
(and, note that the BBF has lists for different topics)

Other work will best be handled individually or privately.  So, you  
should feel free to take messages and communication "offline" if  
things need to get worked out in great detail in order to make  
progress before reporting back to the entire group.

At the first technical standards workshop, we drafted a list of  
technical standards that would be worth working on.  Here's the list...

- standard assembly for DNA, RNA, protein and parts (physical  
composition)
- sharing parts on computer networks
- parts / functional nomenclature
- ontology for parts (avoid reinventing the world, if appropriate)
- functional behavioral description (i.e., quantitative models)
- integrate with publishing framework, culture (e.g., BioBrick Letters)
- qualitative functional descriptions (i.e., works, does not work,  
michelin stars)
- support for searching (people-based, CAD-based)
- DNA construction standards (interface with a roadmap setting  
organization)
- functional composition standards (e.g., signal carriers, signal  
levels, device timing)
- compatability / conflict standards (quantitative, degree)
- cellular environment, context, chassis (e.g., genotype, culture  
conditions)
- characterization standards (for experimental measurements, and  
reporting of
     experiments, e.g., MIAME)
- version management, bug tracking, level and/or quality of description
- source of parts, and use of parts
- coordination with other standards setting organizations (e.g.,IET)
- safety standards (security standards)
- graphical depiction standards
- current OSI status
- abstraction standards
- release or collection standard
- definition of a BioBrick part
- Registries (what is a Registry, communication standards,  
distribution quality)
- genetic code
- documentation / coupling back to the scientific community (SGD)

A small number of groups set out to start working on some of these,  
and report back at the next standards workshop (March 1 at UCSF).   
Here are the four sub groups that got started:

Physical Assembly of BioBrick Parts:
Randy Rettberg, Stephen Davies, Austin Che, Kristina Muller, Raik  
Grunberg, Chris Anderson, John Dueber, Scott Mohr

Push / Pull Parts Across Computer Networks:
Raik Grunberg, Drew Endy, Christopher Mason, Randy Rettberg, Chris  
Anderson, John Dueber, Deepak Chandran, Mac Cowell, Sean Sleight, Matt  
Silver

Functional Composition:
Caroline Ajo-Franklin, Drew Endy, Christopher Mason, Deepak Chandran,

Experiments & Results:
Chris Anderson, Kristian Muller, Drew Endy, John Dueber

The first person listed above for each group was supposed to be the  
leader of the group.  We'll have to check with them to see what they  
have been doing, and find new leaders if needed.

Also, note that there are many technical standards topics that nobody  
is working on.  So, if you'd like start leading work on a particular  
area, make an announcement to this list, set up a page under the  
technical standards section of the BioBricks website on OWW, and go  
for it.  Our goal is to have some progress to report and discuss by  
the March 1 meeting.

I'm going to try to move some of the above information to the web as  
time permits, but I also need to email more of the folks above first,  
so feel free to start building out materials on the web before me if  
you have a spare moment.

I'll also report back with another message drafting how the standards  
setting process might actually work (i.e., the process by which  
BioBrick technical standards get proposed, published, reviewed, and  
accepted).  Of course, we'll have to discuss this, and learn how to  
best get things to happen as we go along.

Be great,
Drew


On Jan 27, 2008, at 2:16 PM, Reshma Shetty wrote:

> Hello,
>
> Yes this list is active.  I'd suggest we coordinate efforts via
> OpenWetWare.  See
> http://openwetware.org/wiki/Synthetic_Biology:BioBricks/ 
> Standardization
> for preliminary ideas for technical standards around BioBrick standard
> biological parts.
>
> Folks should feel free to comment/annotate/change those pages or start
> new ones as needed.
>
> Thanks,
>
> Reshma
>
> On Jan 27, 2008 2:03 PM, Bryan Bishop <kanzure at gmail.com> wrote:
>> Is this list active? Maybe we can seed some links and resources to  
>> get
>> things started?
>>
>> - Bryan
>> ________________________________________
>> Bryan Bishop
>> http://heybryan.org/
>>
>> _______________________________________________
>> Standards mailing list
>> Standards at biobricks.org
>> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>>
>
> _______________________________________________
> Standards mailing list
> Standards at biobricks.org
> http://biobricks.org/mailman/listinfo/standards_biobricks.org