https://hdl.handle.net/1721.1/43714 2026-04-04T19:56:50Z https://hdl.handle.net/1721.1/111011 BBF RFC #111: Inducible expression vector with His tag fusion for purification of RFC25 parts Husser, Mathieu; Narcross, Lauren; Sundarakrishnan, Adithi This Request For Comments (RFC) describes a new expression vector based on the pET expression system and designed for BioBrick RFC25 parts. This design includes all the features of pET expression vectors with a new origin of replication, resistance marker and Multiple Cloning Site (MCS). This MCS contains new restriction sites and a 5’ poly- histidine tag that allows the purification of expressed RFC25 parts. Previous attempts have been prevented by restriction site incompatibility, but using RFC25 parts and their restriction sites enables 5’ fusion to these parts. This new expression vector enables the cloning of RFC25 parts with a 5’ His tag in a single step. This allows the inducible expression of these parts and the easy purification of protein products. 2017-08-24T00:00:00Z https://hdl.handle.net/1721.1/105278 BBF RFC 112: Synthetic Biology Open Language (SBOL) Version 2.1.0 Beal, Jacob; Cox, Robert Sidney; Grünberg, Raik; McLaughlin, James; Nguyen, Tramy; Macklin, Chris; Bissell, Michael; Madsen, Curtis; Roehner, Nicholas; Oberortner, Ernst; Misirli, Goksel; Clancy, Kevin; Pocock, Matthew; Zhang, Zhen; Myers, Chris; Zhang, Michael; Samineni, Meher; Zundel, Zach; Bartley, Bryan; Choi, Kiri; Gennari, John H.; Sauro, Herbert The Synthetic Biology Open Language (SBOL) has been developed as a standard to support the specification and exchange of biological design information. BBF RFC 112 (the SBOL 2.1.0 standard) replaces BBF RFC 108 (the SBOL 2.0 standard), as well as the minor update SBOL 2.0.1. 2016-11-10T00:00:00Z https://hdl.handle.net/1721.1/98369 BBF RFC 108: Synthetic Biology Open Language (SBOL) Version 2.0.0 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 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 standards. 2015-09-07T00:00:00Z https://hdl.handle.net/1721.1/98267 BBF RFC 94: Type IIS Assembly for Bacterial Transcriptional Units: A Standardized Assembly Method for Building Bacterial Transcriptional Units Using the Type IIS Restriction Enzymes BsaI and BbsI 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 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 in 2011 by Weber et al. [1] and is based upon Golden Gate cloning [2]. In this RFC, we describe our proposed MoClo standard for generating a library of bacterial DNA parts for generating four-part transcriptional units (promoter : 5’UTR : CDS : 3’UTR). In this work, we define 5’UTRs as including ribosomal binding sites (RBS) and bi-cistronic design elements (BCDs) [3], and 3’UTRs as transcriptional terminators. The 2012-2014 BostonU iGEM teams completed this work and a more compact library has also been created based on this work [4]. 2015-08-28T00:00:00Z https://hdl.handle.net/1721.1/98266 BBF RFC 107: Copyright and Licensing of BBF RFCs Beal, Jacob; Endy, Drew; Grewal, David; Johnson, Richard; Kahl, Linda In this BioBricks Foundation Request for Comments (BBF RFC), we update and clarify the copyright and licensing notice of BBF RFC documents. 2015-08-28T00:00:00Z https://hdl.handle.net/1721.1/96071 BBF RFC 105: The Intein standard - a universal way to modify proteins after translation 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 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. 2015-03-17T00:00:00Z https://hdl.handle.net/1721.1/96070 BBF RFC 104: BrickClip – rapid assembly of multiple RFC10 BioBricks Trubitsyna, Maryia; Chan, Karen; Cai, Yizhi; Elfick, Alistair; French, Chris 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 donor and acceptor vectors. BrickClip allows assembly of up to six parts from existing parts collections, including the Registry of Standard Biological Parts, in a single reaction, in any desired order. The resulting product is exactly the same as would be obtained from normal RFC10 BioBrick assembly. In contrast to other commonly used methods such as Gibson assembly, BrickClip does not require ordering new oligonucleotides for each assembly; while assembly oligonucleotides are required, these are part-specific and may be re-used in any assembly involving a given part. BrickClip is a special case of a more general assembly method – PaperClip. 