Publications

Authors: Type:

2016

  • N. Roehner and D. Densmore, How to Remember and Revisit Genetic Designs Automatically, Synberc 2016 Spring Retreat , mar, 2016.
    [BibTeX] [Download PDF]
    @Misc{RoehnerDensmoreKNOX,
    author = {N. Roehner and D. Densmore},
    title = {How to Remember and Revisit Genetic Designs Automatically},
    howpublished = {Synberc 2016 Spring Retreat},
    month = mar,
    year = {2016},
    url = {http://cidarlab.org/wp-content/uploads/2016/05/Roehner_2016_Spring_Retreat_v2.pdf}
    }

  • D. Densmore, C. Madsen, and P. Vaidyanathan, Bio Design Automation & Synthesis of Functional Specification, presented at the NSF Kickoff meeting for bioCPS , February, 2016.
    [BibTeX] [Download PDF]
    @Misc{NSFbioCPSKickoff,
    Title = {Bio Design Automation \& Synthesis of Functional Specification},
    Author = {Douglas Densmore and Curtis Madsen and Prashant Vaidyanathan},
    HowPublished = {presented at the NSF Kickoff meeting for bioCPS},
    Month = {February},
    Year = {2016},
    Keywords = {biocps, phoenix},
    URL = {http://cidarlab.org/wp-content/uploads/2016/02/BDA_STL.pptx}
    }

  • L. Ortiz, T. Costa, and D. Densmore, Modular Assembly of an Electronically Integrated Genetic Circuit Library, Poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2016.
    [BibTeX] [Download PDF]
    @Misc{ortiz2016tc,
    author = {Luis Ortiz and Thomas Costa and Douglas Densmore},
    title = {Modular Assembly of an Electronically Integrated Genetic Circuit Library},
    howpublished = {Poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2016},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/Luis-Ortiz-IWBDA-2016-Poster_Small.pdf}
    }

  • I. Turshudzhyan, J. Ospina, A. Durkan, K. Tan, A. Goncharova, J. Kozol, P. Vaidyanathan, N. Roehner, and D. Densmore, Phagebook Alpha: A Software Environment for Social Synthetic Biology, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2016.
    [BibTeX] [Abstract] [Download PDF]
    http://cidarlab.org/wp-content/uploads/2016/09/phagebook-iwbda2016-2.pdf

    @Misc{turshudzhyan2016phagebook,
    author = {Inna Turshudzhyan and Johan Ospina and Allison Durkan and Kristel Tan and Anna Goncharova and Jacob Kozol and Prashant Vaidyanathan and Nicholas Roehner and Douglas Densmore},
    title = {Phagebook Alpha: A Software Environment for Social Synthetic Biology},
    howpublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2016},
    abstract = {http://cidarlab.org/wp-content/uploads/2016/09/phagebook-iwbda2016-2.pdf},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/PhagebookPosterFinal.pdf}
    }

  • P. Vaidyanathan, E. Appleton, C. Madsen, C. Vasile, A. Pacheco, I. Haghighi, N. Roehner, R. Ivison, J. Wang, Y. Agarwal, Z. Chapasko, C. Belta, and D. Densmore, Genetic Systems Engineering, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2016.
    [BibTeX] [Abstract] [Download PDF]
    http://cidarlab.org/wp-content/uploads/2016/09/phoenix.pdf

    @Misc{vaidyanathan2016genetic,
    author = {Prashant Vaidyanathan and Evan Appleton and Curtis Madsen and Cristian-Ioan Vasile and Alan Pacheco and Iman Haghighi and Nicholas Roehner and Rachael Ivison and Junmin Wang and Yash Agarwal and Zachary Chapasko and Calin Belta and Douglas Densmore},
    title = {Genetic Systems Engineering},
    howpublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2016},
    abstract = {http://cidarlab.org/wp-content/uploads/2016/09/phoenix.pdf},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/PhoenixPosterFinal-1.pdf}
    }

  • C. Madsen, P. Vaidyanathan, C. Vasile, R. Ivison, J. Wang, C. Belta, and D. Densmore, Utilizing Signal Temporal Logic to Characterize and Compose Modules in Synthetic Biology, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2016.
    [BibTeX] [Abstract] [Download PDF]
    http://cidarlab.org/wp-content/uploads/2016/09/extended_abstract.pdf

    @Misc{madsen2016stl,
    author = {Curtis Madsen and Prashant Vaidyanathan and Cristian-Ioan Vasile and Rachael Ivison and Junmin Wang and Calin Belta and Douglas Densmore},
    title = {Utilizing Signal Temporal Logic to Characterize and Compose Modules in Synthetic Biology},
    howpublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA)},
    month = {August},
    year = {2016},
    abstract = {http://cidarlab.org/wp-content/uploads/2016/09/extended_abstract.pdf},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/talk.pdf}
    }

  • N. Roehner, E. M. Young, C. A. Voigt, B. D. Gordon, and D. Densmore, “Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems,” ACS Synthetic Biology, 2016. doi:10.1021/acssynbio.5b00232
    [BibTeX] [Download PDF]
    @Article{roehnerDD2016,
    author = {Nicholas Roehner and Eric M. Young and Christopher A. Voigt and D. Benjamin Gordon and Douglas Densmore},
    title = {Double Dutch: A Tool for Designing Combinatorial Libraries of Biological Systems},
    journal = {ACS Synthetic Biology},
    year = {2016},
    month = {April},
    note = {PMID: 27110633},
    day = {25},
    doi = {10.1021/acssynbio.5b00232},
    url = {http://dx.doi.org/10.1021/acssynbio.5b00232}
    }

  • N. Roehner, J. Beal, K. Clancy, B. Bartley, G. Misirli, R. Gruenberg, E. Oberortner, M. Pocock, M. Bissell, C. Madsen, T. Nguyen, M. Zhang, Z. Zhang, Z. Zundel, D. Densmore, J. Gennari, A. Wipat, H. Sauro, and C. J. Myers, “Sharing Structure and Function in Biological Design with SBOL 2.0,” ACS Synthetic Biology, 2016. doi:10.1021/acssynbio.5b00215
    [BibTeX] [Download PDF]
    @Article{doi:10.1021/acssynbio.5b00215,
    author = {Nicholas Roehner and Jacob Beal and Kevin Clancy and Bryan Bartley and Goksel Misirli and Raik Gruenberg and Ernst Oberortner and Matthew Pocock and Michael Bissell and Curtis Madsen and Tramy Nguyen and Michael Zhang and Zhen Zhang and Zach Zundel and Douglas Densmore and John Gennari and Anil Wipat and Herbert Sauro and Chris J. Myers },
    title = {Sharing Structure and Function in Biological Design with SBOL 2.0},
    journal = {ACS Synthetic Biology},
    year = {2016},
    month = {April},
    note = {PMID: 27111421},
    day = {25},
    doi = {10.1021/acssynbio.5b00215},
    url = {
    http://dx.doi.org/10.1021/acssynbio.5b00215
    }
    }

