The BioBricks Foundation:RFC: Difference between revisions
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<h1>RFCs</h1> | |||
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The BioBricks Foundation is dedicated to promoting and protecting the open development, sharing, and reuse of BioBrick™ standard biological parts. Taking inspiration from the Internet Engineering Task Force, we are now implementing a Request for Comments process. A Request for Comments, abbreviated RFC, is a short document that is intended for review by the rest of the community. | The BioBricks Foundation is dedicated to promoting and protecting the open development, sharing, and reuse of BioBrick™ standard biological parts. Taking inspiration from the Internet Engineering Task Force, we are now implementing a Request for Comments process. A Request for Comments, abbreviated RFC, is a short document that is intended for review by the rest of the community. | ||
An RFC might | An RFC might | ||
*propose a standard of some sort (i.e. Tom Knight's 2003 BioBrick physical assembly standard or the Freiburg protein fusion assembly standard) | *propose a standard of some sort (i.e. Tom Knight's 2003 BioBrick™ physical assembly standard or the Freiburg protein fusion assembly standard) | ||
*describe best practices or protocols (i.e. a protocol for assembling two parts) | *describe best practices or protocols (i.e. a protocol for assembling two parts) | ||
*provide information (i.e. a description of how to design transcriptional terminators) | *provide information (i.e. a description of how to design transcriptional terminators) | ||
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===BBF RFC<nowiki></nowiki> 4: Synthetic Biology Diagram Standard=== | ===BBF RFC<nowiki></nowiki> 4: Synthetic Biology Diagram Standard=== | ||
*requested by Mackenzie Cowell | *requested by Mackenzie Cowell | ||
===BBF RFC<nowiki></nowiki> 5: BioBrick Placeholders=== | ===BBF RFC<nowiki></nowiki> 5: BioBrick™ Placeholders=== | ||
*requested by George McArthur IV and Daniel R Tarjan | *requested by George McArthur IV and Daniel R Tarjan | ||
===BBF RFC<nowiki></nowiki> 6: Synthetic Terminators for Transcription Attenuation=== | ===BBF RFC<nowiki></nowiki> 6: Synthetic Terminators for Transcription Attenuation=== | ||
*requested by George McArthur IV and Daniel R Tarjan | *requested by George McArthur IV and Daniel R Tarjan | ||
===BBF RFC<nowiki></nowiki> 7: Original Biobrick distribution data sheet, May 22, 2002=== | ===BBF RFC<nowiki></nowiki> 7: Original Biobrick™ distribution data sheet, May 22, 2002=== | ||
*by Tom Knight | *by Tom Knight | ||
*This is the data sheet accompanying the first public Biobrick distribution | *This is the data sheet accompanying the first public Biobrick™ distribution | ||
*[[Media:BBFRFC7.pdf |RFC Draft]] | *[[Media:BBFRFC7.pdf |RFC Draft]] | ||
===BBF RFC<nowiki></nowiki> 8: Early Biobrick standard design=== | ===BBF RFC<nowiki></nowiki> 8: Early Biobrick™ standard design=== | ||
*by Tom Knight | *by Tom Knight | ||
*Early description of a (now defunct) Biobrick standard | *Early description of a (now defunct) Biobrick™ standard | ||
*[[Media:BBFRFC8.pdf |RFC Draft]] | *[[Media:BBFRFC8.pdf |RFC Draft]] | ||
===BBF RFC<nowiki></nowiki> 9: Idempotent vector design for the standard assembly of Biobricks=== | ===BBF RFC<nowiki></nowiki> 9: Idempotent vector design for the standard assembly of Biobricks™=== | ||
*by Tom Knight, Randall Rettberg, Leon Chan, Drew Endy, Reshma Shetty, Austin Che | *by Tom Knight, Randall Rettberg, Leon Chan, Drew Endy, Reshma Shetty, Austin Che | ||
*Initial detailed motivation and definition of the Biobrick standard | *Initial detailed motivation and definition of the Biobrick standard | ||
*[[Media:BBFRFC9.pdf | RFC Draft]] | *[[Media:BBFRFC9.pdf | RFC Draft]] | ||
===BBF RFC<nowiki></nowiki> 10: Draft standard for Biobrick biological parts=== | ===BBF RFC<nowiki></nowiki> 10: Draft standard for Biobrick™ biological parts=== | ||
*by Tom Knight, May 3, 2007 | *by Tom Knight, May 3, 2007 | ||
*Formal description of the initial Biobrick standard | *Formal description of the initial Biobrick™ standard | ||
*[http://hdl.handle.net/1721.1/45138 DSpace], doi: 1721.1/45138 | *[http://hdl.handle.net/1721.1/45138 DSpace], doi: 1721.1/45138 | ||
