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Browsing Synthetic Biology by Issue Date

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Browsing Synthetic Biology 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.
  • Integrases, Aliens, & Bill Joy 
    Endy, Drew (2013-03-27)
    Research presentation on recent and unpublished work before the MIT Synthetic Biology Working Group on 24 September 2012 in MIT Building 56.
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • "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.
  • 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.
  • 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 ...
  • Assembly of BioBrick standard biological parts using three antibiotic assembly 
    Shetty, Reshma; Lizarazo, Meagan; Rettberg, Randy; Knight, Thomas F., Jr. (Elsevier Inc., 2011-05-20)
    An underlying goal of synthetic biology is to make the process of engineering biological systems easier and more reliable. In support of this goal, we developed BioBrick assembly standard 10 to enable the construction of ...
  • 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 ...
  • 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, ...
  • 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, ...
  • 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 ...
  • 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 ...
  • Documentation of BioBrick parts 
    Slomp, Arend; Ekkers, David (2010-12-05)
    Purpose of this RFC is to improve the information supplied by BioBrick part vendors. Reason to have this RFC is that there would be much more information available which can help improve the search time of the user. ...
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