  • S. B. Carr, “Reliable gene expression and assembly for synthetic biological devices in E. coli through customized promoter insulator elements and automated DNA assembly,” PhD Thesis, Boston University, 2016.
    [BibTeX]
    @PhdThesis{carr2016thesis,
    author = {Carr, Swati Banerjee},
    title = {Reliable gene expression and assembly for synthetic biological devices in E. coli through customized promoter insulator elements and automated DNA assembly},
    school = {Boston University},
    year = {2016}
    }

  • R. Silva, S. Bhatia, and D. Densmore, “A reconfigurable continuous-flow fluidic routing fabric using a modular, scalable primitive,” Lab Chip, vol. 16, pp. 2730-2741, 2016. doi:10.1039/C6LC00477F
    [BibTeX] [Abstract] [Download PDF]
    Microfluidic devices{,} by definition{,} are required to move liquids from one physical location to another. Given a finite and frequently fixed set of physical channels to route fluids{,} a primitive design element that allows reconfigurable routing of that fluid from any of n input ports to any n output ports will dramatically change the paradigms by which these chips are designed and applied. Furthermore{,} if these elements are {"}regular{"} regarding their design{,} the programming and fabrication of these elements becomes scalable. This paper presents such a design element called a transposer. We illustrate the design{,} fabrication and operation of a single transposer. We then scale this design to create a programmable fabric towards a general-purpose{,} reconfigurable microfluidic platform analogous to the Field Programmable Gate Array (FPGA) found in digital electronics.

    @Article{C6LC00477F,
    author = {Silva, Ryan and Bhatia, Swapnil and Densmore, Douglas},
    title = {A reconfigurable continuous-flow fluidic routing fabric using a modular{,} scalable primitive},
    journal = {Lab Chip},
    year = {2016},
    volume = {16},
    pages = {2730-2741},
    abstract = {Microfluidic devices{,} by definition{,} are required to move liquids from one physical location to another. Given a finite and frequently fixed set of physical channels to route fluids{,} a primitive design element that allows reconfigurable routing of that fluid from any of n input ports to any n output ports will dramatically change the paradigms by which these chips are designed and applied. Furthermore{,} if these elements are {"}regular{"} regarding their design{,} the programming and fabrication of these elements becomes scalable. This paper presents such a design element called a transposer. We illustrate the design{,} fabrication and operation of a single transposer. We then scale this design to create a programmable fabric towards a general-purpose{,} reconfigurable microfluidic platform analogous to the Field Programmable Gate Array (FPGA) found in digital electronics.},
    doi = {10.1039/C6LC00477F},
    issue = {14},
    publisher = {The Royal Society of Chemistry},
    url = {http://dx.doi.org/10.1039/C6LC00477F}
    }

  • M. J. Quintin, N. J. Ma, S. Ahmed, S. Bhatia, A. Lewis, F. J. Isaacs, and D. Densmore, “Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE,” ACS Synthetic Biology, iss. ja, p. null, 2016. doi:10.1021/acssynbio.5b00219
    [BibTeX] [Download PDF]
    @Article{doi:10.1021/acssynbio.5b00219,
    author = {Michael James Quintin and Natalie Jing Ma and Samir Ahmed and Swapnil Bhatia and Aaron Lewis and Farren J. Isaacs and Douglas Densmore },
    title = {Merlin: Computer-Aided Oligonucleotide Design for Large Scale Genome Engineering with MAGE},
    journal = {ACS Synthetic Biology},
    year = {2016},
    volume = {0},
    number = {ja},
    pages = {null},
    note = {PMID: 27054880},
    doi = {10.1021/acssynbio.5b00219},
    eprint = { http://dx.doi.org/10.1021/acssynbio.5b00219 },
    url = {
    http://dx.doi.org/10.1021/acssynbio.5b00219
    }
    }

  • S. Bhatia, C. LaBoda, V. Yanez, T. Haddock-Angelli, and D. Densmore, “Permutation Machines,” ACS Synthetic Biology, p. null, 2016. doi:10.1021/acssynbio.5b00226
    [BibTeX] [Download PDF]

  • S. V. Iverson, “Improved modular multipart DNA assembly, development of a DNA part toolkit for E. coli, and applications in traditional biology and bioelectronic systems,” PhD Thesis, Boston University, 2016.
    [BibTeX] [Download PDF]
    @PhdThesis{iverson2016thesis,
    Title = {Improved modular multipart DNA assembly, development of a DNA part toolkit for E. coli, and applications in traditional biology and bioelectronic systems},
    Author = {Iverson, Sonya Victoria},
    School = {Boston University},
    Year = {2016},
    URL = {http://cidarlab.org/wp-content/uploads/2016/03/Iverson_Dissertation_v5.pdf}
    }

  • E. M. Appleton, “A design-build-test-learn tool for synthetic biology,” PhD Thesis, 2016.
    [BibTeX]
    @PhdThesis{appleton2016design,
    author = {Appleton, Evan M},
    title = {A design-build-test-learn tool for synthetic biology},
    year = {2016}
    }

  • R. Sanka, H. Huang, R. Silva, and D. Densmore, MINT – Microfluidic Netlist, poster presented at IWBDA 2016 , 2016.
    [BibTeX] [Abstract] [Download PDF]
    http://cidarlab.org/wp-content/uploads/2016/09/mint-iwbda16.pdf

    @Misc{mintiwbda16,
    author = {Sanka, Radhakrishna and Huang, Haiyao and Silva, Ryan and Densmore, Douglas},
    title = {MINT - Microfluidic Netlist},
    howpublished = {poster presented at IWBDA 2016},
    month = aug,
    year = {2016},
    abstract = {http://cidarlab.org/wp-content/uploads/2016/09/mint-iwbda16.pdf},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/MINT-IWBDA-2016-Poster-Template-copy.pdf}
    }

