Technical Standards Framework

Currently, the BBF is charting a technical standards framework that will serve as the driver and promoter of a high-quality, technical-standards process for synthetic biology based on BioBrick™ parts. It is envisaged that the framework will include the following components:

  • Teaching people, facilitation, and management of community
  • Creating a mechanism for deprecation, promotion, and screening of standard biological parts
  • Providing improved and expanded soft coupling to rewards for quality standards
  • Developing a protocol for dealing with property rights around technical standards
  • Recognizing and celebrating participants.

The BBF was formed to reduce the complexity and cost of producing synthetic living organisms by leveraging time-honored engineering principles of abstraction and standardization. This blend of technology and biology makes it easier for scientists and engineers to work together to develop practical solutions for serious problems facing mankind. A global community initiative, the BBF engages young scientists and engineers, is supported by world-leading institutes and consists of an infrastructure with four key components:

One – Physical assembly standard — changing the sequence of DNA; the resulting reference sequence is compatible with one or more assembly standards.

Two – Reference standard — for making measurements. The BBF is doing this for in vivo genetic functions.

Three – Functional composition standard — What makes a nut fit with a bolt? If they fit its physical assembly; if they stick together when you pull, it’s functional composition.

Four – Data exchange formats — The BBF wants a standard exchange of information with regard to biological parts; we want it to be available openly.

If it’s not compatible in all four ways, it is necessary to explicitly state that it is not compatible.

RFC Process

The BioBricks Foundation is available to provide research and development through our BioBrick™ R&D Services. Give us a call at 650-799-9851.

The BioBricks Foundation delivers its BioBrick™ Research and Development in two ways.

  1. 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).
  2. The second way we deliver our BioBrick™ Research and Development is through our coordination of the BIOFAB’s industrial partners program.

Through its BioBrick™ RFC (Request for Comments) Process, the BioBricks Foundation hosts discussions and editorial work around the development of technical standards. Our BioBrick™ RFC list contains 50+ technical documents to date. Through the BioBrick™ RFC Process, we also host an email discussion list.

An RFC might

  1. propose a standard of some sort (i.e. Tom Knight’s 2003 BioBrick™ physical assembly standard or the Freiburg protein fusion assembly standard)
  2. describe best practices or protocols (i.e. a protocol for assembling two parts)
  3. provide information (i.e. a description of how to design transcriptional terminators)
  4. 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:

The complete list of all assigned RFC numbers and RFC documents (for those submitted) is listed below.

Contents

[edit] 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

[edit] BBF RFC 1: Definition of the nature of a part

  • requested by Kristian Müller and Katja Arndt

[edit] BBF RFC 2: The information stored with a with a part

  • requested by Kristian Müller and Katja Arndt

[edit] BBF RFC 3: Restriction sites for the construction of fusion proteins

  • requested by Kristian Müller and Katja Arndt

[edit] BBF RFC 4: Synthetic Biology Diagram Standard

  • requested by Mackenzie Cowell

[edit] BBF RFC 5: BioBrick™ Placeholders

  • requested by George McArthur IV and Daniel R Tarjan

[edit] BBF RFC 6: Synthetic Terminators for Transcription Attenuation

  • requested by George McArthur IV and Daniel R Tarjan

[edit] 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

[edit] BBF RFC 8: Early BioBrick™ standard design

  • by Tom Knight
  • Early description of a (now defunct) BioBrick™ standard
  • RFC Draft

[edit] 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

[edit] 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

[edit] 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

[edit] 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

[edit] 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

[edit] BBF RFC14: Protein domain fusions in BB-2 assembly

  • by Tom Knight
  • Application of the RFC13 ideas to assembly with BB-2
  • RFC draft

[edit] 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

[edit] 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

[edit] BBF RFC 17: deprecated

[edit] BBF RFC 18: Proposed Conceptual Guidelines for the Design of a BioBrick™ Graphical Language & an Example

[edit] BBF RFC 19: Measuring the Activity of BioBrick™ Promoters Using an In Vivo Reference Standard

  • requested by Jason R Kelly and Drew Endy

[edit] BBF RFC 20: Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts

[edit] 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

[edit] 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

[edit] 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))

[edit] BBF RFC 24: Conversion of Freiburg (Fusion) BioBricks™ to the Silver (BioFusion) format

[edit] 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

[edit] BBF RFC 26: In-Fusion BioBrick™ Assembly

[edit] BBF RFC 27: Fast ligation-free construction of BioBricks™ with PCR & In-Fusion

  • requested by Raik Grünberg

[edit] 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

[edit] BBF RFC 29: Naming of standards of physical composition of BioBrick™ parts

  • by Reshma Shetty and Randy Rettberg
  • DSpace, doi: 1721.1/45137

[edit] BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data

[edit] 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

[edit] 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

[edit] BBF RFC 33: A Core Data Model for Biological System Design

  • requested by Douglas Densmore, J.Christopher Anderson, Timothy Ham, Josh Kittleson, Cesar Rodriquez

[edit] 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

[edit] BBF RFC 35: Context-free grammar representation of design strategies for BioBrick™ constructs