===BBF RFC<nowiki></nowiki> 11: Biobrick assembly standard modifications=== | ===BBF RFC<nowiki></nowiki> 11: Biobrick™ assembly standard modifications=== | ||
*by Tom Knight, July 8, 2008 | *by Tom Knight, July 8, 2008 | ||
*Proposed modification of enzymes to facilitate protein fusions (SpeI/NheI replaces XbaI/SpeI) | *Proposed modification of enzymes to facilitate protein fusions (SpeI/NheI replaces XbaI/SpeI) | ||
*[[Media:BBFRFC11.pdf | RFC Draft]] | *[[Media:BBFRFC11.pdf | RFC Draft]] | ||
===BBF RFC<nowiki></nowiki> 12: Draft Biobrick BB-2 standard for biological parts=== | ===BBF RFC<nowiki></nowiki> 12: Draft Biobrick™ BB-2 standard for biological parts=== | ||
*by Tom Knight, November 19, 2008 | *by Tom Knight, November 19, 2008 | ||
*Formal description of the Biobrick BB-2 standard | *Formal description of the Biobrick™ BB-2 standard | ||
*[http://hdl.handle.net/1721.1/45139 DSpace], doi: 1721.1/45139 | *[http://hdl.handle.net/1721.1/45139 DSpace], doi: 1721.1/45139 | ||
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*[[BBRFC14 | RFC draft]] | *[[BBRFC14 | RFC draft]] | ||
===BBF RFC 15: Innovations Mean Nothing Unless You Use Them -- The New BioScaffold Family of BioBrick Parts To Enable Manipulations Such as Protein Fusions, Library Construction, and Part Domestication=== | ===BBF RFC 15: Innovations Mean Nothing Unless You Use Them -- The New BioScaffold Family of BioBrick™ Parts To Enable Manipulations Such as Protein Fusions, Library Construction, and Part Domestication=== | ||
*by Julie Norville, Angela Belcher and Tom Knight | *by Julie Norville, Angela Belcher and Tom Knight | ||
*[[The BioBricks Foundation:BBFRFC15 | RFC Draft]] | *[[The BioBricks Foundation:BBFRFC15 | RFC Draft]] | ||
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===BBF RFC 17: ''deprecated''=== | ===BBF RFC 17: ''deprecated''=== | ||
===BBF RFC 18: Proposed Conceptual Guidelines for the Design of a BioBrick Graphical Language & an Example=== | ===BBF RFC 18: Proposed Conceptual Guidelines for the Design of a BioBrick™ Graphical Language & an Example=== | ||
*by Eric Fernandez | *by Eric Fernandez | ||
*[http://hdl.handle.net/1721.1/44640 DSpace], doi: 1721.1/44640 | *[http://hdl.handle.net/1721.1/44640 DSpace], doi: 1721.1/44640 | ||
*[[BBF RFC 18 | Add comments here]] | *[[BBF RFC 18 | Add comments here]] | ||
===BBF RFC 19: Measuring the Activity of BioBrick Promoters Using an In Vivo Reference Standard=== | ===BBF RFC 19: Measuring the Activity of BioBrick™ Promoters Using an In Vivo Reference Standard=== | ||
*requested by Jason R Kelly and Drew Endy | *requested by Jason R Kelly and Drew Endy | ||
===BBF RFC 20: Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts=== | ===BBF RFC 20: Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts=== | ||
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*[http://hdl.handle.net/1721.1/46747 DSpace], doi: 1721.1/46747 | *[http://hdl.handle.net/1721.1/46747 DSpace], doi: 1721.1/46747 | ||
===BBF RFC 22: BBΩ-- An Extended BioBricks Assembly Standard that Utilizes Hierarchical Manipulation of Parts to Address Limitations in the Original BioBricks Assembly Standard=== | ===BBF RFC 22: BBΩ-- An Extended BioBricks™ Assembly Standard that Utilizes Hierarchical Manipulation of Parts to Address Limitations in the Original BioBricks Assembly Standard=== | ||
*by Julie Norville, Angela Belcher and Tom Knight | *by Julie Norville, Angela Belcher and Tom Knight | ||
*[[The_BioBricks_Foundation:BBFRFC22|RFC Draft]] | *[[The_BioBricks_Foundation:BBFRFC22|RFC Draft]] |
Revision as of 21:34, 15 June 2010
RFCsThe BioBricks Foundation is dedicated to promoting and protecting the open development, sharing, and reuse of BioBrick™ standard biological parts. Taking inspiration from the Internet Engineering Task Force, we are now implementing a Request for Comments process. A Request for Comments, abbreviated RFC, is a short document that is intended for review by the rest of the community. An RFC might
RFC's are static documents or digital objects like video's intended to get an idea, proposed standard, or method out to the rest of the community for comment. RFC's are numbered, for ease of referencing, and the numbers are assigned by the BBF. Instructions for requesting a BBF RFC number, preparing an RFC, and submitting an RFC to the BBF are described in BBF RFC 0.
