The BioBricks Foundation:RFC

The BioBricks Foundation is available to provide research and development through our BioBrick&trade; R&D Services. Give us a call at 650-799-9851. {| cellspacing="0" The BioBrick&trade; RFC Process Through its BioBrick&trade; RFC Process, the BioBricks Foundation hosts discussions and editorial work around the development of technical standards. Our BioBrick&trade; RFC list contains 50+ technical documents to date. Through the BioBrick&trade; RFC Process, we also host an email discussion list.
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An RFC might
 * propose a standard of some sort (i.e. Tom Knight's 2003 BioBrick&trade; 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

RFCs are static documents or digital objects like videos intended to get an idea, proposed standard, or method out to the rest of the community for comment. RFCs 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
 * [[Media:BBF RFC blank.doc | Word]] (.doc)
 * [[Media:BBF RFC blank.ott | Open Document Format (ODF)]] (.ott)
 * [[Media:BBF RFC blank.stw | OpenOffice.org]] (.stw)
 * [[Media:RFCblank.tex | LaTeX]] (.tex) and [[Media:RFCblank.pdf| 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&trade; 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&trade; distribution data sheet, May 22, 2002

 * by Tom Knight
 * This is the data sheet accompanying the first public BioBrick&trade; distribution
 * [[Media:BBFRFC7.pdf |RFC Draft]]

BBF RFC 8: Early BioBrick&trade; standard design

 * by Tom Knight
 * Early description of a (now defunct) BioBrick&trade; standard
 * [[Media:BBFRFC8.pdf |RFC Draft]]

BBF RFC 9: Idempotent vector design for the standard assembly of BioBricks&trade;

 * by Tom Knight, Randall Rettberg, Leon Chan, Drew Endy, Reshma Shetty, Austin Che
 * Initial detailed motivation and definition of the BioBrick&trade; standard
 * [[Media:BBFRFC9.pdf | RFC Draft]]

BBF RFC 10: Draft standard for BioBrick&trade; biological parts

 * by Tom Knight, May 3, 2007
 * Formal description of the initial BioBrick&trade; standard
 * DSpace, doi: 1721.1/45138

BBF RFC 11: BioBrick&trade; assembly standard modifications

 * by Tom Knight, July 8, 2008
 * Proposed modification of enzymes to facilitate protein fusions (SpeI/NheI replaces XbaI/SpeI)
 * [[Media:BBFRFC11.pdf | RFC Draft]]

BBF RFC 12: Draft BioBrick&trade; BB-2 standard for biological parts

 * by Tom Knight, November 19, 2008
 * Formal description of the BioBrick&trade; 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&trade; 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 18: Proposed Conceptual Guidelines for the Design of a BioBrick&trade; Graphical Language & an Example

 * by Eric Fernandez
 * DSpace, doi: 1721.1/44640
 * Add comments here

BBF RFC 19: Measuring the Activity of BioBrick&trade; 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

 * 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&trade; Assembly Standard that Utilizes Hierarchical Manipulation of Parts to Address Limitations in the Original BioBricks&trade; Assembly Standard

 * by Julie Norville, Angela Belcher and Tom Knight
 * RFC Draft

BBF RFC 23: A New BioBrick&trade; 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&trade; to the Silver (BioFusion) format

 * by Raik Grünberg
 * DSpace, doi: 1721.1/44961
 * Add comments here

BBF RFC 25: Fusion Protein (Freiburg) BioBrick&trade; 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&trade; Assembly

 * by Sean C. Sleight
 * DSpace, doi:1721.1/46328
 * Add comments here

BBF RFC 27: Fast ligation-free construction of BioBricks&trade; 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&trade; 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&trade; 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&trade; constructs

 * requested by Jean Peccoud, Yizhi Cai and Matthew Lux

BBF RFC 37: Fusion protein BioBrick&trade; 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&trade;

 * 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&trade; 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&trade; 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&trade; Parts

 * by Arend Slomp and David Ekkers
 * DSpace, doi: 1721.1/60089

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, Ying Zhang, Ge Gao, and Jing Yang
 * [[Media:BBFRFC53.pdf |RFC draft]]

BBF RFC 54: Abbreviated BioBrick&trade; Prefix and Suffix for More Efficient Primer Design

