The BioBricks Foundation:RFC: Difference between revisions
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Currently, the [http://biobricks.org BioBricks Foundation] 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. | |||
<h1>The BioBrick™ RFC Process</h1> | <h1>The BioBrick™ RFC Process</h1> | ||
<div style="clear: left; text-align: left; float: left; padding: .4em .9em .9em"> | <div style="clear: left; text-align: left; float: left; padding: .4em .9em .9em"> | ||
Through its BioBrick™ RFC Process, the BioBricks Foundation hosts discussions and editorial work around the development of technical standards. Our BioBrick™ RFC list contains | 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 (Request for Comments) Process, the BioBricks Foundation hosts discussions and editorial work around the development of technical standards. Our BioBrick™ RFC list contains 90+ technical documents to date. Through the BioBrick™ RFC Process, we also host an email discussion list. | |||
An RFC might | An RFC might | ||
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*by Hsiao-Ching Lee | *by Hsiao-Ching Lee | ||
*[http://hdl.handle.net/1721.1/60088 DSpace], doi: 1721.1/60088 | *[http://hdl.handle.net/1721.1/60088 DSpace], doi: 1721.1/60088 | ||
===BBF RFC 80: Plug 'n' Play with DNA=== | ===BBF RFC 80: Plug 'n' Play with DNA=== | ||
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===BBF RFC 87: Synthetic Biology Open Language (SBOL) Version 1.1.0=== | ===BBF RFC 87: Synthetic Biology Open Language (SBOL) Version 1.1.0=== | ||
* | *by Michal Galdzicki et al. | ||
*[http://hdl.handle.net/1721.1/73909 DSpace], doi: 1721.1/73909 | |||
===BBF RFC 88: The Golden Gate Standard=== | ===BBF RFC 88: The Golden Gate Standard=== | ||
* | *by Jef Boeke, Leslie Mitchell, Yizhi Cai, Giovanni Stracquadanio, James Chuang, Scott Tan, Margo Heston, Jiarui Wang, Dong Won Kim and Anne Marie Noronha | ||
*[http://hdl.handle.net/1721.1/73912 DSpace], doi: 1721.1/73912 | |||
===BBF RFC 89: The minimum information for a qualified BioBrick=== | ===BBF RFC 89: The minimum information for a qualified BioBrick=== | ||
* | *by Mubing Zhou, Junqiu Zhang and Jiankui He | ||
*[http://hdl.handle.net/1721.1/73910 DSpace], doi: 1721.1/73910 | |||
===BBF RFC 90: The Measurement of rho-independent Transcription Terminator Efficiency=== | ===BBF RFC 90: The Measurement of rho-independent Transcription Terminator Efficiency=== | ||
* | *by Jiankui He, Shui Jing, Mengshi Zhang, Xianggeng Liu, Yao Chen, Boyu Qie, Liuxing Shen, and Zishan Wu | ||
*[http://hdl.handle.net/1721.1/73911 DSpace], doi: 1721.1/73911 | |||
===BBF RFC 91: Phosphorothioate-based BioBrick cloning (Potsdam) Standard=== | |||
*requested by iGEM Team Potsdam 2012, Tobias Baumann, Kristian M. Müller | |||
===BBF RFC 92: The GoldenBricks assembly: A standardized one-shot cloning technique for complete cassette assembly=== | |||
*by Cyrille Pauthenier, Hafez El-Sayyed, William Rostain, Tristan Cerisy, Carolina Gallo Lopez, Raphael Ferreira, Jorgelindo Da Veiga Moreira, Tiffany Souterre, Joachim Eeckhout, Pierre Yves Nogue, Artémis Llamosi, Pierre Parutto, Iryna Nikolayeva, Mohamed Machat, Clément Marquet, Anna Młynarczyk, Aurore THELIE, Thomas Landrain, Andrew Tolonen, Nicolas Pollet, Jean-Loup Faulon, Alfonso Jaramillo | |||
*[http://hdl.handle.net/1721.1/74561 DSpace], doi: 1721.1/74561 | |||
===BBF RFC 93: Synthetic Biology Open Language Visual (SBOL Visual) Version 1.0.0=== | |||
*by Jacqueline Quinn, Jacob Beal, Swapnil Bhatia, Patrick Cai, Joanna Chen, Kevin Clancy, Nathan Hillson, Michal Galdzicki, Akshay Maheshwari, Umesh P, Matthew Pocock, Cesar Rodriguez, Guy-Bart Stan, Drew Endy | |||
*[http://hdl.handle.net/1721.1/78249 DSpace], doi: 1721.1/78249 | |||
</div> | </div> | ||
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Revision as of 10:54, 31 March 2013
Currently, the BioBricks Foundation 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:
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. The BioBrick™ RFC ProcessThe 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.