2015-03-17T00:00:00Z https://hdl.handle.net/1721.1/96069 BBF RFC 106: A Standard Type IIS Syntax for Plants 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 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 Golden Braid (GB2.0) and Golden Gate Modular Cloning (MoClo) are in common use, particularly for the assembly of plasmids for delivery to plant cells. Many characterised plant parts compatible with Type IIS mediated assembly are available outside of the Registry of Standard Parts, as well as plasmids with the features necessary for delivery of DNA to plants cells via the shuttle chassis, Agrobacterium tumefaciens. This RFC describes a consensus Type IIS syntax for plant parts to allow assembly into complete eukaryotic transcriptional units in plasmid vectors that contain the necessary features for transfection of plant chassis. We use Marchantia polymorpha, a primitive and easy-to-engineer liverwort and Nicotiana benthamiana a model plant as exemplar chassis. 2015-03-17T00:00:00Z https://hdl.handle.net/1721.1/81957 BBF RFC 101: Logic Gene Module Standard Wang, Lingjue; Tong, Yin; Zhou, Liqun; Ni, Zhuangdian; Zhu, Xiaodan; Li, Hanrun 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 paper, we collect several frequently-used logic modules and the corresponding classic gene structure. 2013-11-01T00:00:00Z https://hdl.handle.net/1721.1/81826 BBF RFC97: Genetic Circuit Standard 1.0 Wang, Lingjue; Zhu, Xiaodan; Li, Hanrun; He, Huiyu; Ni, Zhuangdian; Zhou, Liqun 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 should be included in a description of a genetic circuit. We have therefore develop the technique standard for recording a genetic circuits. This standard will help the sharing of genetic circuits’ information among synthetic biology community. 2013-10-29T00:00:00Z https://hdl.handle.net/1721.1/81334 Open Sequence Initiative: a part submission standard to complement modern DNA assembly techniques 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. 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 standardization is BioBrick RFC[10], introduced in 2003 by Tom Knight at MIT. BioBricks are stored on a standard plasmid, pSB1C3, which contains prefix and suffix sequences flanking the DNA sequence specifying a biological part. The prefix and suffix sequences contain two pairs of 6 base-pair (bp) restriction enzyme sites (EcoRI+XbaI and SpeI+PstI), which can be used for both part assembly and quality control. BioBricks are intended to be well- characterized biological parts, such as genes or promoters, that function in a predictable fashion and can be readily combined to make complex systems. The rules of the RFC[10] BioBrick assembly method require that none of the restriction sites used in the prefix and suffix be present in the parts themselves. This requirement can be an onerous imposition for iGEM teams developing large, novel parts, such as genes or entire operons that are obtained by amplifying DNA sequences from environmental samples or microorganisms. While iGEM teams may use methods such as site-directed mutagenesis to remove illegal restriction sites from a part's sequence, it is certainly possible that this mutation will alter the functionality of the part – a very undesirable outcome. In addition, the mutagenesis of illegal restriction sites is an unnecessary burden on teams, given the limited time and resources available to teams during each year’s iGEM competition. Efforts spent mutagenizing sites would be better spent characterizing and improving parts. This RFC proposes an alternative submission standard to eliminate these problems. 2013-10-06T00:00:00Z https://hdl.handle.net/1721.1/81333 Standard for Synthesis of Customized Peptides by Non-Ribosomal Peptide Synthetases 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 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 peptides (NRPs) of user-defined sequence and structure. 2013-10-04T00:00:00Z https://hdl.handle.net/1721.1/81332 HiCT: High Throughput Protocols For CPE Cloning And Transformation 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 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 Throughput Circular Extension Cloning and Transformation (HiCT). Description of construct libraries generated by the HiCT method can be found at http://2013.igem.org/Team:Heidelberg/Indigoidine. This RFC also points out further optimization strategies with regard to construct stability, reduction of transformation background and the generation of competent cells. 2013-10-04T00:00:00Z https://hdl.handle.net/1721.1/81331 GenBrick – A Rapid Multi-Part Assembly Method for BioBricks Gasiūnaitė, Lina; Lewicka, Aleksandra; Pashkuleva, Hristiana; Villanueva, Hugo; Thornton, Harry; Trubitsyna, Maryia; French, Chris 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, without recloning or reamplification. 