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
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: Synthetic Biology Open Language Visual (SBOLv) Specification
- by Cesar Rodriguez, Suzie Bartram, Anusuya Ramasubramanian, and Drew Endy
- DSpace, doi: 1721.1/49523
BBF RFC 17: deprecated
BBF 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
- requested by Jason R Kelly and Drew Endy
BBF RFC 20: Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts
BBF RFC 21: BglBricks Assembly Standard
- by J. Christopher Anderson, John E. Dueber, Mariana Leguia, Gabriel C. Wu, Jonathan A. Goler, Adam P. Arkin, and Jay D. Keasling
- 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
- 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
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
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
- by Sergio G. Peisajovich, Andrew Horwitz, Oliver Hoeller, Benjamin Rhau & Wendell Lim
- DSpace, doi:1721.1/46721
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
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: deprecated
BBF RFC 37: Fusion protein BioBrick™ assembly standard with optional linker extension
- by Mojca Benčina and Roman Jerala
- DSpace, doi: 1721.1/46705
- replaces BBF RFC 36
BBF RFC 38: Building Blocks - Standard Large DNA/Genome Construction
- by Jef Boeke and James DiCarlo
- DSpace, doi: 1721.1/49417
BBF RFC 39: The USER cloning standard
- by Christian Schrøder Kaas, Niels Bjørn Hansen, Hans Jasper Genee, Lars Ronn Olsen, Claudia Matos, Mads Tvillinggaard Bonde; Bjarne Gram Hansen
- DSpace, doi:1721.1/49522
BBF RFC 40: How to Build Kinetic Models of BioBricks™
- by Emma Weeding, Jason Houle, Ben Swiniarski, Patrick Smadbeck, Kristen Lindblad, Katherine Volzing, Poonam Srivastava, Vassilios Sotiropoulos, Kostas Biliouris, Yiannis Kaznessis
- DSpace, doi: 1721.1/49504
BBF RFC 41: Units for Promoter Measurement in Mammalian Cells
- by Velten, Lars; Iwamoto, Nao; Hiller, Corinna; Uckelmann, Hannah; Zhu, Chenchen; Zhao, Bingqing; Richter, Daniela; Hundeshagen, Phillip; Reichenzeller, Michaela; Keienburg, Jens; Eils, Roland
- DSpace, doi: 1721.1/49501
BBF RFC 42: RA-PCR, a method for the generation of randomized promoter libraries
- by Velten, Lars; Haas, Simon; Rademacher, Anne; Meyer, Hannah; Eils, Roland
- DSpace, doi: 1721.1/49502
BBF RFC 43: Design of specific mammalian promoters by in silico prediction
- by Tim Heinemann, Stephen Krämer, Lars Velten, Anna-Lena Kranz, Tobias Bauer, Rainer Konig, Marti Bernardo, Jens Keienburg, Roland Eils, and Nao Iwamoto
- DSpace, doi: 1721.1/49520
BBF RFC 44: Bioscaffold-Linker
- by Petros Mina and Nigel Savery
- DSpace, doi: 1721.1/49505
BBF RFC 45: Cloning Standard for Mammalian BioBrick™ Parts and Devices
- by Michael Bartoschek, Douaa Mugahid, Anne Rademacher, Hannah Meyer, Lars Velten, Yara Reis, Jens Keienburg, Roland Eils
- DSpace, doi: 1721.1/49503
BBF RFC 46: Large-Scale Peptide Modification on BioBrick™ Proteins
- by Feng Tian, GuoQiang Chen, Zhao Wang
- DSpace, doi: 1721.1/49521
BBF RFC 47: BioBytes Assembly Standard