The complete list of all assigned RFC numbers and RFC documents (for those submitted) is listed below. BBF RFC 0: Instructions to BBF RFC Authors
BBF RFC 1: Definition of the nature of a part
BBF RFC 2: The information stored with a with a part
BBF RFC 3: Restriction sites for the construction of fusion proteins
BBF RFC 4: Synthetic Biology Diagram Standard
BBF RFC 5: BioBrick™ Placeholders
BBF RFC 6: Synthetic Terminators for Transcription Attenuation
BBF RFC 7: Original Biobrick™ distribution data sheet, May 22, 2002
BBF RFC 8: Early Biobrick™ standard design
BBF RFC 9: Idempotent vector design for the standard assembly of Biobricks™
BBF RFC 10: Draft standard for Biobrick™ biological parts
BBF RFC 11: Biobrick™ assembly standard modifications
BBF RFC 12: Draft Biobrick™ BB-2 standard for biological parts
BBF RFC 13: Rethinking the boundaries and composition of coding regions
BBF RFC14: Protein domain fusions in BB-2 assembly
BBF RFC 15: Innovations Mean Nothing Unless You Use Them -- The New BioScaffold Family of BioBrick™ Parts To Enable Manipulations Such as Protein Fusions, Library Construction, and Part Domestication
BBF RFC 16: Synthetic Biology Open Language Visual (SBOLv) Specification
BBF RFC 17: deprecatedBBF RFC 18: Proposed Conceptual Guidelines for the Design of a BioBrick™ Graphical Language & an Example
BBF RFC 19: Measuring the Activity of BioBrick™ Promoters Using an In Vivo Reference Standard
BBF RFC 20: Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts
BBF RFC 21: BglBricks Assembly Standard
BBF RFC 22: BBΩ-- An Extended BioBricks™ Assembly Standard that Utilizes Hierarchical Manipulation of Parts to Address Limitations in the Original BioBricks Assembly Standard
BBF RFC 23: A New Biobrick Assembly Strategy Designed for Facile Protein Engineering
BBF RFC 24: Conversion of Freiburg (Fusion) Biobricks to the Silver (BioFusion) format
BBF RFC 25: Fusion Protein (Freiburg) Biobrick assembly standard
BBF RFC 26: In-Fusion BioBrick Assembly
BBF RFC 27: Fast ligation-free construction of BioBricks with PCR & In-Fusion
BBF RFC 28: A method for combinatorial multi-part assembly based on the Type IIs restriction enzyme AarI
BBF RFC 29: Naming of standards of physical composition of BioBrick parts
BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data
BBF RFC 31: Provisional BioBrick Language (PoBoL)
BBF RFC 32: Revised draft of an RDF-based framework for the exchange and integration of Synthetic Biology data
BBF RFC 33: A Core Data Model for Biological System Design
BBF RFC 34: A Promoter Measurement Kit for Bacillus subtilis
BBF RFC 35: Context-free grammar representation of design strategies for BioBrick constructs
BBF RFC 36: deprecatedBBF RFC 37: Fusion protein BioBrick assembly standard with optional linker extension
BBF RFC 38: Building Blocks - Standard Large DNA/Genome Construction
BBF RFC 39: The USER cloning standard
BBF RFC 40: How to Build Kinetic Models of BioBricks
BBF RFC 41: Units for Promoter Measurement in Mammalian Cells
BBF RFC 42: RA-PCR, a method for the generation of randomized promoter libraries
BBF RFC 43: Design of specific mammalian promoters by in silico prediction
BBF RFC 44: Bioscaffold-Linker
BBF RFC 45: Cloning Standard for Mammalian BioBrick Parts and Devices
BBF RFC 46: Large-Scale Peptide Modification on BioBrick Proteins
BBF RFC 47: BioBytes Assembly Standard
BBF RFC 48: Automatic Biological Circuit Design
BBF RFC 49: Draft Characterization Standard for describing Biosensor Sensitivity Tuners
BBF RFC 50: Synthetic Biology Data Transfer Protocol (SB/DTP)
deprecated by authors 5/12/2010 BBF RFC 51: Final Expression Vectors for RFC 10 Expression parts
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