[BBF Standards] Deepak's Format Proposal [Re: Two separate standards]

[Deepak Chandran]

Ralf,

   I think your (1),(2), and (3) points for describing a format is good. 
At the same time, there should also be a list of requirements for a 
format. Any standard format should:

1) be able to represent any biological device/system
2) provide syntax that define connections between devices
3) have sufficient information for another person to model/analyze the 
device/system
4) have sufficient information for another person to reconstruct the 
entire device/system
5) avoid redundant information (or even strictly no redundant information)

that was just a quick list. You may add or remove items.

The idea of a wiki is nice. That way, we can all post various examples 
(challenges) to it.

--Deepak

Ralph Santos wrote:
> Deepak,
>
> I think your proposal to try and write out a format is a good idea.  I 
> think it would be useful if it were treated a bit like a project or an 
> event for the working group:  Set up a wiki page for it, put the 
> objectives and any guidelines there, with an empty section to let 
> people link in their format writeups.
>
> I'd also be interested to hear what you think should go into a 
> writeup, or more broadly what you'd be looking for in a writeup to 
> determine whether it is capable of describing all the iGEM projects.  
> Just to make it clear, I'm thinking more along the lines of basic 
> essential requirements, not criteria for an optimal solution.  I think 
> that would be useful in providing some common basis to compare and 
> contrast the submitted writeups.  Of course the people doing the 
> writeups would be completely free to address or ignore the criteria 
> you state as they see fit.
>
> Do you have any notions on the format for a writeup?  I could imagine 
> a writeup could take on a number of forms:
>
> (1) A set of rules telling a reader how to write an arbitrary system 
> in the submitter's format
> (2) A set of example descriptions demonstrating by example
> (3) A set of *annotated* descriptions made up of examples plus 
> comments describing how the  rules are applied in the examples
>
> Of course, there are combinations of the above not to mention other 
> ways besides those I mentioned.
>
> What are your thoughts?
>
> ---ralf
>
>
> Deepak Chandran wrote:
>> Hello Josh, Drew, and rest,
>>
>>    While it seems logical to first have standard definitions for 
>> promoter, rbs, coding regions, terminators, etc. before working on 
>> standards for devices and systems, I think the two are somewhat 
>> independent. People have been building biological circuits 
>> successfully (iGEM students for example). What I am proposing is for 
>> some of us (myself included) to write out a format that can represent 
>> all of the iGEM projects. This format can allow others to take iGEM 
>> projects (and any other such projects) and connect them together to 
>> form larger circuits without having to understand the details of the 
>> project itself. All these circuits will be represented in the 
>> standard language so that one does not need to reconstruct an entire 
>> device to reuse it. I think this is very much possible while the 
>> standards on promoters/rbs/etc are still pending. It is also a bit 
>> easier maybe, because many concepts can be borrowed from engineering 
>> disciplines.
>>
>> --Deepak
>>
>>   
>