2013-10-04T00:00:00Z https://hdl.handle.net/1721.1/81330 The AutoAnnotator - Standardized annotation of protein-encoding BioBricks 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 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 features, for instance transmembrane regions, are very interesting and informative when viewing a part. However, this information is not presented or very hard to find in most part descriptions and requires the user to use external websites to obtain it. To resolve this issue we propose a standardized table containing this information. For this purpose we developed a web tool, called the AutoAnnotator, in JavaScript gathering this information and providing the standardized table for the user to copy. 2013-10-04T00:00:00Z https://hdl.handle.net/1721.1/78249 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 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. 2013-03-31T00:00:00Z https://hdl.handle.net/1721.1/74561 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 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 10 BioBrick assembly standard. 2012-11-05T00:00:00Z https://hdl.handle.net/1721.1/73912 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 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 that we use the term “promoter” here to refer to both the promoter and the 5’ UTR, which we currently define as a single part. Future iterations of this standard will incorporate subdivision of currently defined parts e.g. into promoter and 5’ UTR. The standard makes use of the type IIS restriction enzyme BsaI to generate standardized and user­‐defined ‘signature overhangs’, thus enabling directional and seamless TU assembly. RFC88 is supported by the Yeast Standardized Collection of Parts for Expression (SCoPE), a repository of subcloned and sequence verified parts compatible with this assembly standard. The Yeast SCoPE is currently populated by a large number of S. cerevisiae promoters and terminators that facilitate expression and characterization of non­‐native ORFs. 2012-10-11T00:00:00Z https://hdl.handle.net/1721.1/73911 The Measurement of rho‐independent Transcription Terminator Efficiency He, Jiankui; Jing, Shui; Zhang, Mengshi; Liu, Xianggeng; Chen, Yao; Qie, Boyu; Shen, Liuxing; Wu, Zishan 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 equation model, it can be expressed in PoPS. 2012-10-11T00:00:00Z https://hdl.handle.net/1721.1/73910 The minimum information for a qualified BioBrick Zhou, Mubing; Zhang, Junqiu; He, Jiankui 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 standardization will reduce the time to locate and find a BioBrick. So it is essential to create a default template of storing the information of BioBricks. 2012-10-11T00:00:00Z https://hdl.handle.net/1721.1/73909 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. 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 biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a common computational representation. 2012-10-11T00:00:00Z https://hdl.handle.net/1721.1/67887 Creating native registry functions to accommodate mutant libraries Xu, Kenneth O.; Walters, Eric M. 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 would become filled with parts and eventually become unmanageable to navigate. If the mutants were added directly to the source’s page, it could become unwieldy and unintuitive to find. We propose a system of adding a few features to the registry that SHALL allow a user-friendly method of visualizing mutant offspring and siblings while condensing the registry as much as possible when mutants are introduced to allow for easier navigation. 2011-12-29T00:00:00Z https://hdl.handle.net/1721.1/67700 PCR - Ligation Assembly Standard for BioBrick Parts He, Tony PeiYuan; Campbell, Alexander; Zhou, Stefanie Yifan 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 assembly method will involve the use of standard BioBrick restriction enzyme systems, PCR purification kit, ligase system, and a PCR polymerase system. 2011-12-15T00:00:00Z https://hdl.handle.net/1721.1/66485 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 This BBF RFC provides a method in which standardized parts can be easily created for Neurospora crassa. 2011-10-17T00:00:00Z https://hdl.handle.net/1721.1/66484 "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 This Request for Comments (RFC) describes a strategy for using homology-based assembly methods to assemble parts from a library in any order. 2011-10-17T00:00:00Z https://hdl.handle.net/1721.1/66172 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 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 biology. We define: 1. the vocabulary, a set of preferred terms and 2. the core data model, a common computational representation. 2011-10-03T00:00:00Z https://hdl.handle.net/1721.1/60094 Detailed Information Standard Culviner, Peter; Pantalone, Nathaniel; Sagstetter, Mary; Sandock, Sarah; Vrana, Justin; Wu, Yue The purpose of this standard is to increase the required information that must accompany any parts submitted to the Registry of Standard Biological Parts. This will give users of the parts better assurance of their authenticity and promote better Registry maintenance. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60093 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 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, and therefore it is can be expressed in PoPS [1] 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60092 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 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, BBa_K337049) enabling rapid experimental characterization of any miRNA-BS of choice. We recommend a new standard unit, RKDU (relative knock-down unit) to describe the knock-down efficiency of a miRNA-BS in a specific cell type. pSMB_miMeasure allows for an easy and fast measurement of RKDU while providing effective normalization against variance stemming from differences in transfection efficiency and from other sources. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60091 miTuner - a kit for microRNA based gene expression tuning 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 The purpose of this RFC is to introduce a modular expression tuning kit for use in mammalian cells. The kit enables the regulation of the gene expression of any gene of interest (GOI) based on synthetic microRNAs, endogenous microRNAs or a combination of both. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60090 General updating scheme for the design and construction of assembly vectors that are compatible with BBF RFC 10 and BBF RFC 28 Billerbeck, Sonja; Zwicky, Katharina; Lang, Moritz; Pestalozzi, Luzius; Rosenberger, George; Constantinescu, Simona; Ambegoda, Thanuja; Sotiriadis, Elsa BBF RFC 75 intends to link the BBF RFC 28-based combinatorial multi-part assembly method to BBF RFC 10. Its aim is to easily redesign an expression vector to make it compatible to BBF RFC 10 for the construction of fusion proteins based on BBF RFC 28. These vectors can then directly be used for expression of the fusion protein. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60089 Documentation of BioBrick parts Slomp, Arend; Ekkers, David 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. Furthermore it should supply the information in such a way that no contact is needed with the creator of the BioBrick part. It should create a default template for all information of BioBrick parts and devices. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60088 Construction a RBS library with different translational activity Lee, Hsiao-Ching 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 genetic circuit design lies in selecting well-matched genetic components that when coupled, reliably and consistently act in a desired behavior. Although the parameter values are calculated by model equations, it is hard to select the biobricks that reliably implements a desired cellular function with quantitative values. To overcome this problem, the RBSs were designed to control the expression of downstream genes when necessary. This protocol will describe how to generate a RBS library with different ribosome binding affinities. The degenerated primers designed for PCR are used to generate mutations in RBS regions, while the mutated RBS activity are assayed using green fluorescence protein on a low copy number plasmid. In addition, a library of RBS's with different transcriptional strength can be built to fit the specific parameter values derived from model equations. Because the reporter protein activity has a positive correlation to RBS translational activity, we can design customizable RBS translational strengths for application. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60087 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 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, an inducible promoter drives the expression of the second reporter, YFP in the case of the part tested. The constitutively expressed reporter protein (R1) serves as normalization factor for the inducible reporter (R2) by simple division. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60086 Standard for the Electronic Distribution of SBOLv Diagrams Johnson, Jeffrey; Galdzicki, Michal; Sauro, Herbert M 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 to readers by establishing a systematic scheme for linking diagrams of synthetic biological mechanisms to reference information on the Registry of Standard Biological Parts [1]. Through the use of standard diagrams based on SBOL-visual (BBF RFC 16) symbols, we hope to facilitate communication about synthetic DNA constructs between research groups. This standard applies the use of the established SBOLv symbols on the Web to clearly represent synthetic constructs. Linking these diagrams using http URLs to reference information at the Registry provides a method to retrieve contextual reference information about components of DNA constructs. Use of standardized diagrams in engineering promotes fast and accurate communication between researchers, which in turn promotes effective re-use of biological parts. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60085 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 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 augmented with domain-specific knowledge. Here we propose a standard for a RESTful (Richardson, 2007) API which facilitates the discovery and publication of models of functional biological units. This API is designed to produce parts models which can be automatically combined into complete, simulatable models of entire systems. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60084 A New Standard to Connect BioBrick Parts for Precise Extraction of an Enzyme Digestion Product Uekusa, Kousuke; Iguchi, Seiko This BioBricks Foundation Request for Comments (BBF RFC) introduces a new standard to connect BioBrick parts using BglI site. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60083 Building Protein Domain Based Composite Biobricks for Mammalian Expression Systems Balint, Balint L; Keret, Ophir; Brazda, Peter; Demeny, Mate; 2010 Debrecen-Hungary, iGEM 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 designed to be used in mammalian expression systems. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60082 Recombination Based Part Assembly Deming, Laura; Slusarczyk, Adrian; Jiao, Yunxin; iGEM, 2010 MIT Here we propose a new recombination-based assembly standard, optimized to allow for efficient cloning of mammalian vectors. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60081 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 This document provides recommendations for licensing of community-created biological parts, especially in BioBrick standard. 2010-12-05T00:00:00Z https://hdl.handle.net/1721.1/60080 DTU Synthetic Promoter Library Standard Fortuna, Patrick; Trolle, Thomas; Borch, Martin Malthe; Haugaard, Anastasiya; Kjaergaard, Maya Friis; Iversen, Lisa Blanc; Jollmann, Annemi; Sander, Anja; Frederiksen, Juliet; Slodkowicz, Grzegorz The purpose of this RFC is to outline a method for generating a BioBrick compatible Synthetic Promoter Library (SPL) within bacteria in order to fine-tune the expression of BioBrick parts and devices. 2010-12-04T00:00:00Z https://hdl.handle.net/1721.1/59957 Standard Biological Part Automatic Modeling Database Language (MoDeL) Wang, Zhen; Liao, Chen; Jiang, Hao; Yao, Xiaomo; Jiang, Kun This BioBricks Foundation Request for Comments (BBF RFC) describes the Standard Biological Part Automatic Modeling Database Language (MoDeL). MoDeL provides a language and syntax standard for automatic modeling databases used by synthetic biology software. Meanwhile, MoDeL allows detailed description of biological complex, and presents the concept of Chain-Node Model. 2010-11-09T00:00:00Z https://hdl.handle.net/1721.1/59851 Promoter and Coding Sequence Considerations for Caenorhabditis elegans and Other Eukaryotes Palmer, Chris; Halliday, Geoff Our primary aim is to provide a standard format for protein-coding BioBricks intended for eukaryotes, especially in the nematode worm Caenorhabditis elegans, so that future teams will be able to correctly take advantage of the Kozak consensus sequence and its power to manipulate gene expression levels. There are currently, in fact, at least three protein-coding BioBricks with Kozak sequences that correctly conform to this convention, designed for yeast, (BBa_K165057, BBa_K165058, and BBa_K165059) but their format has not been documented or standardized. Since this is so important to full exploitation of current and future eukaryotic chassis, we feel it must be codified. 2010-11-07T00:00:00Z https://hdl.handle.net/1721.1/59803 Fast multiple gene fragment ligation method based on homologous recombination Wang, Ruiyan; Shi, Zhenyu; Li, Teng; Chen, Guoqiang With the established BioBrick Assembly standards, ligation of different parts has to be accomplished step by step. It can be time-consuming when dealing with multiple fragment ligation. BBF RFC 62 is developed aimed at completing the ligation of multiple fragments quickly and efficiently based on homologous recombination. 2010-10-31T00:00:00Z https://hdl.handle.net/1721.1/59802 Fast multiple gene fragment ligation method based on Type IIs restriction enzyme DraIII Shi, Zhenyu; Li, Teng; Chen, Guoqiang With the established BioBrick Assembly standards, ligation of different parts has to be accomplished step by step. It can be time-consuming when dealing with multiple fragment ligation. BBF RFC 61 is developed aimed at completing the ligation of multiple fragments quickly and efficiently based on Type II restriction enzyme DraIII. 