  • A. A. K. Nielsen, B. S. Der, J. Shin, P. Vaidyanathan, V. Paralanov, E. A. Strychalski, D. Ross, D. Densmore, and C. A. Voigt, “Genetic circuit design automation,” Science, vol. 352, iss. 6281, 2016. doi:10.1126/science.aac7341
    [BibTeX] [Abstract] [Download PDF]
    As synthetic biology techniques become more powerful, researchers are anticipating a future in which the design of biological circuits will be similar to the design of integrated circuits in electronics. Nielsen et al. describe what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering.Science, this issue p. 10.1126/science.aac7341INTRODUCTIONCells respond to their environment, make decisions, build structures, and coordinate tasks. Underlying these processes are computational operations performed by networks of regulatory proteins that integrate signals and control the timing of gene expression. Harnessing this capability is critical for biotechnology projects that require decision-making, control, sensing, or spatial organization. It has been shown that cells can be programmed using synthetic genetic circuits composed of regulators organized to generate a desired operation. However, the construction of even simple circuits is time-intensive and unreliable.RATIONALEElectronic design automation (EDA) was developed to aid engineers in the design of semiconductor-based electronics. In an effort to accelerate genetic circuit design, we applied principles from EDA to enable increased circuit complexity and to simplify the incorporation of synthetic gene regulation into genetic engineering projects. We used the hardware description language Verilog to enable a user to describe a circuit function. The user also specifies the sensors, actuators, and {\textquotedblleft}user constraints file{\textquotedblright} (UCF), which defines the organism, gate technology, and valid operating conditions. Cello (www.cellocad.org) uses this information to automatically design a DNA sequence encoding the desired circuit. This is done via a set of algorithms that parse the Verilog text, create the circuit diagram, assign gates, balance constraints to build the DNA, and simulate performance.RESULTSCello designs circuits by drawing upon a library of Boolean logic gates. Here, the gate technology consists of NOT/NOR logic based on repressors. Gate connection is simplified by defining the input and output signals as RNA polymerase (RNAP) fluxes. We found that the gates need to be insulated from their genetic context to function reliably in the context of different circuits. Each gate is isolated using strong terminators to block RNAP leakage, and input interchangeability is improved using ribozymes and promoter spacers. These parts are varied for each gate to avoid breakage due to recombination. Measuring the load of each gate and incorporating this into the optimization algorithms further reduces evolutionary pressure.Cello was applied to the design of 60 circuits for Escherichia coli, where the circuit function was specified using Verilog code and transformed to a DNA sequence. The DNA sequences were built as specified with no additional tuning, requiring 880,000 base pairs of DNA assembly. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts). Across all circuits, 92\% of the 412 output states functioned as predicted.CONCLUSIONOur work constitutes a hardware description language for programming living cells. This required the co-development of design algorithms with gates that are sufficiently simple and robust to be connected by automated algorithms. We demonstrate that engineering principles can be applied to identify and suppress errors that complicate the compositions of larger systems. This approach leads to highly repetitive and modular genetics, in stark contrast to the encoding of natural regulatory networks. The use of a hardware-independent language and the creation of additional UCFs will allow a single design to be transformed into DNA for different organisms, genetic endpoints, operating conditions, and gate technologies.Genetic programming using Cello.A user specifies the desired circuit function in Verilog code, and this is transformed into a DNA sequence. An example circuit is shown (0xF6); red and blue curves are predicted output states for populations of cells, and solid black distributions are experimental flow cytometry data. The outputs are shown for all combinations of sensor states; plus and minus signs indicate the presence or absence of input signal. RBS, ribosome binding site; RPU, relative promoter unit; YFP, yellow fluorescent protein.Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits for Escherichia coli (880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92\% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization.

    @Article{Nielsenaac7341,
    Title = {Genetic circuit design automation},
    Author = {Nielsen, Alec A. K. and Der, Bryan S. and Shin, Jonghyeon and Vaidyanathan, Prashant and Paralanov, Vanya and Strychalski, Elizabeth A. and Ross, David and Densmore, Douglas and Voigt, Christopher A.},
    Journal = {Science},
    Year = {2016},
    Number = {6281},
    Volume = {352},
    Abstract = {As synthetic biology techniques become more powerful, researchers are anticipating a future in which the design of biological circuits will be similar to the design of integrated circuits in electronics. Nielsen et al. describe what is essentially a programming language to design computational circuits in living cells. The circuits generated on plasmids expressed in Escherichia coli required careful insulation from their genetic context, but primarily functioned as specified. The circuits could, for example, regulate cellular functions in response to multiple environmental signals. Such a strategy can facilitate the development of more complex circuits by genetic engineering.Science, this issue p. 10.1126/science.aac7341INTRODUCTIONCells respond to their environment, make decisions, build structures, and coordinate tasks. Underlying these processes are computational operations performed by networks of regulatory proteins that integrate signals and control the timing of gene expression. Harnessing this capability is critical for biotechnology projects that require decision-making, control, sensing, or spatial organization. It has been shown that cells can be programmed using synthetic genetic circuits composed of regulators organized to generate a desired operation. However, the construction of even simple circuits is time-intensive and unreliable.RATIONALEElectronic design automation (EDA) was developed to aid engineers in the design of semiconductor-based electronics. In an effort to accelerate genetic circuit design, we applied principles from EDA to enable increased circuit complexity and to simplify the incorporation of synthetic gene regulation into genetic engineering projects. We used the hardware description language Verilog to enable a user to describe a circuit function. The user also specifies the sensors, actuators, and {\textquotedblleft}user constraints file{\textquotedblright} (UCF), which defines the organism, gate technology, and valid operating conditions. Cello (www.cellocad.org) uses this information to automatically design a DNA sequence encoding the desired circuit. This is done via a set of algorithms that parse the Verilog text, create the circuit diagram, assign gates, balance constraints to build the DNA, and simulate performance.RESULTSCello designs circuits by drawing upon a library of Boolean logic gates. Here, the gate technology consists of NOT/NOR logic based on repressors. Gate connection is simplified by defining the input and output signals as RNA polymerase (RNAP) fluxes. We found that the gates need to be insulated from their genetic context to function reliably in the context of different circuits. Each gate is isolated using strong terminators to block RNAP leakage, and input interchangeability is improved using ribozymes and promoter spacers. These parts are varied for each gate to avoid breakage due to recombination. Measuring the load of each gate and incorporating this into the optimization algorithms further reduces evolutionary pressure.Cello was applied to the design of 60 circuits for Escherichia coli, where the circuit function was specified using Verilog code and transformed to a DNA sequence. The DNA sequences were built as specified with no additional tuning, requiring 880,000 base pairs of DNA assembly. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts). Across all circuits, 92\% of the 412 output states functioned as predicted.CONCLUSIONOur work constitutes a hardware description language for programming living cells. This required the co-development of design algorithms with gates that are sufficiently simple and robust to be connected by automated algorithms. We demonstrate that engineering principles can be applied to identify and suppress errors that complicate the compositions of larger systems. This approach leads to highly repetitive and modular genetics, in stark contrast to the encoding of natural regulatory networks. The use of a hardware-independent language and the creation of additional UCFs will allow a single design to be transformed into DNA for different organisms, genetic endpoints, operating conditions, and gate technologies.Genetic programming using Cello.A user specifies the desired circuit function in Verilog code, and this is transformed into a DNA sequence. An example circuit is shown (0xF6); red and blue curves are predicted output states for populations of cells, and solid black distributions are experimental flow cytometry data. The outputs are shown for all combinations of sensor states; plus and minus signs indicate the presence or absence of input signal. RBS, ribosome binding site; RPU, relative promoter unit; YFP, yellow fluorescent protein.Computation can be performed in living cells by DNA-encoded circuits that process sensory information and control biological functions. Their construction is time-intensive, requiring manual part assembly and balancing of regulator expression. We describe a design environment, Cello, in which a user writes Verilog code that is automatically transformed into a DNA sequence. Algorithms build a circuit diagram, assign and connect gates, and simulate performance. Reliable circuit design requires the insulation of gates from genetic context, so that they function identically when used in different circuits. We used Cello to design 60 circuits for Escherichia coli (880,000 base pairs of DNA), for which each DNA sequence was built as predicted by the software with no additional tuning. Of these, 45 circuits performed correctly in every output state (up to 10 regulators and 55 parts), and across all circuits 92\% of the output states functioned as predicted. Design automation simplifies the incorporation of genetic circuits into biotechnology projects that require decision-making, control, sensing, or spatial organization.},
    DOI = {10.1126/science.aac7341},
    Eprint = {http://science.sciencemag.org/content/352/6281/aac7341.full.pdf},
    ISSN = {0036-8075},
    Publisher = {American Association for the Advancement of Science},
    URL = {http://science.sciencemag.org/content/352/6281/aac7341}
    }