- by David Lloyd, Kelly Robinson, Erin Garside, Justin Fedor, Doug Ridgway, Michael Ellison
- DSpace, doi: 1721.1/49518
BBF RFC 48: Automatic Biological Circuit Design
- requested by Wei Pan, Bo Ding, Yu He, Yuwei Cui, Jiahao Li, Xiaomo Yao,
BBF RFC 49: Draft Characterization Standard for describing Biosensor Sensitivity Tuners
- requested by James Brown, Vivian Mullin, Megan Stanley, Alan Walbridge
BBF RFC 50: Synthetic Biology Data Transfer Protocol (SB/DTP)
- requested by Cesar A. Rodriguez & Drew Endy
- RFC Draft
deprecated by authors 5/12/2010
BBF RFC 51: Final Expression Vectors for RFC 10 Expression parts
- requested by Kristian M. Mueller
BBF RFC 52: Information Standard for BioBrick Parts
- requested by Arend Slomp (a....@igemgroningen.com)
BBF RFC 53: USTC MetaPart Assembly Standard -- Extending RFC 10 to Enable Scarless Protein Fusion with Type IIS Restriction Enzyme EarI and SapI
- requested by Hao Jiang, Yang Zhang, Ruijun Zhu, Chang Liu, Duo An, and Ge Gao
BBF RFC 54: Abbreviated BioBrick Prefix and Suffix for More Efficient Primer Design
- requested by (from Osaka) Teoh Shao Thing shaothing@yahoo.com, Shuhei Yasumoto shuhei_yasumoto@yahoo.co.jp, Tadashi Nakamura tadasi.nakamura@gmail.com, Takahiro Saka takahiro9bttf@yahoo.co.jp, Kousuke Torigata colt_m16a4@yahoo.co.jp, Takino Rie doudemo-iinosa@hotmail.co.jp, Saya Kakuda kakuda150@gmail.com, Lin Youfeng yuto@w4.dion.ne.jp, Toshiyuki Otake viva_softbank_hawks@yahoo.ne.jp, Yuki Miyatake million.miles.miles.away@gmail.com, Hirayama Ikumi eating218sobabouro@yahoo.co.jp, Takuro A. Kagaya tkagaya@bio.sci.osaka-u.ac.jp, Naoaki Ono nono@ist.osaka-u.ac.jp and (from Edinburgh) Donal Stewart donal.stewart@ed.ac.uk, John Roger Wilson-Kanamori s0458094@sms.ed.ac.uk, Meng Lu s0971303@sms.ed.ac.uk, William Rostain s0789154@sms.ed.ac.uk, Maria Kowal s0801029@sms.ed.ac.uk, Richard Partridge-Hicks s0784083@sms.ed.ac.uk, Sarah Hunt sarah0674115@hotmail.co.uk, Marta Bereska martabereska@gmail.com, Hannah Fraser hpf2102@columbia.edu, Matthew Coombes contradictory@hotmail.co.uk, Damian Barnard dkbarnard@gmail.com, Alistair Elfick Alistair.Elfick@ed.ac.uk, Chris French C.French@ed.ac.uk
BBF RFC 55: Standard Biological Part Automatic Modeling Database Language
- requested by Hao Jiang haojiang@mail.ustc.edu.cn, Chen Liao, Zhen Wang, Xiaomo Yao, and Kun Jiang
BBF RFC 56: “Part Flavors” For Peptide-Coding Parts
- by Chris Anderson
- DSpace, doi: 1721.1/59011
BBF RFC 57: Assembly of BioBricks by the Gibson Method
- requested by Bill Collins, Hannah Copley, Peter Emmrich, Will Handley, Anja Hohmann, Emily Knott, Paul Masset, Ben Reeve, Theo Sanderson
BBF RFC 58: Absolute measurement of bacterial promoter strength in cell-free system by qPCR
- requested by Michal Lower and Anna Olchowik
BBF RFC 59: Quantitative measurement of mamallian cell invasion by bacteria using flow cytometry
- requested by Michal Lower and Anna Olchowik
BBF RFC 60: Open licensing of BioBrick parts
- requested by Michal Lower and Anna Olchowik
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