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 90+ technical documents to date. Through the BioBrick™ RFC Process, we also host an email discussion list. An RFC might
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.
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
BBF RFC 52: Information Standard for BioBrick™ Parts
BBF RFC 53: USTC MetaPart Assembly Standard -- Extending RFC 10 to Enable Scarless Protein Fusion with Type IIS Restriction Enzyme EarI and SapI
BBF RFC 54: Abbreviated BioBrick™ Prefix and Suffix for More Efficient Primer Design
BBF RFC 55: Standard Biological Part Automatic Modeling Database Language (MoDeL)
BBF RFC 56: “Part Flavors” For Peptide-Coding Parts
BBF RFC 57: Assembly of BioBricks by the Gibson Method
BBF RFC 58: Absolute measurement of bacterial promoter strength in cell-free system by qPCR
BBF RFC 59: Quantitative measurement of mamallian cell invasion by bacteria using flow cytometry
BBF RFC 60: Open licensing of BioBrick™ parts
BBF RFC 61: Fast multiple gene fragment ligation method based on Type IIs restriction enzyme DraIII
BBF RFC 62: Fast multiple gene fragment ligation method based on homologous recombination
BBF RFC 63: DTU Synthetic Promoter Library Standard
BBF RFC 64: Building Protein Domain Based Composite BioBricks
BBF RFC 65: Recombination Based Part Assembly
BBF RFC 66: A RESTful API for Supporting Automated BioBrick Model Assembly
BBF RFC 67: Detailed Information Standard
BBF RFC 68: Standard for the Electronic Distribution of SBOLv Diagrams
BBF RFC 69: A New Standard to Connect BioBrick™ Parts for Precise Extraction of an Enzyme Digestion Product
BBF RFC 70: Standard Emulsification assay
BBF RFC 71: Phage Modification Standard
BBF RFC 72: miTuner - a kit for microRNA based gene expression tuning in mammalian cells
BBF RFC 73: miMeasure -- a standard for microRNA binding site characterization in mammalian cells
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
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
BBF RFC 76: A Simple Alternative to Shuttle Vector DNA Manipulation by Homologous Recombination in S. cerevisiae
BBF RFC 77: Promoter and Coding Sequence Considerations for Caenorhabditis elegans and Other Eukaryotes
BBF RFC 78: Novel Normalization Standard using Fluorescence
BBF RFC 79: Construction a RBS library with different translational activity
BBF RFC 80: Plug 'n' Play with DNA
BBF RFC 81: "BioSandwich" - a homology based assembly method using a library of standard parts
BBF RFC 82: Reusable rapid assembly of genetic parts for Neurospora crassa
BBF RFC 83: PCR - Ligation Assembly Standard for BioBrick Parts
BBF RFC 84: Synthetic Biology Open Language (SBOL) Version 1.0.0
BBF RFC 85: A method for making constructs with interchangeable regions in the middle
BBF RFC 86: Creating native registry functions to accommodate mutant libraries
BBF RFC 87: Synthetic Biology Open Language (SBOL) Version 1.1.0
BBF RFC 88: The Golden Gate Standard
BBF RFC 89: The minimum information for a qualified BioBrick
BBF RFC 90: The Measurement of rho-independent Transcription Terminator Efficiency
BBF RFC 91: Phosphorothioate-based BioBrick cloning (Potsdam) Standard
BBF RFC 92: The GoldenBricks assembly: A standardized one-shot cloning technique for complete cassette assembly
BBF RFC 93: Synthetic Biology Open Language Visual (SBOL Visual) Version 1.0.0
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