[BBF Standards] functional composition of BioBrick parts?

[Deepak Chandran]

Hello BioBricks Standards group,

    I have been doing some work in constructing simple file formats for 
representing parts as well as interfacing between them (connecting 
them). Simulating a model is kept as an objective when designing the 
file. The file format is intended to be human readable and concise, so 
that a user would not be intimidated to adopt it. Of course, this format 
is still in the 'experimenting' stage, but if anyone is interested, feel 
free to contact me.

--Deepak
Herbert Sauro Lab,
Bioengineering, Univ. Washington,
Seattle, WA
> My apologies - the March 1st meeting!
> Caroline
>
> On Jan 29, 2008 10:13 AM, Caroline Ajo-Franklin <CAjo-Franklin at lbl.gov> wrote:
>   
>> Hi Drew & Members of the Standards working group,
>>   At the November workshop, Alistair Elfick, Christopher Mason, Barry
>> Canton, Reshma Shetty, Kim de Mora, Matthieu Buprelle, Vincent
>> Rouilly, Scott Mohr, and myself met and outlined two initial goals for
>> our working group:
>> 1) to determine the variability of in vivo fluorescence measurements
>> of identical strains across different labs
>> 2) to draft a standard for transcriptional devices
>>  While this was an excellent start, we haven't yet gotten farther. We
>> are eager to have something in hand for the March 31 meeting, so your
>> reminder is quite welcome.
>>
>> Standards working group, could I please get some volunteers to help
>> who have access to a FACS machine and would be interested in making a
>> handful of in vivo fluorescence measurements before the March 31st
>> meeting? This experiment is designed to answer the question: How much
>> does the relative fluorescence of two (or three) GFP-expressing E.coli
>> strains vary between different labs assuming identical media & growth
>> conditions? It would be great to get measurements from several labs
>> spread across the world.
>>  Could I also get some volunteers interested in drafting a standard
>> sheet for transcriptional devices to be presented at the March 31st
>> meeting? The goal here is to articulate the minimum description of a
>> transcriptional device which would enable its use in a higher order
>> device, and would build upon substantial starts present in the
>> Registry documentation and in the literature.
>>
>>  If you interested in joining the struggle to standardize biological
>> parts through either of these efforts, please drop me an e-mail by
>> this Sunday Feb 2.
>>
>> Best-
>> Caroline
>>
>>
>> On Jan 27, 2008 3:53 PM, Drew Endy <endy at mit.edu> wrote:
>>     
>>> Hi Caroline, Chris, Deepak,
>>>
>>>
>>> The Technical Standards Group at the BBF recently launched.
>>>
>>> A number of new folks have signed up and are anxious to help.
>>>
>>> At the November BBF workshop we expressed an interest in working together on
>>> standard(s) that define how BioBrick parts function so that, when two parts
>>> are combined, the resulting behavior of the composite part is as expected,
>>> and not some surprising emergent property.  Has there been any progress?
>>> Who is leading our discussion?  Can we get a report / update?  Should we
>>> recruit more people to help with this topic?  E.g., I know that Reshma
>>> Shetty and Jason Kelly have been working on a PoPS level standard.
>>>
>>> The next workshop is coming up on March 1 at UCSF and we're hoping to be
>>> able to discuss progress and plans to continue to take things forward.
>>>
>>> If you haven't signed up for the mailing list, here's the URL to do so:
>>>
>>> Standards mailing list
>>> Standards at biobricks.org
>>> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>>>
>>> Thanks / be great!
>>> Drew
>>>
>>>
>>> Begin forwarded message:
>>>
>>> From: "Julius B. Lucks" <julius at younglucks.com>
>>> Date: January 27, 2008 5:11:56 PM EST
>>> To: standards at biobricks.org
>>> Subject: [BBF Standards] Starting off discussions
>>>
>>> Maybe a good place to start discussions is for the 4 topic leaders to
>>> send something to the list saying a little bit about the topic, and
>>> what needs to get done before March 1.  That would be very helpful
>>> for those of us new to the discussions to figure out where we can
>>> jump in and help out.
>>>
>>>
>>> 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.
>>>
>>>
>>>
>>> Cheers,
>>>
>>> Julius
>>>
>>> ------------------------------------------------------------------------
>>> ----------------
>>> http://www.openwetware.org/wiki/User:Julius_B._Lucks
>>> ------------------------------------------------------------------------
>>> ----------------
>>>
>>>
>>> _______________________________________________
>>> Standards mailing list
>>> Standards at biobricks.org
>>> http://biobricks.org/mailman/listinfo/standards_biobricks.org
>>>
>>>
>>>       
>>
>> --
>> Caroline Ajo-Franklin, Ph.D.
>> Staff Scientist, Biological Nanostructures Facility
>> The Molecular Foundry
>> Lawrence Berkeley National Laboratory
>> phone: 510.486.4299
>> e-mail: CAjo-Franklin at lbl.gov
>>
>>     
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