  • A. Lashkaripour, L. Ortiz, M. Pavan, R. Sanka, and D. Densmore, Cell-Free Transcription and Translation Reactions with Droplet Microfluidics, talk presented at the Engineering Biology Research Consortium (EBRC) , 2016.
    [BibTeX] [Download PDF]
    @Misc{EBRC16,
    author = {Lashkaripour, Ali and Ortiz, Luis and Pavan, Marilene and Sanka, Radhakrishna and Densmore, Douglas},
    title = {Cell-Free Transcription and Translation Reactions with Droplet Microfluidics},
    howpublished = {talk presented at the Engineering Biology Research Consortium (EBRC)},
    month = Nov,
    year = {2016},
    url = {http://cidarlab.org/wp-content/uploads/2016/11/Ali-EBRC.pdf}
    }

2015

  • A. Pacheco, R. Silva, S. Iverson, T. Haddock, and D. Densmore, Multicellular Logic through Conversion of Genetic Circuit Outputs into Electrical Signals, poster presented at Synberc: Fall 2015 , September, 2015.
    [BibTeX] [Download PDF]
    @Misc{PachecoSynberc62015,
    Title = {Multicellular Logic through Conversion of Genetic Circuit Outputs into Electrical Signals},
    Author = {Pacheco, Alan and Silva, Ryan and Iverson, Sonya and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at Synberc: Fall 2015},
    Month = {September},
    Year = {2015},
    Keywords = {posters, synthetic biology},
    URL = {http://cidarlab.org/wp-content/uploads/2016/02/Synberc_TweeColi_Poster_Pacheco.pdf}
    }

  • A. Durkan, K. Lewis, I. Turshudzhyan, K. L. Fort, N. Roehner, P. Vaidyanathan, and D. Densmore, Phagebook, poster presented at Synberc: Fall 2015 , September, 2015.
    [BibTeX] [Abstract] [Download PDF]
    http://cidarlab.org/wp-content/uploads/2016/09/phagebook-iwbda2016-2.pdf

    @Misc{turshudzhyan2015phagebooksynberc,
    author = {Allison Durkan and Kathleen Lewis and Inna Turshudzhyan and Kara Le Fort and Nicholas Roehner and Prashant Vaidyanathan and Douglas Densmore},
    title = {Phagebook},
    howpublished = {poster presented at Synberc: Fall 2015},
    month = {September},
    year = {2015},
    abstract = {http://cidarlab.org/wp-content/uploads/2016/09/phagebook-iwbda2016-2.pdf},
    url = {http://cidarlab.org/wp-content/uploads/2016/09/Phagebook-Poster-synberc-2015.pdf}
    }

  • R. Silva, Heuckroth Aaron, C. Huang, A. Rolfe, and D. Densmore, MakerFluidics: Microfluidics for all, poster presented at Synberc: Fall 2015 , September, 2015.
    [BibTeX] [Download PDF]
    @Misc{SilvaSynberc2015,
    Title = {MakerFluidics: Microfluidics for all},
    Author = {Silva, Ryan and Heuckroth, Aaron, and Huang, Cassie and Rolfe, Aparna and Densmore, Douglas},
    HowPublished = {poster presented at Synberc: Fall 2015},
    Month = {September},
    Year = {2015},
    Keywords = {posters, synthetic biology},
    URL = {http://cidarlab.org/wp-content/uploads/2016/02/Synberc_MakerFluidics_Poster_Silva.pdf}
    }

  • E. Appleton, P. Vaidyanathan, A. Pacheco, I. Haghighi, C. Vasile, C. Madsen, N. Roehner, Y. Agarwal, Z. Chapasko, C. Belta, and D. Densmore, Phoenix: A Design-Build-Test-Learn Tool, talk presented at the Synberc 2015 Fall Retreat , September, 2015.
    [BibTeX]
    @Misc{AppletonSynBERCPhoenix2015,
    Title = {Phoenix: A Design-Build-Test-Learn Tool},
    Author = {Evan Appleton and Prashant Vaidyanathan and Alan Pacheco and Iman Haghighi and Christian-loan Vasile and Curtis Madsen and Nicholas Roehner and Yash Agarwal and Zachary Chapasko and Calin Belta and Douglas Densmore},
    HowPublished = {talk presented at the Synberc 2015 Fall Retreat},
    Month = {September},
    Year = {2015},
    Keywords = {phoenix, cidar}
    }

  • C. Belta, D. Densmore, V. Kumar, and R. Weiss, CPS: Frontier: Collaborative Research: bioCPS for Engineering Living Cells, poster presented at the NSF CPS PI Meeting 2015 , November, 2015.
    [BibTeX]
    @Misc{nsfcps2015,
    Title = {CPS: Frontier: Collaborative Research: bioCPS for Engineering Living Cells},
    Author = {Calin Belta and Doug Densmore and Vijay Kumar and Ron Weiss},
    HowPublished = {poster presented at the NSF CPS PI Meeting 2015 },
    Month = {November},
    Year = {2015}
    }