 * by Thing, Teoh Shao; Yasumoto, Shuhei; Nakamura, Tadashi; Saka, Takahiro; Torigata, Kousuke; Rie, Takino; Kakuda, Saya; Youfeng, Lin; Otake, Toshiyuki; Miyatake, Yuki; Ikumi, Hirayama; Kagaya, Takuro A.; Ono, Naoaki; Stewart, Donal; Wilson-Kanamori, John Roger; Lu, Meng; Rostain, William; Kowal, Maria; Partridge-Hicks, Richard; Hunt, Sarah; Bereska, Marta; Fraser, Hannah; Coombes, Matthew; Barnard, Damian; Elfick, Alistair; French, Chris
 * DSpace; doi: 1721.1/59800

BBF RFC 55: Standard Biological Part Automatic Modeling Database Language (MoDeL)

 * by Zhen Wang, Chen Liao, Hao Jiang, Xiaomo Yao, Kun Jiang
 * DSpace, doi:1721.1/59957

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

 * by Anna Olchowik, Michał Lower, Cherry Moreno, Jarosław Pankowski
 * DSpace, doi: 1721.1/60093

BBF RFC 59: Quantitative measurement of mamallian cell invasion by bacteria using flow cytometry

 * by Michal Lower and Anna Olchowik
 * DSpace, doi: 1721.1/59801

BBF RFC 60: Open licensing of BioBrick&trade; parts

 * by Michał Lower, Anna Olchowik, Jarosław Pankowski, Milena Bażlekowa, Marta Błaszkiewicz, Dominik Cysewski, Kamil Koper, Joanna Leszczyńska, Cherry Moreno and Anna Puławska
 * DSpace, doi: 1721.1/60081

BBF RFC 61: Fast multiple gene fragment ligation method based on Type IIs restriction enzyme DraIII

 * by Zhenyu SHI, Teng LI, and Guoqiang CHEN
 * DSpace, doi: 1721.1/59802

BBF RFC 62: Fast multiple gene fragment ligation method based on homologous recombination

 * by Ruiyan WANG, Zhenyu SHI, Teng LI, Guoqiang CHEN
 * DSpace, doi: 1721.1/59803

BBF RFC 63: DTU Synthetic Promoter Library Standard

 * by Patrick Fortuna, Thomas Trolle, Martin Malthe Borch, Anastasiya Haugaard, Maya Friis Kjærgaard, Lisa Blanc Iversen, Annemi Jollmann, Anja Sander, Juliet Frederiksen and Grzegorz Slodkowicz
 * DSpace, doi: 1721.1/60080

BBF RFC 64: Building Protein Domain Based Composite BioBricks

 * by Balint L. Balint, Ophir Keret, Peter Brazda, Mate Demeny and 2010 Debrecen-Hungary iGEM team
 * DSpace, doi: 1721.1/60083

BBF RFC 65: Recombination Based Part Assembly

 * by Laura Deming, Adrian Slusarczyk, Yunxin Jiao, and the 2010 MIT iGEM team
 * DSpace, doi: 1721.1/60082

BBF RFC 66: A RESTful API for Supporting Automated BioBrick Model Assembly

 * by Jannetta S. Steyn, Anil Wipat, Jennifer Hallinan, Matthew Pocock, Rachel May Boyd, Harsh Sheth, Alan Koh, Phil Hall, Deena Tsu, Steven Woodhouse and Younus Essa
 * DSpace, doi: 1721.1/60085

BBF RFC 67: Detailed Information Standard

 * by Peter Culviner, Nathaniel Pantalone, Mary Sagstetter, Sarah Sandock, Justin Vrana, Yue Wu
 * DSpace, 1721.1/60094

BBF RFC 68: Standard for the Electronic Distribution of SBOLv Diagrams

 * by Jeff Johnson, Michal Galdzicki, Herbert Sauro
 * DSpace, doi: 1721.1/60086

BBF RFC 69: A New Standard to Connect BioBrick&trade; Parts for Precise Extraction of an Enzyme Digestion Product