  • requested by Jean Peccoud, Yizhi Cai and Matthew Lux

[edit] BBF RFC 36: deprecated

[edit] 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

[edit] BBF RFC 38: Building Blocks – Standard Large DNA/Genome Construction

  • by Jef Boeke and James DiCarlo
  • DSpace, doi: 1721.1/49417

[edit] 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

[edit] 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

[edit] 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

[edit] 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

[edit] 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

[edit] BBF RFC 44: Bioscaffold-Linker

  • by Petros Mina and Nigel Savery
  • DSpace, doi: 1721.1/49505

[edit] 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

[edit] BBF RFC 46: Large-Scale Peptide Modification on BioBrick™ Proteins

  • by Feng Tian, GuoQiang Chen, Zhao Wang
  • DSpace, doi: 1721.1/49521

[edit] BBF RFC 47: BioBytes Assembly Standard

  • by David Lloyd, Kelly Robinson, Erin Garside, Justin Fedor, Doug Ridgway, Michael Ellison
  • DSpace, doi: 1721.1/49518

[edit] BBF RFC 48: Automatic Biological Circuit Design

  • requested by Wei Pan, Bo Ding, Yu He, Yuwei Cui, Jiahao Li, Xiaomo Yao,

[edit] BBF RFC 49: Draft Characterization Standard for describing Biosensor Sensitivity Tuners

  • requested by James Brown, Vivian Mullin, Megan Stanley, Alan Walbridge

[edit] 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

[edit] BBF RFC 51: Final Expression Vectors for RFC 10 Expression parts

  • requested by Kristian M. Mueller

[edit] BBF RFC 52: Information Standard for BioBrick™ Parts

  • requested by Arend Slomp (a….@igemgroningen.com)

[edit] 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

[edit] BBF RFC 54: Abbreviated BioBrick™ 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

[edit] 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

[edit] BBF RFC 56: “Part Flavors” For Peptide-Coding Parts

  • by Chris Anderson
  • DSpace, doi: 1721.1/59011

[edit] 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

[edit] BBF RFC 58: Absolute measurement of bacterial promoter strength in cell-free system by qPCR

[edit] 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

[edit] BBF RFC 60: Open licensing of BioBrick™ parts

[edit] 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

[edit] 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

[edit] BBF RFC 63: DTU Synthetic Promoter Library Standard

  • requested by Thomas Trolle, Patrick Fortuna, and Martin Malthe Borch

[edit] BBF RFC 64: Building Protein Domain Based Composite BioBricks

  • requested by Balint L. Balint, Ophir Keret, Peter Brazda and Mate Demeny

[edit] BBF RFC 65: Recombination Based Part Assembly

  • requested by Laura Deming, Adrian Lukas Slusarczyk, and Yunxin Jiao

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

  • requested 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

[edit] BBF RFC 67: Detailed Information Standard

  • requested by Peter Culviner, Nathaniel Pantalone, Mary Sagstetter, Sarah Sandock, Justin Vrana, Yue Wu

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

  • requested by Jeff Johnson, Michal Galdzicki, Herbert Sauro

[edit] BBF RFC 69: A New Standard to Connect BioBrick™ Parts for Precise Extraction of an Enzyme Digestion Product.”

  • requested by Kousuke Uekusa and Seiko Iguchi

[edit] BBF RFC 70: Standard Emulsification assay

  • requested by Pieter van Boheemen and Eva Brinkman

[edit] 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

[edit] BBF RFC 72: miTuner – a kit for microRNA based gene expression tuning in mammalian cells

  • requested 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

[edit] BBF RFC 73: miMeasure — a standard for microRNA binding site characterization in mammalian cells

  • requested 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

[edit] 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.

[edit] 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

  • requested by Sonja Billerbeck, Katharina Zwicky, Moritz Lang, Luzius Pestalozzi, George Rosenberger, Simona Constantinescu, Thanuja Ambegoda, Elsa Sotiriadis

[edit] 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

[edit] BBF RFC 77: Promoter and Coding Sequence Formats for C. elegans

  • requested by Chris Palmer and Geoff Halliday

[edit] BBF RFC 78: Novel Normalization Standard using Fluorescence

  • requested by Syed Habib Tahir Bukhari, Ashwini Rahul Akkineni, Adithya Ananth, Victor Gordeev, Svea Grieb, Sarah Mansour, Mareike Roth, Charanya Sampathkumar, Lucas Schirmer, Jonathan Tam

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

  • requested by Hsiao-Ching Lee

[edit]

 

 

 

 

 

 

 

The BioBricks Foundation is available to provide research and development through our BioBrick™ R&D Services. Give us a call at 650-799-9851. The BioBricks Foundation delivers its BioBrick™ 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™ Research and Development is through our coordination of the BIOFAB’s industrial partners program.

 

Through its BioBrick™ RFC Process, the BioBricks Foundation hosts discussions and editorial work around the development of technical standards. Our BioBrick™ RFC list contains 50+ technical documents to date. Through the BioBrick™ RFC Process, we also host an email discussion list.

An RFC might

1.propose a standard of some sort (i.e. Tom Knight’s 2003 BioBrick™ physical assembly standard or the Freiburg protein fusion assembly standard)

2.describe best practices or protocols (i.e. a protocol for assembling two parts)

3.provide information (i.e. a description of how to design transcriptional terminators)

4.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

▪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