  • N. Roehner and D. Densmore, Double Dutch: A Tool for Designing Libraries of Variant Metabolic Pathways, poster presented at the SynBERC 2014 Spring Retreat , March, 2015.
    [BibTeX] [Download PDF]
    @Misc{nic_roehner_IWBDA_2015,
    Title = {Double Dutch: A Tool for Designing Libraries of Variant Metabolic Pathways},
    Author = {Roehner, Nicholas and Densmore, Douglas},
    HowPublished = {poster presented at the SynBERC 2014 Spring Retreat},
    Month = {March},
    Year = {2015},
    Timestamp = {2015.09.01},
    URL = {http://cidarlab.org/wp-content/uploads/2015/09/roehner_synberc_2015_poster.pdf}
    }

  • A. Heuckroth, C. Huang, R. Silva, S. Iverson, T. Haddock, A. Pacheco, and D. Densmore, Accessible Microfluidic Mold Fabrication Using 3D Printing, poster presented at the Synberc 2015 Spring Retreat, Berkeley CA , March, 2015.
    [BibTeX] [Download PDF]
    @Misc{HeuckrothSynBERCS2015,
    Title = {Accessible Microfluidic Mold Fabrication Using 3D Printing},
    Author = {Heuckroth, Aaron and Huang, Cassie and Silva, Ryan and Iverson, Sonya and Haddock, Traci and Pacheco, Alan and Densmore, Douglas},
    HowPublished = {poster presented at the Synberc 2015 Spring Retreat, Berkeley CA},
    Month = {March},
    Year = {2015},
    Keywords = {fluigi, microfluidics, 3D-printing, 3D printing, mold, fabrication, design},
    Timestamp = {2015.03.30},
    URL = {http://cidarlab.org/wp-content/uploads/2015/03/accessible-microfluidics-SynBERC-S2015.pdf}
    }

  • S. Iverson, J. Beal, T. Haddock, and D. Densmore, E. coli MoClo assembly & part library: Applications in traditional biological research, poster presented at the Systems and Synthetic Biology Summer School in Italy , July, 2015.
    [BibTeX] [Download PDF]
    @Misc{iverson_SSBSS15,
    Title = {E. coli MoClo assembly \& part library: Applications in traditional biological research},
    Author = {Iverson, Sonya and Beal, Jake and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at the Systems and Synthetic Biology Summer School in Italy},
    Month = {July},
    Year = {2015},
    Owner = {Sonya Iverson},
    Timestamp = {2015.11.29},
    URL = {http://cidarlab.org/wp-content/uploads/2015/04/SSBSS15.pdf}
    }

  • N. Roehner and D. Densmore, Double Dutch: A Tool for Designing Libraries of Variant Metabolic Pathways, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.
    [BibTeX] [Download PDF]
    @Misc{nic_roehner_IWBDA_doubledutch_2015,
    Title = {Double Dutch: A Tool for Designing Libraries of Variant Metabolic Pathways},
    Author = {Roehner, Nicholas and Densmore, Douglas},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {August},
    Year = {2015},
    Timestamp = {2015.09.01},
    URL = {http://cidarlab.org/wp-content/uploads/2015/09/double_dutch_camera_ready.pdf}
    }

  • K. Lewis, A. Durkan, Turshudzhyan, K. Le Fort, N. Roehner, P. Vaidyanathan, and D. Densmore, Phagebook, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.
    [BibTeX] [Download PDF]
    @Misc{LewisPhagebookIWBDA2015,
    Title = {Phagebook},
    Author = {Lewis, Kathleen and Durkan, Allison and Turshudzhyan and Le Fort, Kara and Roehner, Nicholas and Vaidyanathan, Prashant and Densmore, Douglas},
    HowPublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {August},
    Year = {2015},
    Timestamp = {2015.09.01},
    URL = {http://cidarlab.org/wp-content/uploads/2015/09/Phagebook-Poster-3.pdf}
    }

  • E. Appleton, E. Oberortner, P. Vaidyanathan, Z. Chapasko, Y. Pacheco Alan andAgarwal, N. Roehner, T. Haddock, and D. Densmore, Phoenix: An automated design-build, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , August, 2015.
    [BibTeX] [Download PDF]
    @Misc{AppletonPhoenixIWBDA2015,
    Title = {Phoenix: An automated design-build},
    Author = {Appleton, Evan and Oberortner, Ernst and Vaidyanathan, Prashant and Chapasko, Zachary and Pacheco, Alan andAgarwal, Yash and Roehner, Nicholas and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {August},
    Year = {2015},
    Owner = {Evan Appleton},
    URL = {http://cidarlab.org/wp-content/uploads/2015/09/IWBDA_Poster.pdf}
    }

  • T. Haddock, D. Densmore, E. Appleton, S. Carr, S. Iverson, and M. De Freitas, 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, BioBricks Foundation Request for Comments , August, 2015.
    [BibTeX] [Download PDF]
    @Misc{iverson_SSBSS15_RFC,
    Title = {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},
    Author = {Haddock, Traci and Densmore, Douglas and Appleton, Evan and Carr, Swati and Iverson, Sonya and De Freitas, Monique},
    HowPublished = {BioBricks Foundation Request for Comments},
    Month = {August},
    Year = {2015},
    Owner = {Sonya Iverson},
    Timestamp = {2015.11.29},
    URL = {http://dspace.mit.edu/bitstream/handle/1721.1/98267/BBFRFC94.pdf?sequence=1}
    }

  • P. Vaidyanathan, B. S. Der, S. Bhatia, N. Roehner, R. Silva, C. A. Voigt, and D. Densmore, “A Framework for Genetic Logic Synthesis,” Proceedings of the IEEE, vol. 103, iss. 11, pp. 2196-2207, 2015. doi:10.1109/JPROC.2015.2443832
    [BibTeX]
    @Article{vaidyanathanframework,
    Title = {A Framework for Genetic Logic Synthesis},
    Author = {Vaidyanathan, P. and Der, B.S. and Bhatia, S. and Roehner, N. and Silva, R. and Voigt, C.A. and Densmore, D.},
    Journal = {Proceedings of the IEEE},
    Year = {2015},
    Number = {11},
    Pages = {2196-2207},
    Volume = {103},
    DOI = {10.1109/JPROC.2015.2443832},
    ISSN = {0018-9219},
    Keywords = {Crosstalk;DNA;Encoding;Logic gates;Proteins;RNA;Boolean;digital;genetic;logic;synthesis;synthetic biology;transcription}
    }