2010-10-31T00:00:00Z https://hdl.handle.net/1721.1/59801 Quantitative measurement of mammalian cell invasion by bacteria using flow cytometry Lower, Michal; Olchowik, Anna Purpose of this RFC is to provide method of measurement of bacterial invasion into mammalian cells. Also this RFC defines Percent of INvasion (PIN) unit. 2010-10-31T00:00:00Z https://hdl.handle.net/1721.1/59800 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 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. 2010-10-31T00:00:00Z https://hdl.handle.net/1721.1/59011 BBF RFC 56: “Part Flavors” For Peptide-Coding Parts Anderson, J. Chris “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 concept to other types of parts. A CDS part flavor is intended to address the problem of how to precisely describe compositions of parts that differ by the presence of 5’ and 3’ spacers, presence or absence of start codons, stop codons, and ribosome binding sites, etc. The goal is to be able to describe these in such a way that grammar-based software tools (such as Genocad or Eugene) could register the grammatical equivalence of two parts. This facilitates automated design strategies in which an abstract device (such as promoter.rbs.CDS.terminator) can be instantiated to grammatically correct compositions (such as r0040.b0034.E0040.b0015). The concept is an extension of RFC 13 which proposes to describe CDS parts as “head,” “internal,” “special,” or “tail” domains. The difference is a little subtle, it has nothing to do with what the part encodes per se, but rather seeks to distinguish the translation-related properties of the encoded part and separate them into grammatically-equivalent categories, and in so doing allows for there being more “flavors” of part that can exist (and already do exist). I describe the concept here since we’ve been using this concept for the past 2 years or so, and there are already a number of parts whose descriptions are written with the flavor notations described herein in the Registry. This document serves as a guide to interpreting the codes. This may also be of value to others as a means of distinguishing their different types of parts. 2010-10-11T00:00:00Z https://hdl.handle.net/1721.1/49523 BBF RFC 16: Synthetic Biology Open Language Visual (SBOLv) Specification Rodriguez, Cesar; Bartram, Suzie; Ramasubramanian, Anusuya; Endy, Drew 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 parts during the development of biological devices. It is targeted for use by biological engineers in forward engineering projects. It encourages and supports model-driven engineering. 2009-11-01T19:39:55Z https://hdl.handle.net/1721.1/49522 The USER cloning standard Kaas, Christian Schrøder; Hansen, Niels Bjørn; Genee, Hans Jasper; Olsen, Lars Rønn; Matos, Cláudia; Bonde, Mads Tvillinggaard; Hansen, Bjarne Gram This BioBricks Foundation Request for Comments (BBF RFC) provides information about the design of uracil-containing primers used for USER cloning and USER fusion. 2009-11-01T18:17:28Z https://hdl.handle.net/1721.1/49521 Large-Scale Peptide Modification on BioBrick Proteins Tian, Feng; Chen, GuoQiang; Wang, Zhao With the established BioBrick Assembly standards, fusion proteins with diversified functions are easy to manipulate. However, we realized that the existing BBF RFC do not clearly defining the standard for peptide display on BioBrick proteins. Considering the promising use of specific small peptide modification on functional proteins, targeting to specific cell types, for example, we proposed a standard for small peptide modification on BioBrick proteins. 2009-10-30T22:12:05Z https://hdl.handle.net/1721.1/49520 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 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 sequences and b) further introduce standards to provide compatibility with data formats introduced in this RFC. Description of promoters generated by this method can be found at http://2009.igem.org/Team:Heidelberg/HEARTBEAT_database. 2009-10-30T22:02:45Z https://hdl.handle.net/1721.1/49518 BBF RFC 47: BioBytes Assembly Standard Ellison, Michael; Ridgway, Doug; Fedor, Justin; Garside, Erin; Robinson, Kelly; Lloyd, David 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, it allows for greater speed and efficiency in assembling these components. This document defines a standard for genetic parts compatible with the assembly system and describes detailed protocols for the construction of such parts and their rapid assembly. Although the original motivation for the method was to produce whole synthetic genomes, the design allows for any type of DNA construction. 