BBF RFC 31

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(New page: Add your comments to RFC 31 here. See BBF_RFC_20 for an example how comments can be formatted and signed.)
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The RFC is available at [http://hdl.handle.net/1721.1/45536]
Add your comments to RFC 31 here. See [[BBF_RFC_20]] for an example how comments can be formatted and signed.
Add your comments to RFC 31 here. See [[BBF_RFC_20]] for an example how comments can be formatted and signed.
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=[[User:Vincent_Rouilly | Vincent]], 16th May 2009=
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Hi,
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it is a good surprise to read about some new PoBoL development.
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I fully agree with the authors that the Synthetic Biology community needs an open and standarized data model to represent BioBricks. Please find below some comments about the proposal. I hope they are clear and useful.
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'''> related to [6. Motivation]'''
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What about compatibility with existing DNA sequence standards, and their respective tools ? I understand that SynBio will require some specific features, but is it really required to start from scratch. Defining a standard that would extend on previous standards might help us to avoid reinventing the wheel, as well as reaching out other communities (in terms of people and software solutions / infrastructures). At least, I would be interested to read about the authors' reasons not to consider, at all, any of the existing standards to represent DNA sequences.
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I would also find useful if the authors could describe two or three relevant scenarii where such a data format would be required.
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'''> related to [10.1.1 Class BioBrick]'''
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Is there a concept of unicity for a BioBrick ? Or is it accepted for the proposed standard to have duplicates ? For example, two Biobricks with same DNASequences, same Format, but different ShortDescriptions ?
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Also, if unicity is required, at which level ? in the same lab or in the all world ?
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Would it be useful to consider unique identifiers ?
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"The BioBrick class May be extended at any time". This built-in flexibility might be difficult to deal with when people try to practically implement the scheme.
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'''> related to [10.1.3 BioBrickBasic]'''
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Quick clarification: Let's say that I use direct DNA synthesis to get a 5kb (4 genes) metabolic pathway, with prefix/suffix chosen to satisfy a particular BioBrick standard (+ not incompatible restriction sites in the 5kb). From what I understand, this would constitute a BioBrickBasic instance, no ? 
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'''> related to [10.1.5 BioBrickFormat]'''
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Recombinant DNA is a method amongst others to put together 2 pieces of DNA. For example, in vitro recombination could very well become a popular way of physically assembling DNA (no resulting scar). It looks like this proposed scheme only considers Recombinant DNA-type assemblies. Is it a limitation ? Is it ok ? Or are we saying that pieces of DNA using homology recombination for assembly will never be considered as BioBricks ?
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'''> related to [Class Sample]'''
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What if the sample is a PCR product (linear DNA, no vector) ?
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How would you distinguish between a mini-prep in buffer, dry DNA, or a stab ?
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At the end, I am not sure that this type of information is very useful. I would prefer to see a community agreement on key attributes before getting into those details that are more relevant to a Laboratory Information System.
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'''> General comments'''
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Could the authors comment on the impact of such information model on the current MIT registry, and on future registries ?
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Characterisation of Biobricks is one of the highest priorities for our community.  How the authors suggest to integrate this new type of information in the current scheme ? Will it be part of the standard or will it require a different system ?

Revision as of 12:36, 15 May 2009

The RFC is available at [1] Add your comments to RFC 31 here. See BBF_RFC_20 for an example how comments can be formatted and signed.

Vincent, 16th May 2009

Hi,

it is a good surprise to read about some new PoBoL development. I fully agree with the authors that the Synthetic Biology community needs an open and standarized data model to represent BioBricks. Please find below some comments about the proposal. I hope they are clear and useful.

> related to [6. Motivation]

What about compatibility with existing DNA sequence standards, and their respective tools ? I understand that SynBio will require some specific features, but is it really required to start from scratch. Defining a standard that would extend on previous standards might help us to avoid reinventing the wheel, as well as reaching out other communities (in terms of people and software solutions / infrastructures). At least, I would be interested to read about the authors' reasons not to consider, at all, any of the existing standards to represent DNA sequences.

I would also find useful if the authors could describe two or three relevant scenarii where such a data format would be required.


> related to [10.1.1 Class BioBrick]

Is there a concept of unicity for a BioBrick ? Or is it accepted for the proposed standard to have duplicates ? For example, two Biobricks with same DNASequences, same Format, but different ShortDescriptions ? Also, if unicity is required, at which level ? in the same lab or in the all world ? Would it be useful to consider unique identifiers ?

"The BioBrick class May be extended at any time". This built-in flexibility might be difficult to deal with when people try to practically implement the scheme.

> related to [10.1.3 BioBrickBasic]

Quick clarification: Let's say that I use direct DNA synthesis to get a 5kb (4 genes) metabolic pathway, with prefix/suffix chosen to satisfy a particular BioBrick standard (+ not incompatible restriction sites in the 5kb). From what I understand, this would constitute a BioBrickBasic instance, no ?


> related to [10.1.5 BioBrickFormat]

Recombinant DNA is a method amongst others to put together 2 pieces of DNA. For example, in vitro recombination could very well become a popular way of physically assembling DNA (no resulting scar). It looks like this proposed scheme only considers Recombinant DNA-type assemblies. Is it a limitation ? Is it ok ? Or are we saying that pieces of DNA using homology recombination for assembly will never be considered as BioBricks ?

> related to [Class Sample]

What if the sample is a PCR product (linear DNA, no vector) ? How would you distinguish between a mini-prep in buffer, dry DNA, or a stab ?

At the end, I am not sure that this type of information is very useful. I would prefer to see a community agreement on key attributes before getting into those details that are more relevant to a Laboratory Information System.

> General comments

Could the authors comment on the impact of such information model on the current MIT registry, and on future registries ?

Characterisation of Biobricks is one of the highest priorities for our community. How the authors suggest to integrate this new type of information in the current scheme ? Will it be part of the standard or will it require a different system ?

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