  • H. Huang, “Fluigi: An end-to-end Software Workflow for Microfluidic Design,” PhD Thesis, Boston University, 2015.
    [BibTeX] [Download PDF]
    @PhdThesis{Huang2014,
    Title = {Fluigi: An end-to-end Software Workflow for Microfluidic Design},
    Author = {Huang, Haiyao},
    School = {Boston University},
    Year = {2015},
    URL = {http://cidarlab.org/wp-content/uploads/2016/02/ch_2015_thesis.pdf}
    }

  • S. Iverson, T. L. Haddock, J. Beal, and D. Densmore, “CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enables Rapid Combinatorial Design for Synthetic and Traditional Biology,” ACS Synthetic Biology, iss. ja, p. null, 2015. doi:10.1021/acssynbio.5b00124
    [BibTeX] [Download PDF]
    @Article{doi:10.1021/acssynbio.5b00124,
    Title = {CIDAR MoClo: Improved MoClo Assembly Standard and New E. coli Part Library Enables Rapid Combinatorial Design for Synthetic and Traditional Biology},
    Author = {Sonya Iverson and Traci L. Haddock and Jacob Beal and Douglas Densmore},
    Journal = {ACS Synthetic Biology},
    Year = {2015},
    Note = {PMID: 26479688},
    Number = {ja},
    Pages = {null},
    Volume = {0},
    DOI = {10.1021/acssynbio.5b00124},
    Eprint = { http://dx.doi.org/10.1021/acssynbio.5b00124 },
    Owner = {Obdurate_2},
    Timestamp = {2015.11.02},
    URL = {http://dx.doi.org/10.1021/acssynbio.5b00124}
    }

2014

  • E. Oberortner, S. Bhatia, E. Lindgren, and D. Densmore, “A Rule-Based Design Specification Language for Synthetic Biology,” J. Emerg. Technol. Comput. Syst. Special Issue on Synthetic Biology, vol. 11, iss. 3, p. 25:1–25:19, 2014. doi:10.1145/2641571
    [BibTeX] [Download PDF]
    @Article{Oberortner:2014:RDS:2711453.2641571,
    Title = {A Rule-Based Design Specification Language for Synthetic Biology},
    Author = {Oberortner, Ernst and Bhatia, Swapnil and Lindgren, Erik and Densmore, Douglas},
    Journal = {J. Emerg. Technol. Comput. Syst. Special Issue on Synthetic Biology},
    Year = {2014},
    Month = dec,
    Number = {3},
    Pages = {25:1--25:19},
    Volume = {11},
    Acmid = {2641571},
    Address = {New York, NY, USA},
    Articleno = {25},
    DOI = {10.1145/2641571},
    ISSN = {1550-4832},
    Issue_date = {December 2014},
    Keywords = {Synthetic biology, design, language, rule, specification, template},
    Numpages = {19},
    Owner = {Aaron},
    Publisher = {ACM},
    Timestamp = {2015.01.28},
    URL = {http://doi.acm.org/10.1145/2641571}
    }

  • E. Oberortner and D. Densmore, An Ecosystem of Rule-Based Design Tools and Languages, poster presented at the Synberc 2014 Spring Retreat, Berkeley CA , March, 2014.
    [BibTeX] [Abstract] [Download PDF]
    The synthetic biology design paradigm recursively decomposes a system into smaller sub-systems that can be designed independently. Then, those sub-systems are composed to resultantly build a functioning system. We develop an ecosystem of tools, languages, and standards for an automated in silico design of DNA sequences, Parts, Devices, and Systems compliant with biological rules and constraints. Here, we present two tools of this ecosystem – -Sparrow and miniEugene — and their automated data exchange. Sparrow is a rule-based system to discover knowledge of biological data and rules on designing novel biological systems. For the time being, Sparrow supports importing data (e.g. parts, devices, or designs) and querying data based on characteristics (e.g. type, strength, media, or growth rate). miniEugene arranges the composition of a system’s sub-systems according to a given set of constraints. We support constraints regarding the position, orientation, and count of a system’s sub-components, as well as their pair-wise occurrence and regulatory interactions among them. In this ecosystem, we support an automated data exchange using the SBOL standard data format and scientific workflow systems. We demonstrate an automated workflow between Sparrow and miniEugene on designing a genetic Priority Encoder circuit. This solution enables to customize and automate synthetic biology workflows rapidly — the ultimate goal of the Eugene ecosystem.

    @Misc{SynBERCEcosystem2014,
    Title = {An Ecosystem of Rule-Based Design Tools and Languages},
    Author = {Ernst Oberortner and Douglas Densmore},
    HowPublished = {poster presented at the Synberc 2014 Spring Retreat, Berkeley CA},
    Month = {March},
    Year = {2014},
    Abstract = {The synthetic biology design paradigm recursively decomposes a system into smaller sub-systems that can be designed independently. Then, those sub-systems are composed to resultantly build a functioning system.
    We develop an ecosystem of tools, languages, and standards for an automated in silico design of DNA sequences, Parts, Devices, and Systems compliant with biological rules and constraints. Here, we present two tools of this ecosystem - -Sparrow and miniEugene -- and their automated data exchange.
    Sparrow is a rule-based system to discover knowledge of biological data and rules on designing novel biological systems. For the time being, Sparrow supports importing data (e.g. parts, devices, or designs) and querying data based on characteristics (e.g. type, strength, media, or growth rate).
    miniEugene arranges the composition of a system's sub-systems according to a given set of constraints. We support constraints regarding the position, orientation, and count of a system's sub-components, as well as their pair-wise occurrence and regulatory interactions among them.
    In this ecosystem, we support an automated data exchange using the SBOL standard data format and scientific workflow systems. We demonstrate an automated workflow between Sparrow and miniEugene on designing a genetic Priority Encoder circuit. This solution enables to customize and automate synthetic biology workflows rapidly -- the ultimate goal of the Eugene ecosystem.},
    Keywords = {eugene, CIDAR, synthetic biology, software},
    Timestamp = {2014.04.07},
    URL = {http://cidarlab.org/wp-content/uploads/2014/04/Oberortner_SynBERC_Spring2014_Poster-1.pdf}
    }