2009-10-29T23:42:34Z https://hdl.handle.net/1721.1/49505 Bioscaffold-Linker Mina, Petros; Savery, Nigel 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 assembly standard 10 (RFC10) and hence allows utilization of most of the current biobricks database. 2009-10-21T02:36:41Z https://hdl.handle.net/1721.1/49504 How to Build Kinetic Models of BioBricks Weeding, Emma; Houle, Jason; Swiniarski, Ben; Smadbeck, Patrick; Lindblad, Kristen; Volzing, Katherine; Srivastava, Poonam; Sotiropoulos, Vassilios; Biliouris, Kostas; Kaznessis, Yiannis This BioBricks Foundation Request for Comments (BBF RFC) provides instructions on how to automatically generate a model of any BioBrick sequence. These models can be used in computer simulations of the dynamic behavior of all molecular components of the BioBrick. 2009-10-21T02:07:22Z https://hdl.handle.net/1721.1/49503 Cloning Standard for Mammalian BioBrick Parts and Devices Bartoschek, Michael; Mugahid, Douaa; Rademacher, Anne; Meyer, Hannah; Velten, Lars; Reis, Yara; Keienburg, Jens; Eils, Roland To introduce a common cloning standard for BioBrick parts that find application in mammalian cells. 2009-10-21T01:45:14Z https://hdl.handle.net/1721.1/49502 RA-PCR, a method for the generation of randomized promoter libraries Velten, Lars; Haas, Simon; Rademacher, Anne; Meyer, Hannah; Eils, Roland The purpose of this RFC is to provide instructions for the synthesis of promoters in mammalian cells that are active at a desired cellular condition (where a cellular condition is specified by the activity of a set of transcription factors of interest). The method generates a library of promoters putatively active under the desired condition. This RFC also provides instructions on how to screen the libraries generated by this method in order to obtain functional promoters. Description of promoters generated by this method can be found at http://2009.igem.org/Team:Heidelberg/Project_Synthetic_promoters. 2009-10-21T01:24:36Z https://hdl.handle.net/1721.1/49501 Units for Promoter Measurement in Mammalian Cells Velten, Lars; Iwamoto, Nao; Hiller, Corinna; Uckelmann, Hannah; Zhu, Chenchen; Zhao, Bingqing; Richter, Daniela; Hundeshagen, Phillip; Reichenzeller, Michaela; Keienburg, Jens; Eils, Roland The purpose of this RFC is to provide units for the characterization of promoter strength for use in mammalian cells. RMPU is mRNA based and directly proportional to PoPS, whereas REU is protein based and not proportional to PoPS. 2009-10-21T01:18:06Z https://hdl.handle.net/1721.1/49417 BBF RFC 38: RFC 38: Building Blocks - Standard Large DNA/Genome Construction DiCarlo, James; Boeke, Jef 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. Furthermore, current Biobrick construction standards [RFC 10,11,12 etc.] rely heavily on restriction enzyme based methods, which can be sequence, cost and time restrictive. This is especially true of large DNA assembly, where 100% control of over DNA sequence may be mandatory, such as in whole genome assembly. We propose a novel standard, The Building Block Method, for both the construction of standard parts and their assembly This Building Block standard can be either A) an interchangeable or B) a non-interchangeable format, based on the desired use of the part. 2009-10-07T21:51:51Z https://hdl.handle.net/1721.1/46747 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 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 assembly reaction, BglBricks parts contain a scar sequence of GGATCT between the two parts. This sequence conveniently translates as Gly-Ser in the zero frame, a commonly-used linker in protein engineering. BglBricks has previously been called the “BglBrick” standard, and is also referred to as Assembly standard 21. A consolidated description of the standard is available at: http://openwetware.org/wiki/Template:AndersonLab:BglBrick_Standard 2009-09-18T14:38:40Z https://hdl.handle.net/1721.1/46721 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 This BioBricks Foundation Request for Comments (BBF RFC) describes an alternative assembly standard based on the Type IIS restriction enzyme AarI. 2009-09-16T14:12:33Z https://hdl.handle.net/1721.1/46705 BBF RFC 37: Fusion protein BioBrick assembly standard with optional linker extension Bencina, Mojca; Jerala, Roman 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) and RFC 10 standard and supports in-frame fusion and controlled potentially infinite extension of linker between protein fusion domains. BBF RFC 37 replaces BBF RFC 36. 2009-09-02T17:09:25Z https://hdl.handle.net/1721.1/46701 BBF RFC 36: Fusion protein BioBrick assembly standard with optional linker extension Jerala, Roman 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) and RFC 10 standard and supports in-frame fusion and controlled potentially infinite extension of linker between protein fusion domains. 