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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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  • Bartley, Bryan; Beal, Jacob; Clancy, Kevin; Misirli, Goksel; Roehner, Nicholas; Sauro, Herbert; Oberortner, Ernst; Madsen, Curtis; Pocock, Matthew; Wipat, Anil; Nguyen, Tramy; Zhang, Zhen; Myers, Chris; Gennari, John H.; Bissell, Michael (2015-09-07)
    The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information in synthetic biology, filling a need not satisfied by other pre-existing ...
  • Haddock, Traci L.; Densmore, Douglas M.; Appleton, Evan; Carr, Swati; Iverson, Sonya; De Freitas, Monique; Jin, Shawn; Awtry, Jake; Desai, Devina; Lozanoski, Thomas; Shah, Pooja; Agarwal, Yash; Lewis, Kathleen; Pacheco, Alan (2015-08-28)
    This RFC94 describes an assembly standard based on the Type IIS restriction enzymes BsaI and BbsI (also called BpiI). This assembly standard is based upon the Modular Cloning (MoClo) assembly strategy, which was introduced ...
  • Beal, Jacob; Endy, Drew; Grewal, David; Johnson, Richard; Kahl, Linda (2015-08-28)
    In this BioBricks Foundation Request for Comments (BBF RFC), we update and clarify the copyright and licensing notice of BBF RFC documents.
  • Trubitsyna, Maryia; Chan, Karen; Cai, Yizhi; Elfick, Alistair; French, Chris (2015-03-17)
    This BioBrick Foundation Request for Comments (BBF RFC 104) describes a new approach to multiple part DNA assembly – BrickClip, which does not require use of any restriction enzymes, nor cloning of the parts to specific ...
  • Rutten, Virginia; Munabi, Angelina; Riche, Fergus; Lewy, Guy; Wilson, Hugh; Pipan, Miha; Bhate, Salil; Nghiem, Trang-Anh; Kaufhold, Will; Haseloff, Jim; Rubert, Alba; González, Alejandra; Quijano, Alfredo; Llopis, Ivan; Gavaldá, Jose; Estellés, Lucía; Vásquez, Marta; Orzáez, Diego; Deal, Cara; Gray, Jessica; Spiegel, Mischa; Monsey, Steven; Middlemiss, Alistair; Day, Jack; Patron, Nicola (2015-03-17)
    Here we define a standard syntax for assembling standard parts for expression in plant cells, extensible to all other eukaryotes. Variations of the Type IIS mediated cloning method known as Golden Gate Cloning, most notably ...
  • Ahlmann-Eltze, Constantin; Bunne, Charlotte; Büscher, Magdalena; Gleixner, Jan; Horn, Max; Huhn, Anna; Klughammer, Nils; Kreft, Jakob; Schäfer, Elisabeth; Schmelas, Carolin; Schmitz, Silvan; Waldhauer, Max; Bayer, Philipp; Krämer, Stephen; Neugebauer, Julia; Wehler, Pierre; Beaudouin, Joel; Di Ventura, Barbara; Eils, Roland (2015-03-17)
    This Request for Comments (RFC) proposes a new standard that allows for easy and flexible cloning of intein constructs and thus makes this technology accessible to the synthetic biology community.
  • Wang, Lingjue; Tong, Yin; Zhou, Liqun; Ni, Zhuangdian; Zhu, Xiaodan; Li, Hanrun (2013-11-01)
    This Request for Comments (RFC) describes a new framework for standardize logic gene relations among gene circuits. Each type of logic module in gene circuit can be summarized in a standard device in electronics. In this ...
  • Wang, Lingjue; Zhu, Xiaodan; Li, Hanrun; He, Huiyu; Ni, Zhuangdian; Zhou, Liqun (2013-10-29)
    Current, there is well adopted documentation of biobricks. The Registry of Standard Biology Part set the standard documentation for biobrick. However, there is no standard way to document a genetic circuit, what information ...
  • Hammerling, Michael J.; Gottel, Neil R.; Alnahas, Razan N.; Slater, Ben; Huang, Yunle; Okasheh, Yousef; Howard, Marco; Mortensen, Catherine; Monk, Jordan; Detelich, Madeline; Lannan, Ryan S.; Pitaktong, Areen; Weaver, Evan; Das, Siddharth; Barrick, Jeffrey E. (2013-10-06)
    The discipline of synthetic biology emphasizes the application of engineering principles such as standardization, abstraction, modularity, and rational design to complex biological systems. The archetypical example of such ...
  • Gasiūnaitė, Lina; Lewicka, Aleksandra; Pashkuleva, Hristiana; Villanueva, Hugo; Thornton, Harry; Trubitsyna, Maryia; French, Chris (2013-10-04)
    This BioBricks Foundation Request for Comments (BBF RFC) describes a novel approach, GenBrick, for the rapid assembly of multiple BioBrick RFC10-compatible parts in a single reaction, with completely flexible part order, ...
  • Wolf, Christopher; Albrecht, Florian; Brüggenthies, Johanna; Brunner, Andreas; Ciccone, Rosario; Fischer, Katrin; Froehlich, Fabian; Funke, Louise; Morath, Volker; Polte, Ingmar; Reichart, Leonie; Schneider, Philipp; Truong, Jeffery (2013-10-04)
    For protein-encoding BioBricks a large number of useful parameters, such as the amino acid sequence or the molecular weight, can easily be computed. Furthermore alignments against databases and predictions of various ...
  • Beer, Ralf; Christiansen, Tania; Herbst, Konrad; Ignatiadis, Nikolaos; Kats, Ilia; Kurzawa, Nils; Meichsner, Johanna; Rabe, Sophie; Riedel, Anja; Sachs, Joshua; Schessner, Julia; Schmidt, Florian; Walch, Philipp; Adlung, Lorenz; Genereith, Katharina; Georgi, Fanny; Heinemann, Tim; Meyer, Hannah; Niopek, Dominik; Di Ventura, Barbara; Eils, Roland (2013-10-04)
    The purpose of this RFC is to provide instructions for a rapid and cost efficient cloning and transformation method which allows for the manufacturing of multi-fragment plasmid constructs in a parallelized manner: High ...
  • Beer, Ralf; Christiansen, Tania; Herbst, Konrad; Ignatiadis, Nikos; Kats, Ilia; Kurzawa, Nils; Meichsner, Johanna; Rabe, Sophie; Riedel, Anja; Sachs, Joshua; Schessner, Julia; Schmidt, Florian; Walch, Philipp; Adlung, Lorenz; Genreith, Katharina; Georgi, Fanny; Heinemann, Tim; Meyer, Hannah; Niopek, Dominik; Di Ventura, Barbara; Eils, Roland (2013-10-04)
    The purpose of this RFC is to introduce a standardized framework for the engineering of customizable non-ribosomal peptide synthetases (NRPS) and their application for in vivo and in vitro synthesis of short non-ribosomal ...
  • 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.
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
  • 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 ...
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