 * by Kousuke Uekusa and Seiko Iguchi
 * DSpace, doi: 1721.1/60084

BBF RFC 70: Standard Emulsification assay

 * requested by Pieter van Boheemen and Eva Brinkman

BBF RFC 71: Phage Modification Standard

 * requested by Emily Chang, Eric Finlay, Jason Gao, Kevin Yang, Marianne Park, Melody Wang, Phillip Chu, Shing Hei Zhan, Vicki Ma, Alina Chan, Rafael Saer, Joanne Fox and Eric Lagally

BBF RFC 72: miTuner - a kit for microRNA based gene expression tuning in mammalian cells

 * by Aastha Mathur, Alejandro Macias Torre, Aleksandra Kolodziejczyk, Dmytro Mayilo, Elena Cristiano, Jan-Ulrich Schad, Jude Al Sabah, Laura-Nadine Schuhmacher, Lea Flocke, Lorenz Adlung, Philipp Bayer, Rebecca Berrens, Stefan Neumann, Stefan Kleinsorg, Stephen Krämer, Thomas Uhlig, Xiaoting Wu, Rudolf Pisa, Jens Keienburg, Dirk Grimm and Roland Eils
 * DSpace, doi: 1721.1/60091

BBF RFC 73: miMeasure -- a standard for microRNA binding site characterization in mammalian cells

 * by Aastha Mathur, Alejandro Macias Torre, Aleksandra Kolodziejczyk, Dmytro Mayilo, Elena Cristiano, Jan-Ulrich Schad, Jude Al Sabah, Kathleen Boerner, Laura-Nadine Schuhmacher, Lea Flocke, Lorenz Adlung, Philipp Bayer, Rebecca Berrens, Stefan Neumann, Stefan Kleinsorg, Stephen Krämer, Thomas Uhlig, Xiaoting Wu, Rudolf Pisa, Jens Keienburg, Dirk Grimm and Roland Eils
 * DSpace, doi: 1721.1/60092

===BBF RFC 74: "Biological integrated circuits”—a framework for devices using fixed and variable parts, a methodology for rapid prototyping of systems using these devices, and a notation to describe the resulting devices and systems===
 * requested by Julie E. Norville, Angela M. Belcher, and Thomas F. Knight, Jr.

BBF RFC 75: General updating scheme for the design and construction of assembly vectors that are compatible with BBF RFC28 and Tom Knight's original assembly standard

 * by Sonja Billerbeck, Katharina Zwicky, Moritz Lang, Luzius Pestalozzi, George Rosenberger, Simona Constantinescu, Thanuja Ambegoda, Elsa Sotiriadis
 * DSpace, 1721.1/60090

BBF RFC 76: A Simple Alternative to Shuttle Vector DNA Manipulation by Homologous Recombination in S. cerevisiae

 * requested by Alice Meng, Elaine Chang, Amanda Hay, Brian Landry, Brenden McDearmon, Zachary Knudsen

BBF RFC 77: Promoter and Coding Sequence Considerations for Caenorhabditis elegans and Other Eukaryotes

 * by Chris Palmer and Geoff Halliday
 * DSpace, doi: 1721.1/59851

BBF RFC 78: Novel Normalization Standard using Fluorescence

 * by Syed Habib Tahir Bukhari, Ashwini Rahul Akkineni, Adithya Ananth, Victor Gordeev, Svea Grieb, Sarah Mansour, Mareike Roth, Charanya Sampathkumar, Lucas Schirmer, Jonathan Tam
 * DSpace, doi: 1721.1/60087

BBF RFC 79: Construction a RBS library with different translational activity

 * by Hsiao-Ching Lee
 * DSpace, 1721.1/60088


 * }
 * }

BioBrick&trade; Research and Development
The BioBricks Foundation delivers its BioBrick&trade; Research and Development in two ways. First, we do this through technical standards related to measurement of genetic functions inside cells via the BioBricks Foundation's partnership with BIOFAB. The BIOFAB: International Open Facility Advancing Biotechnology (BIOFAB) was founded in December 2009 as the world's first biological design-build facility. This professionally staffed public-benefit facility was initiated by a grant from the National Science Foundation (NSF) and is led by bioengineers from UC Berkeley and Stanford University. The BIOFAB is operated in partnership with Lawrence Berkeley National Laboratory (LBNL), the BioBricks Foundation (BBF), and the Synthetic Biology Engineering Research Center (SynBERC). The second way we deliver our BioBrick&trade; Research and Development is through our coordination of the BIOFAB's industrial partners program.