  • E. Oberortner, A. Lewis, and D. Densmore, Towards Rule-based Knowledge Systems for Synthetic Biology, presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2014.
    [BibTeX] [Download PDF]
    @Misc{OberortnerIWBDA2014,
    Title = {Towards Rule-based Knowledge Systems for Synthetic Biology},
    Author = {Oberortner, E. and Lewis, A. and Densmore, D.},
    HowPublished = {presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {June},
    Year = {2014},
    Booktitle = {International Workshop on Biodesign Automation (IWBDA)},
    Journal = {IWBDA},
    Keywords = {eugene},
    Timestamp = {2014.08.25},
    URL = {http://cidarlab.org/wp-content/uploads/2014/08/OberortnerIWBDA2014.pdf}
    }

  • S. Iverson, J. Beal, T. Haddock, and D. Densmore, Efficient Modular, Mulitpart and Multiplex DNA Assembly System, poster presented at the Syn Bio Boston and IWBDA , June, 2014.
    [BibTeX] [Download PDF]
    @Misc{iverson_IWBDA14,
    Title = {Efficient Modular, Mulitpart and Multiplex DNA Assembly System},
    Author = {Iverson, Sonya and Beal, Jake and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at the Syn Bio Boston and IWBDA},
    Month = {June},
    Year = {2014},
    Owner = {Sonya Iverson},
    Timestamp = {2015.11.29},
    URL = {http://cidarlab.org/wp-content/uploads/2015/11/Syn-Bio-Boston-2014.pdf}
    }

  • S. Paige, P. Vaidyanathan, M. Bates, J. C. Anderson, and D. Densmore, Clotho 3.0: An Improved Common Framework for Synthetic Biology Computing, poster presented at Synthetic Biology Boston , June, 2014.
    [BibTeX] [Download PDF]
    @Misc{PaigeClothoSBB2014,
    Title = {Clotho 3.0: An Improved Common Framework for Synthetic Biology Computing},
    Author = {Paige, S. and Vaidyanathan, P. and Bates, M. and Anderson, J.C. and Densmore, D.},
    HowPublished = {poster presented at Synthetic Biology Boston},
    Month = {June},
    Year = {2014},
    Keywords = {clotho},
    Timestamp = {2014.08.25},
    URL = {http://cidarlab.org/wp-content/uploads/2014/08/PaigeClothoSBB20141.pdf}
    }

  • S. Paige, S. Iverson, A. Heuckroth, S. Carr, T. Haddock, and D. Densmore, The Boston University Center of Synthetic Biology (CoSBi) ICE Repository, poster presented at the Internaional Workshop on Bio-Design Automation (IWBDA) , June, 2014.
    [BibTeX] [Download PDF]
    @Misc{PaigeICEIWBDA2014,
    Title = {The Boston University Center of Synthetic Biology (CoSBi) ICE Repository},
    Author = {Paige, S. and Iverson, S. and Heuckroth, A. and Carr, S. and Haddock, T. and Densmore, D.},
    HowPublished = {poster presented at the Internaional Workshop on Bio-Design Automation (IWBDA)},
    Month = {June},
    Year = {2014},
    Owner = {Kirrei},
    Timestamp = {2014.08.26},
    URL = {http://cidarlab.org/wp-content/uploads/2014/08/PaigeICEIWBDA2014.pdf}
    }

  • J. McNamara, S. Lightfoot, K. Drinkwater, E. Appleton, and K. Oye, “Designing safety policies to meet evolving needs: iGEM as a testbed for proactive and adaptive risk management.,” ACS Synthetic Biology, in press., 2014.
    [BibTeX]
    @Article{McNamara2014,
    Title = {Designing safety policies to meet evolving needs: iGEM as a testbed for proactive and adaptive risk management.},
    Author = {McNamara, J. and Lightfoot, S. and Drinkwater, K. and Appleton, E. and Oye, K.},
    Journal = {ACS Synthetic Biology, in press.},
    Year = {2014},
    Timestamp = {2014.08.25}
    }

  • M. J. Smanski, S. Bhatia, D. Zhao, Y. Park, L. B A Woodruff, G. Giannoukos, D. Ciulla, M. Busby, J. Calderon, R. Nicol, B. D. Gordon, D. Densmore, and C. A. Voigt, “Functional optimization of gene clusters by combinatorial design and assembly,” Nat Biotech, vol. advance online publication, 2014.
    [BibTeX] [Abstract] [Download PDF]
    Large microbial gene clusters encode useful functions, including energy utilization and natural product biosynthesis, but genetic manipulation of such systems is slow, difficult and complicated by complex regulation. We exploit the modularity of a refactored Klebsiella oxytoca nitrogen fixation (nif) gene cluster (16 genes, 103 parts) to build genetic permutations that could not be achieved by starting from the wild-type cluster. Constraint-based combinatorial design and DNA assembly are used to build libraries of radically different cluster architectures by varying part choice, gene order, gene orientation and operon occupancy. We construct 84 variants of the nifUSVWZM operon, 145 variants of the nifHDKY operon, 155 variants of the nifHDKYENJ operon and 122 variants of the complete 16-gene pathway. The performance and behavior of these variants are characterized by nitrogenase assay and strand-specific RNA sequencing (RNA-seq), and the results are incorporated into subsequent design cycles. We have produced a fully synthetic cluster that recovers 57% of wild-type activity. Our approach allows the performance of genetic parts to be quantified simultaneously in hundreds of genetic contexts. This parallelized design-build-test-learn cycle, which can access previously unattainable regions of genetic space, should provide a useful, fast tool for genetic optimization and hypothesis testing.

    @Article{Smakski_func_opt_2014,
    Title = {Functional optimization of gene clusters by combinatorial design and assembly},
    Author = {Smanski, Michael J and Bhatia, Swapnil and Zhao, Dehua and Park, YongJin and B A Woodruff, Lauren and Giannoukos, Georgia and Ciulla, Dawn and Busby, Michele and Calderon, Johnathan and Nicol, Robert and Gordon, D Benjamin and Densmore, Douglas and Voigt, Christopher A},
    Journal = {Nat Biotech},
    Year = {2014},
    Month = nov,
    Volume = {advance online publication},
    Abstract = {Large microbial gene clusters encode useful functions, including energy utilization and natural product biosynthesis, but genetic manipulation of such systems is slow, difficult and complicated by complex regulation. We exploit the modularity of a refactored Klebsiella oxytoca nitrogen fixation (nif) gene cluster (16 genes, 103 parts) to build genetic permutations that could not be achieved by starting from the wild-type cluster. Constraint-based combinatorial design and DNA assembly are used to build libraries of radically different cluster architectures by varying part choice, gene order, gene orientation and operon occupancy. We construct 84 variants of the nifUSVWZM operon, 145 variants of the nifHDKY operon, 155 variants of the nifHDKYENJ operon and 122 variants of the complete 16-gene pathway. The performance and behavior of these variants are characterized by nitrogenase assay and strand-specific RNA sequencing (RNA-seq), and the results are incorporated into subsequent design cycles. We have produced a fully synthetic cluster that recovers 57% of wild-type activity. Our approach allows the performance of genetic parts to be quantified simultaneously in hundreds of genetic contexts. This parallelized design-build-test-learn cycle, which can access previously unattainable regions of genetic space, should provide a useful, fast tool for genetic optimization and hypothesis testing.},
    ISSN = {1546-1696},
    Publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
    Timestamp = {2014.12.08},
    URL = {http://dx.doi.org/10.1038/nbt.3063}
    }

