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Browsing Requests for Comments (RFCs) by Title

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  • Abbreviated BioBrick Prefix and Suffix for More Efficient Primer Design 
    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 (2010-10-31)
    This Request for Comments (RFC) modifies the assembly standard for biological parts proposed in BBF RFC 10 by removing the NotI restriction site from the BioBrick Prefix and Suffix.
  • BBF RFC 16: Synthetic Biology Open Language Visual (SBOLv) Specification 
    Rodriguez, Cesar; Bartram, Suzie; Ramasubramanian, Anusuya; Endy, Drew (2009-11-01)
    Synthetic Biology Open Language Visual (SBOLv) is a graphical notation that supports biological device development. It provides a formal notation for describing the physical composition of basic parts into composite ...
  • BBF RFC 21: BglBricks Assembly Standard 
    Anderson, J Christopher; Dueber, John E; Leguia, Mariana; Wu, Gabriel C; Goler, Jonathan A; Arkin, Adam P; Keasling, Jay D (2009-09-18)
    The BglBricks standard has been developed as an alternative to the original XbaI/SpeI standard primarily to provide a solution to the issue of generating translational-fusion parts. When joined together in a standard ...
  • BBF RFC 26: In-Fusion BioBrick Assembly 
    Sleight, Sean (2009-07-09)
    This BioBricks Foundation Request for Comments (BBF RFC) describes a method to assemble two BioBricks using the Clontech In-Fusion PCR Cloning Kit while maintaining BioBrick standard formats.
  • BBF RFC 28: A method for combinatorial multi-part assembly based on the Type IIs restriction enzyme AarI 
    Peisajovich, Sergio G.; Horwitz, Andrew; Hoeller, Oliver; Rhau, Benjamin; Lim, Wendell (2009-09-16)
    This BioBricks Foundation Request for Comments (BBF RFC) describes an alternative assembly standard based on the Type IIS restriction enzyme AarI.
  • BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data 
    Grunberg, Raik (2009-04-24)
    This Request for Comments (RFC) suggests a framework for the description, exchange and interlinking of Synthetic Biology data. The framework would create an open process for the evolution and “rolling” standardization ...
  • BBF RFC 36: Fusion protein BioBrick assembly standard with optional linker extension 
    Jerala, Roman (2009-09-01)
    This RFC 36 describes an extension of the original BioBrick assembly standard (BBF RFC 10) and Freiburg assembly standard (BBF RFC 25). The Fusion Assembly strategy described here is fully compatible with RFC 25 (Freiburg) ...
  • BBF RFC 37: Fusion protein BioBrick assembly standard with optional linker extension 
    Bencina, Mojca; Jerala, Roman (2009-09-02)
    This RFC 37 describes an extension of the original BioBrick assembly standard (BBF RFC 10) and Freiburg assembly standard (BBF RFC 25). The Fusion Assembly strategy described here is fully compatible with RFC 25 (Freiburg) ...
  • BBF RFC 38: RFC 38: Building Blocks - Standard Large DNA/Genome Construction 
    DiCarlo, James; Boeke, Jef (2009-10-07)
    The physical assembly of standard parts is currently a non-standard process, which can either come from direct genome PCR with restriction enzyme sites incorporated into the PCR primers, or overlap assembly PCR. ...
  • BBF RFC 47: BioBytes Assembly Standard 
    Ellison, Michael; Ridgway, Doug; Fedor, Justin; Garside, Erin; Robinson, Kelly; Lloyd, David (2009-10-29)
    The BioBytes assembly method provides a new high-throughput way of assembling plasmids as well as other large DNA constructs. Using a bead-linked assembly of genetic parts with long (12 bp) standardized sticky ends, ...
  • BBF RFC 56: “Part Flavors” For Peptide-Coding Parts 
    Anderson, J. Chris (2010-10-11)
    “Part Flavors” are a means of describing the grammatical properties of parts. Specifically, this is introduced as a means of describing parts that encode peptides (CDS parts), but there may be value to extrapolating the ...
  • "BioSandwich", a homology-based assembly method using a library of standard parts 
    Abbas, Yassen; Crossman, Allan; Fletcher, Eugene; French, Chris; Gibson, Clare; Isapanie, Sylvia; Kopec, Lukasz; Lee, Mun Ching; Li, Di; Tynan-O'Mahony, Fionn (2011-10-17)
    This Request for Comments (RFC) describes a strategy for using homology-based assembly methods to assemble parts from a library in any order.
  • Bioscaffold-Linker 
    Mina, Petros; Savery, Nigel (2009-10-21)
    Protein fusions are currently not supported by most assembly standards. This assembly standard aims to provide the basis of a solution to a biobrick-friendly protein fusion mechanism that supports the current favorite ...
  • Building Protein Domain Based Composite Biobricks for Mammalian Expression Systems 
    Balint, Balint L; Keret, Ophir; Brazda, Peter; Demeny, Mate; 2010 Debrecen-Hungary, iGEM (2010-12-05)
    The purpose of this RFC is to describe a method that allows the design of protein domain based parts, starting with gene centered information and translate these informations into BBF RFC 25 compatible part. The method is ...
  • Cloning Standard for Mammalian BioBrick Parts and Devices 
    Bartoschek, Michael; Mugahid, Douaa; Rademacher, Anne; Meyer, Hannah; Velten, Lars; Reis, Yara; Keienburg, Jens; Eils, Roland (2009-10-21)
    To introduce a common cloning standard for BioBrick parts that find application in mammalian cells.
  • Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts 
    Che, Austin (2009-03-30)
    This Request for Comments (RFC) modifies the assembly standard for biological parts proposed in BBF RFC 10 by replacing PstI with SbfI and dropping other sequence constraints. This change relaxes the constraints on the ...
  • Construction a RBS library with different translational activity 
    Lee, Hsiao-Ching (2010-12-05)
    The first step in programming and controlling cell behavior is to establish a library of well-defined components, a.k.a. "biobricks", that serve as the building blocks of artificial gene networks. The main challenge in ...
  • Conversion of Freiburg (Fusion) Biobricks to the Silver (BioFusion) format 
    Grunberg, Raik (2009-03-30)
    This Request for Comments (RFC) describes a strategy for converting Biobricks from the Freiburg (aka Fusion) format to the Silver lab (aka BioFusion) format.
  • Creating native registry functions to accommodate mutant libraries 
    Xu, Kenneth O.; Walters, Eric M. (2011-12-29)
    The current registry system accommodates normal parts fairly well but has difficulty when adding mutant libraries. If all mutant offspring were added as new parts, the registry would be comprehensive but the parts registry ...
  • Design of Specific Mammalian Promoters by in silico Prediction 
    Heinemann, Tim; Kramer, Stephen; Velten, Lars; Kranz, Anna-Lena; Bauer, Tobias; Faura, Marti Bernardo; Konig, Rainer; Keienburg, Jens; Eils, Roland; Iwamoto, Nao (2009-10-30)
    The purpose of this RFC is to provide a) a method for the design of rational synthetic promoter sequences based on a statistical analysis about the spatial preference of transcription factor binding sites in human promoter ...
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