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Browsing Requests for Comments (RFCs) by Issue Date

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Browsing Requests for Comments (RFCs) by Issue Date

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  • Synthetic Biology Open Language Visual (SBOL Visual), version 1.0.0 
    Quinn, Jacqueline; Beal, Jacob; Bhatia, Swapnil; Cai, Patrick; Chen, Joanna; Clancy, Kevin; Hillson, Nathan; Galdzicki, Michal; Maheshwari, Akshay; P, Umesh; Pocock, Matthew; Rodriguez, Cesar; Stan, Guy-Bart; Endy, Drew (2013-03-31)
    In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language Visual standard (SBOL Visual) to enable consistent, human-readable depiction of genetic designs.
  • The GoldenBricks assembly: A standardized one-shot cloning technique for complete cassette assembly 
    Pauthenier, Cyrille; El-Sayyed, Hafez; Rostain, William; Cerisy, Tristan; Lopez, Carolina Gallo; Ferreira, Raphael; Moreira, Jorgelindo Da Veiga; Souterre, Tiffany; Eeckhout, Joachim; Nogue, Pierre Yves; Llamosi, Artemis; Parutto, Pierre; Nikolayeva, Iryna; Machat, Mohamed; Marquet, Clement; Młynarczyk, Anna; Thelie, Aurore; Landrain, Thomas; Tolonen, Andrew; Pollet, Nicolas; Faulon, Jean-Loup; Jaramilo, Alfonso (2012-11-05)
    BBF RFC 92 proposes a new standard assembly method for the Parts Registry. The method makes one-shot cloning of a complete eukaryotic or prokaryotic cassette possible in one day while keeping compatibility with the BBF RFC ...
  • The Measurement of rho‐independent Transcription Terminator Efficiency 
    He, Jiankui; Jing, Shui; Zhang, Mengshi; Liu, Xianggeng; Chen, Yao; Qie, Boyu; Shen, Liuxing; Wu, Zishan (2012-10-11)
    The purpose of this RFC is to provide standard methodology for the measurement of the absolute strength of terminators in bacteria. Because we have characterized the performance of terminator in E. coli and used a simple ...
  • Synthetic Biology Open Language (SBOL) Version 1.1.0 
    Galdzicki, Michal; Wilson, Mandy; Rodriguez, Cesar A.; Pocock, Matthew R.; Oberortner, Ernst; Adam, Laura; Adler, Aaron; Anderson, J. Christopher; Beal, Jacob; Cai, Yizhi; Chandran, Deepak; Densmore, Douglas; Drory, Omri A.; Endy, Drew; Gennari, John H.; Grünberg, Raik; Ham, Timothy S.; Hillson, Nathan J.; Johnson, Jeffrey D.; Kuchinsky, Allan; Lux, Matthew W.; Madsen, Curtis; Misirli, Goksel; Myers, Chris J.; Olguin, Carlos; Peccoud, Jean; Plahar, Hector; Platt, Darren; Roehner, Nicholas; Sirin, Evren; Smith, Trevor F.; Stan, Guy-Bart; Villabos, Alan; Wipat, Anil; Sauro, Herbert M. (2012-10-11)
    In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.1.0 to enable the electronic exchange of information describing DNA components used in synthetic ...
  • Yeast Golden Gate: Standardized Assembly of S. cerevisiae Transcriptional Units 
    Boeke, Jef; Mitchell, Leslie; Cai, Yizhi; Stracquadanio, Giovanni; Chuang, James; Tan, Scott; Heston, Margo; Wang, Jiarui; Kim, Dong Won; Noronha, Anne Marie (2012-10-11)
    BBF RFC 88 describes a new standard for the assembly of basic Saccharomyces cerevisiae transcriptional units (TUs) consisting of a promoter/5’untranslated region (UTR), open reading frame (ORF), and 3’UTR/terminator. Note ...
  • The minimum information for a qualified BioBrick 
    Zhou, Mubing; Zhang, Junqiu; He, Jiankui (2012-10-11)
    Since the information of many existing BioBricks is incomplete, thus the usage of the BioBricks will be affected. It is necessary to standardize the minimum information required for a qualified BioBrick. Furthermore this ...
  • 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 ...
  • PCR - Ligation Assembly Standard for BioBrick Parts 
    He, Tony PeiYuan; Campbell, Alexander; Zhou, Stefanie Yifan (2011-12-15)
    This Request for Comments (RFC) describes a novel method for the assembly of standard BioBrick parts. This assembly method for BioBrick parts is an improvement upon the conventional methods of BioBrick part assembly. This ...
  • Reusable rapid assembly of genetic parts for Neurospora crassa 
    Odsen, Raymond; Baretta, Kayla; Zakrewski, Helena; Simpson, Michael; Guo, Yuan; Pelech, Murray; Foster, Adam; Ridgway, Douglas; Ellison, Michael (2011-10-17)
    This BBF RFC provides a method in which standardized parts can be easily created for Neurospora crassa.