2009-09-01T16:15:53Z https://hdl.handle.net/1721.1/46328 BBF RFC 26: In-Fusion BioBrick Assembly Sleight, Sean 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. 2009-07-09T18:53:13Z https://hdl.handle.net/1721.1/45537 Provisional BioBrick Language (PoBoL) Galdzicki, Michal; Chandran, Deepak; Nielsen, Alec; Morrison, Jason; Cowell, Mackenzie; Grünberg, Raik; Sleight, Sean; Sauro, Herbert This BioBricks Foundation Request for Comments (BBF RFC) describes a semantic markup language for publishing and sharing information about BioBricks on the World Wide Web. This BBF RFC includes the recommendation for the minimal information expected when creating a Provisional BioBrick Language (PoBoL) description of BioBricks and for the implementation of the language using Web Ontology Language (OWL). 2009-05-15T18:05:32Z https://hdl.handle.net/1721.1/45143 BBF RFC 30: Draft of an RDF-based framework for the exchange and integration of Synthetic Biology data Grunberg, Raik 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 of data models. It describes how data and data models are to be published, how they are exchanged and integrated between different parties, and how they can be extended, corrected and interlinked in a decentralized fashion. These goals are achieved by embracing the RDF (Resource Description Framework), a set of W3C standards. A one-sentence summary of this proposal would there- fore be: “Use RDF according to the W3C standards.” The PoBoL pro ject (Provisional BioBrick Ontology Language, http://pobol.org) is based on this idea. This RFC does not describe a data model per se but only outlines a possible architecture and rules of data exchange. 2009-04-24T22:16:06Z https://hdl.handle.net/1721.1/45140 Fusion Protein (Freiburg) Biobrick assembly standard Grünberg, Raik; Arndt, Katja; Müller, Kristian This Request for Comments (RFC) describes an extension to the original BioBrick assembly standard (BBF RFC 10). The Fusion Assembly strategy described here is fully backwards compatible with RFC 10 and supports the construction of in frame fusion proteins. 2009-04-18T22:42:57Z https://hdl.handle.net/1721.1/45139 Draft Standard for Biobrick BB-2 Biological Parts Knight, Tom This standard defines the required sequence properties for a Biobrick(R) BB-2 standard biological part. It does not define any functional characteristics of the parts, nor does it motivate any aspect of these standards. 2008-11-19T00:00:00Z https://hdl.handle.net/1721.1/45138 Draft Standard for Biobrick Biological Parts Knight, Tom This standard defines the required sequence properties for a Biobrick(tm) standard biological part. It does not define any functional characteristics of the parts, nor does it motivate any aspect of these standards. All sequences defined herein are specified in the 5' to 3' direction. 2007-05-03T00:00:00Z https://hdl.handle.net/1721.1/45137 Naming of standards of physical composition of BioBrick parts Rettberg, Randy; Shetty, Reshma This BioBricks Foundation Request for Comments (BBF RFC) proposes a naming convention for standards of physical composition of BioBrick parts in which assembly standards are named according to the BBF RFC that specifies the standard. 2009-04-17T21:23:35Z https://hdl.handle.net/1721.1/44962 Constraint Relaxation of RFC 10 for Assembling Standard Biological Parts Che, Austin 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 part sequence while maintaining compatibility with existing parts that use RFC 10. 2009-03-30T22:29:13Z https://hdl.handle.net/1721.1/44961 Conversion of Freiburg (Fusion) Biobricks to the Silver (BioFusion) format Grunberg, Raik This Request for Comments (RFC) describes a strategy for converting Biobricks from the Freiburg (aka Fusion) format to the Silver lab (aka BioFusion) format. 2009-03-30T18:33:51Z https://hdl.handle.net/1721.1/44960 Instructions to BBF RFC Authors Tarjan, Daniel; Sleight, Sean; Shetty, Reshma; Ridgway, Doug; Rettberg, Randy; McArthur, George; Mayer, Antonia; Knight, Tom; French, Chris; Endy, Drew; de Mora, Kim; Elfick, Alistair; Cowell, Mackenzie; Che, Austin; Anderson, Chris This BioBricks Foundation Request for Comments (BBF RFC) provides in- formation about the preparation and submission of BBF RFCs to The Bio- Bricks Foundation (BBF). 2008-11-10T00:00:00Z https://hdl.handle.net/1721.1/44640 Proposed Conceptual Guidelines for the Design of a BioBrick Graphical Language & an Example Fernandez, Eric As we update the current BioBrick symbols we have an opportunity to look at the end users of a BioBrick Graphical language and develop design guidelines so that the new symbols best suit their needs. This document explores those needs, looks at the design principles necessary to meet them, and puts those principles into practice by showing an example of a new set of BioBrick symbols. 2009-03-12T04:06:23Z