The BioBricks Foundation:RFC: Difference between revisions
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===BBF RFC 95: Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques=== | ===BBF RFC 95: Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques=== | ||
* | *by Michael J. Hammerling, Neil R. Gottel, Razan N. Alnahas, Ben Slater, Yunle Huang, Yousef Okasheh, Marco Howard, Catherine Mortensen, Jordan Monk, Madeline Detelich, Ryan S. Lannan, Areen Pitaktong, Evan Weaver, Siddharth Das, and Jeffrey E. Barrick | ||
*[http://hdl.handle.net/1721.1/81334 DSpace], doi: 1721.1/81334 | |||
===BBF RFC 96: The AutoAnnotator - Standardized annotation of protein-encoding BioBricks=== | ===BBF RFC 96: The AutoAnnotator - Standardized annotation of protein-encoding BioBricks=== | ||
* | *by Christopher Wolf, Florian Albrecht, Johanna Brüggenthies, Andreas Brunner, Rosario Ciccone, Katrin Fischer, Fabian Froehlich, Louise Funke, Volker Morath, Ingmar Polte, Leonie Reichart, Philipp Schneider, Jeffery Truong | ||
*[http://hdl.handle.net/1721.1/81330 DSpace], doi: 1721.1/81330 | |||
===BBF RFC 97: Genetic Circuit Standard 1.0=== | ===BBF RFC 97: Genetic Circuit Standard 1.0=== | ||
* | *by Lingjue Wang, Xiaodan Zhu, Hanrun Li, Huiyu He, Zhuangdian Ni, Liqun Zhou | ||
*[http://hdl.handle.net/1721.1/81826 DSpace], doi: 1721.1/81826 | |||
===BBF RFC 98: Genbrick - A Rapid Multi-part Assembly Method for BioBricks=== | |||
*by Lina Gasiūnaitė, Aleksandra Lewicka, Hristiana Pashkuleva, Hugo Villanueva, Harry Thornton, Maryia Trubitsyna, Chris French | |||
*[http://hdl.handle.net/1721.1/81331 DSpace], doi: 1721.1/81331 | |||
===BBF RFC 99: HiCT: High Throughput Protocols for CPE Cloning and Transformation=== | |||
*by Ralf Beer, Tania Christiansen, Konrad Herbst, Nikolaos Ignatiadis, Ilia Kats, Nils Kurzawa, Johanna Meichsner, Sophie Rabe, Anja Riedel, Joshua Sachs, Julia Schessner, Florian Schmidt, Philipp Walch, Lorenz Adlung, Katharina Genereith, Fanny Georgi, Tim Heinemann, Hannah Meyer, Dominik Niopek, Barbara Di Ventura, Roland Eils | |||
*[http://hdl.handle.net/1721.1/81332 DSpace], doi: 1721.1/81332 | |||
===BBF RFC 100: Standard for Synthesis of Customized Peptides by Non-Ribosomal Peptide Synthetases=== | |||
*by Ralf Beer, Tania Christiansen, Konrad Herbst, Nikos Ignatiadis, Ilia Kats, Nils Kurzawa, Johanna Meichsner, Sophie Rabe, Anja Riedel, Joshua Sachs, Julia Schessner, Florian Schmidt, Philipp Walch, Lorenz Adlung, Katharina Genreith, Fanny Georgi, Tim Heinemann, Hannah Meyer, Dominik Niopek, Barbara Di Ventura, Roland Eils | |||
*[http://hdl.handle.net/1721.1/81333 DSpace], doi: 1721.1/81333 | |||
===BBF RFC 101: Logic Gene Module Standard=== | |||
*requested by Yin Tong, Lingjue Wang, Liqun Zhou, Zhuangdian Ni, Xiaodan Zhu, Hanrun Li | |||
*[http://hdl.handle.net/1721.1/81957 DSpace], doi: 1721.1/81957 | |||
===BBF RFC 102: Genetic Circuit Standard 2.0=== | |||
*requested by Mike Wong | |||
===BBF RFC 103: The Michigan Standard=== | |||
*requested by Joshua Abramson | |||
===BBF RFC 104: BrickClip - rapid assembly of multiple RFC10 BioBricks=== | |||
*requested by Maryia Trubitsyna, Karen Chan, Yizhi Cai, Alistair Elfick, Chris French | |||
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Revision as of 07:31, 20 June 2014
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
BBF RFC 94: The Modular Cloning Assembly: Standardized Assembly of Bacterial Transcriptional Units Using Type IIS Restriction Enzymes BsaI and BpiI
BBF RFC 95: Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques
BBF RFC 96: The AutoAnnotator - Standardized annotation of protein-encoding BioBricks
BBF RFC 97: Genetic Circuit Standard 1.0
BBF RFC 98: Genbrick - A Rapid Multi-part Assembly Method for BioBricks
BBF RFC 99: HiCT: High Throughput Protocols for CPE Cloning and Transformation
BBF RFC 100: Standard for Synthesis of Customized Peptides by Non-Ribosomal Peptide Synthetases
BBF RFC 101: Logic Gene Module Standard
BBF RFC 102: Genetic Circuit Standard 2.0
BBF RFC 103: The Michigan Standard
BBF RFC 104: BrickClip - rapid assembly of multiple RFC10 BioBricks
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