  • "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.
  • Title: Synthetic Biology Open Language (SBOL) Version 1.0.0 
    Wipat, Anil; Villalobos, Alan; Stan, Guy-Bart; Smith, Trevor; Sauro, Herbert; Roehner, Nicholas; Pocock, Matthew; Plahar, Hector; Peccoud, Jean; Myers, Chris; Misirli, Goksel; Madsen, Curtis; Lux, Matthew; Kuchinsky, Allan; Ham, Timothy; Grünberg, Raik; Gennari, John; Endy, Drew; Drory, Omri; Densmore, Douglas; Chandran, Deepak; Beal, Jacob; Anderson, J. Christopher; Adler, Aaron; Adam, Laura; Rodriguez, Cesar; Wilson, Mandy; Galdzicki, Michal (2011-10-03)
    In this BioBricks Foundation Request for Comments (BBF RFC), we specify the Synthetic Biology Open Language (SBOL) Version 1.0.0 to enable the electronic exchange of information describing DNA components used in synthetic ...
  • Standard for the Electronic Distribution of SBOLv Diagrams 
    Johnson, Jeffrey; Galdzicki, Michal; Sauro, Herbert M (2010-12-05)
    A common method for publicly distributing design diagrams on the Web would enhance understanding of the mechanisms and intended function of synthetic DNA constructs. We aim to improve the usefulness of the depicted design ...
  • Novel Normalization Standard using Fluorescence 
    Bukhari, Syed Habib Tahir; Akkineni, Ashwini Rahul; Ananth, Adithya; Gordeev, Victor; Grieb, Svea; Mansour, Sarah; Roth, Mareike; Sampathkumar, Charanya; Schirmer, Lucas; Tam, Jonathan (2010-12-05)
    The Biotec_Dresden Team 2010 developed an approach where two fluorescent proteins are simultaneously expressed. The fact that one reporter, in our case RFP, is constitutively expressed allows to monitor cell growth. Secondly, ...
  • 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 ...
  • miMeasure – a standard for miRNA binding site characterization in mammalian cells 
    Adlung, Lorenz; Sabah, Jude Al; Bayer, Philipp; Berrens, Rebecca; Cristiano, Elena; Flocke, Lea; Kleinsorg, Stefan; Kolodziejczyk, Aleksandra; Kraemer, Stephen; Torre, Alejandro Macias; Mathur, Aastha; Mayilo, Dmytro; Neumann, Stefan; Niopek, Dominik; Pisa, Rudolf; Schad, Jan-Ulrich; Schumacher, Laura-Nadine; Uhlig, Thomas; Wu, Xiaoting; Keienburg, Jens; Boerner, Kathleen; Grimm, Dirk; Eils, Roland (2010-12-05)
    This RFC proposes a standard for the quantitative characterization of miRNA binding sites (miRNA-BS) in mammalian cells. The miMeasure standard introduces a ready-to-use standard measurement plasmid (pSMB_miMeasure, ...
  • A New Standard to Connect BioBrick Parts for Precise Extraction of an Enzyme Digestion Product 
    Uekusa, Kousuke; Iguchi, Seiko (2010-12-05)
    This BioBricks Foundation Request for Comments (BBF RFC) introduces a new standard to connect BioBrick parts using BglI site.
  • Measurement of bacterial promoter absolute activity and determination of dynamic performance in cell-free expression system by qPCR 
    Olchowik, Anna; Lower, Michal; Moreno, Cherry; Pankowski, Jaroslaw (2010-12-05)
    The purpose of this RFC is to provide standard methodology for the measurement of the absolute strength of bacterial promoters. The absolute activity can be experimentally measured in Moles of RNA per Moles of DNA in time, ...
  • Open licensing of BioBrick parts 
    Lower, Michal; Olchowik, Anna; Pankowski, Jaroslaw; Bazlekowa, Milena; Blaszkiewicz, Marta; Cysewski, Dominik; Koper, Kamil; Lesczynska, Joanna; Moreno, Cherry; Pulawska, Anna (2010-12-05)
    This document provides recommendations for licensing of community-created biological parts, especially in BioBrick standard.
  • Recombination Based Part Assembly 
    Deming, Laura; Slusarczyk, Adrian; Jiao, Yunxin; iGEM, 2010 MIT (2010-12-05)
    Here we propose a new recombination-based assembly standard, optimized to allow for efficient cloning of mammalian vectors.
  • A RESTful API for Supporting Automated BioBrick Model Assembly 
    Steyn, J S; Boyd, R M; Essa, Y; Hall, P; Koh, A; Sheth, H; Tsu, D; Woodhouse, S; Hallinan, J; Wipat, A; Pocock, M R (2010-12-05)
    Constructing simulatable models for BioBricks by hand is a complex and time-consuming task. The time taken could be reduced by using Computer Aided Design (CAD) tools to aid in designing models, but these tools need to be ...
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