The BioBricks Foundation:RFC

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RFCs 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 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) provide information (i.e. a description of how to design transcriptional terminators) simply comment, extend, or replace an earlier RFC 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. Blank templates for drafting a BBF RFC are available Word (.doc) Open Document Format (ODF) (.ott) OpenOffice.org (.stw) LaTeX (.tex) and Corresponding PDF (.pdf) 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 by Chris Anderson, Austin Che, Mackenzie Cowell, Alistair Elfick, Kim de Mora, Drew Endy, Chris French, Tom Knight, Antonia Mayer, George McArthur, Randy Rettberg, Douglas Ridgway, Reshma Shetty, Sean Sleight, and Daniel Tarjan DSpace, doi: 1721.1/44960 Add comments here BBF RFC 1: Definition of the nature of a part requested by Kristian Müller and Katja Arndt BBF RFC 2: The information stored with a with a part requested by Kristian Müller and Katja Arndt BBF RFC 3: Restriction sites for the construction of fusion proteins requested by Kristian Müller and Katja Arndt BBF RFC 4: Synthetic Biology Diagram Standard requested by Mackenzie Cowell BBF RFC 5: BioBrick Placeholders requested by George McArthur IV and Daniel R Tarjan BBF RFC 6: Synthetic Terminators for Transcription Attenuation requested by George McArthur IV and Daniel R Tarjan BBF RFC 7: Original Biobrick distribution data sheet, May 22, 2002 by Tom Knight This is the data sheet accompanying the first public Biobrick distribution RFC Draft BBF RFC 8: Early Biobrick standard design by Tom Knight Early description of a (now defunct) Biobrick standard RFC Draft BBF RFC 9: Idempotent vector design for the standard assembly of Biobricks by Tom Knight, Randall Rettberg, Leon Chan, Drew Endy, Reshma Shetty, Austin Che Initial detailed motivation and definition of the Biobrick standard RFC Draft BBF RFC 10: Draft standard for Biobrick biological parts by Tom Knight, May 3, 2007 Formal description of the initial Biobrick standard DSpace, doi: 1721.1/45138 BBF RFC 11: Biobrick assembly standard modifications by Tom Knight, July 8, 2008 Proposed modification of enzymes to facilitate protein fusions (SpeI/NheI replaces XbaI/SpeI) RFC Draft BBF RFC 12: Draft Biobrick BB-2 standard for biological parts by Tom Knight, November 19, 2008 Formal description of the Biobrick BB-2 standard DSpace, doi: 1721.1/45139 BBF RFC 13: Rethinking the boundaries and composition of coding regions by Tom Knight Logical split of the protein coding region into domains RFC draft BBF RFC14: Protein domain fusions in BB-2 assembly by Tom Knight Application of the RFC13 ideas to assembly with BB-2 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 by Julie Norville, Angela Belcher and Tom Knight RFC Draft BBF RFC 16: BioBrick Open Graphical Language (BOGL) requested by Cesar Rodriguez, Drew Endy, and others TBA BBF RFC 17: deprecated BBF RFC 18: Proposed Conceptual Guidelines for the Design of a BioBrick Graphical Language & an Example by Eric Fernandez DSpace, doi: 1721.1/44640 Add comments here BBF RFC 19: Measuring the Activity of BioBrick Promoters Using an In Vivo Reference Standard requested by Jason R Kelly and Drew Endy BBF RFC 20: Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts by Austin Che DSpace, doi: 1721.1/44962 Add comments here BBF RFC 21: BglBricks Assembly Standard requested by J. Christopher Anderson, John E. Dueber, Jonathan A. Goler, Adam P. Arkin, and Jay D. Keasling 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 RFC Draft BBF RFC 23: A New Biobrick Assembly Strategy Designed for Facile Protein Engineering by Karmella Haynes, Ira Phillips and Pamela Silver (Original technical report available at DSpace, PDF (direct link)) BBF RFC 24: Conversion of Freiburg (Fusion) Biobricks to the Silver (BioFusion) format by Raik Grünberg DSpace, doi: 1721.1/44961 Add comments here BBF RFC 25: Fusion Protein (Freiburg) Biobrick assembly standard by Kristian M. Müller, Katja M. Arndt, the 2007 Freiburg iGEM team, and Raik Grünberg DSpace; doi:1721.1/45140 BBF RFC 26: In-Fusion BioBrick Assembly by Sean C. Sleight DSpace, doi:1721.1/46328 Add comments here BBF RFC 27: Fast ligation-free construction of BioBricks with PCR & In-Fusion requested by Raik Grünberg BBF RFC 28: A method for combinatorial multi-part assembly based on the Type IIs restriction enzyme AarI requested by Sergio G. Peisajovich, Noah Helman, Andrew Horwitz, Reid Williams, Michael Chen & Wendell Lim BBF RFC 29: Naming of standards of physical composition of BioBrick parts by Reshma Shetty and Randy Rettberg DSpace, doi: 1721.1/45137 BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data by Raik Grünberg DSpace, doi: 1721.1/45143 Add comments here BBF RFC 31: Provisional BioBrick Language (PoBoL) by Michal Galdzicki, Deepak Chandran, Alec Nielsen, Jason Morrison, Mackenzie Cowell, Raik Grünberg, Sean Sleight, Herbert Sauro DSpace, doi: 1721.1/45537 Add comments here BBF RFC 32: Revised draft of an RDF-based framework for the exchange and integration of Synthetic Biology data requested by Raik Grünberg and Michal Galdzicki BBF RFC 33: A Core Data Model for Biological System Design requested by Douglas Densmore, J.Christopher Anderson, Timothy Ham, Josh Kittleson, Cesar Rodriquez BBF RFC 34: A Promoter Measurement Kit for Bacillus subtilis requested by Geoff Baldwin, James Brown, Jane Calvert, Vincent Danos, Kim de Mora, Alistair Elfick, Paul Freemont, Chris French, Emma Frow, Jennifer Hallinan, Matt Pocock, Vincent Rouilly, Anil Wipat, Goksel Misirli, Jan-Willem Veening, Leendert Hamoen BBF RFC 35: Context-free grammar representation of design strategies for BioBrick constructs requested by Jean Peccoud, Yizhi Cai and Matthew Lux BBF RFC 36: Fusion protein BioBrick assembly standard with optional linker extension requested by Roman Jerala