  • K. A. Oye, K. Esvelt, E. Appleton, F. Catteruccia, G. Church, T. Kuiken, S. B. Lightfoot, J. McNamara, A. Smidler, and J. P. Collins, “Regulating gene drives,” Science, vol. 345, iss. 6197, pp. 626-628, 2014.
    [BibTeX] [Download PDF]
    @Article{Oye2014,
    Title = {Regulating gene drives},
    Author = {Oye, Kenneth A. and Esvelt, Kevin and Appleton, Evan and Catteruccia, Flaminia and Church, George and Kuiken, Todd and Lightfoot, Shlomiya Bar-Yam and McNamara, Julie and Smidler, Andrea and Collins, James P.},
    Journal = {Science},
    Year = {2014},
    Note = {ACS Synthetic Biology, 2014. In press.},
    Number = {6197},
    Pages = {626-628},
    Volume = {345},
    Timestamp = {2014.08.25},
    URL = {http://www.sciencemag.org/content/345/6197/626.summary}
    }

  • H. Huang and D. Densmore, “Integration of microfluidics into the synthetic biology design flow,” Lab on a Chip, vol. 14, iss. 18, pp. 3459-3474, 2014.
    [BibTeX] [Download PDF]
    @Article{huang2014integration,
    Title = {Integration of microfluidics into the synthetic biology design flow},
    Author = {Huang, Haiyao and Densmore, Douglas},
    Journal = {Lab on a Chip},
    Year = {2014},
    Number = {18},
    Pages = {3459--3474},
    Volume = {14},
    Publisher = {Royal Society of Chemistry},
    URL = {http://pubs.rsc.org/en/content/articlelanding/2014/lc/c4lc00509k#!divAbstract}
    }

  • J. Beal, T. E. Wagner, T. Kitada, O. Azizgolshani, J. M. Parker, D. Densmore, and R. Weiss, “Model-Driven Engineering of Gene Expression from RNA Replicons,” ACS Synthetic Biology, 2014. doi:10.1021/sb500173f
    [BibTeX] [Download PDF]

  • E. Appleton, J. Tao, C. F. Wheatley, D. H. Desai, T. M. Lozanoski, P. D. Shah, J. A. Awtry, S. S. Jin, T. L. Haddock, and D. M. Densmore, “Owl: Electronic Datasheet Generator,” ACS Synthetic Biology, vol. 3, iss. 12, pp. 966-968, 2014. doi:10.1021/sb500053j
    [BibTeX] [Download PDF]
    @Article{doi:10.1021/sb500053j,
    Title = {Owl: Electronic Datasheet Generator},
    Author = {Appleton, Evan and Tao, Jenhan and Wheatley, F. Carter and Desai, Devina H. and Lozanoski, Thomas M. and Shah, Pooja D. and Awtry, Jake A. and Jin, Shawn S. and Haddock, Traci L. and Densmore, Douglas M.},
    Journal = {ACS Synthetic Biology},
    Year = {2014},
    Note = {PMID: 25524100},
    Number = {12},
    Pages = {966-968},
    Volume = {3},
    DOI = {10.1021/sb500053j},
    Eprint = { http://dx.doi.org/10.1021/sb500053j },
    Owner = {Aaron},
    Timestamp = {2015.01.28},
    URL = {http://dx.doi.org/10.1021/sb500053j}
    }

  • D. M. Densmore and S. Bhatia, “Bio-design automation: software + biology + robots,” Trends in Biotechnology, vol. 32, iss. 3, pp. 111-113, 2014. doi:10.1016/j.tibtech.2013.10.005
    [BibTeX] [Download PDF]
    @Article{Densmore2014111,
    Title = {Bio-design automation: software + biology + robots },
    Author = {Douglas M. Densmore and Swapnil Bhatia},
    Journal = {Trends in Biotechnology },
    Year = {2014},
    Number = {3},
    Pages = {111 - 113},
    Volume = {32},
    DOI = {10.1016/j.tibtech.2013.10.005},
    ISSN = {0167-7799},
    Keywords = {design automation},
    URL = {http://www.sciencedirect.com/science/article/pii/S0167779913002230}
    }

  • E. Oberortner and D. Densmore, “Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems,” ACS Synthetic Biology, p. null, 2014. doi:10.1021/sb500352b
    [BibTeX] [Abstract] [Download PDF]
    miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system—the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology (www.eugenecad.org).

    @Article{doi:10.1021/sb500352b,
    Title = {Web-Based Software Tool for Constraint-Based Design Specification of Synthetic Biological Systems},
    Author = {Oberortner, Ernst and Densmore, Douglas},
    Journal = {ACS Synthetic Biology},
    Year = {2014},
    Note = {PMID: 25426642},
    Number = {0},
    Pages = {null},
    Volume = {0},
    Abstract = { miniEugene provides computational support for solving combinatorial design problems, enabling users to specify and enumerate designs for novel biological systems based on sets of biological constraints. This technical note presents a brief tutorial for biologists and software engineers in the field of synthetic biology on how to use miniEugene. After reading this technical note, users should know which biological constraints are available in miniEugene, understand the syntax and semantics of these constraints, and be able to follow a step-by-step guide to specify the design of a classical synthetic biological system—the genetic toggle switch.1 We also provide links and references to more information on the miniEugene web application and the integration of the miniEugene software library into sophisticated Computer-Aided Design (CAD) tools for synthetic biology (www.eugenecad.org). },
    DOI = {10.1021/sb500352b},
    Eprint = { http://dx.doi.org/10.1021/sb500352b },
    Owner = {Aaron},
    Timestamp = {2015.02.02},
    URL = {
    http://dx.doi.org/10.1021/sb500352b
    }
    }

  • H. Huang and D. Densmore, Fluigi: Microfluidic Device Synthesis for Synthetic Biology, poster presented at Synthetic Biology: Boston , 2014.
    [BibTeX] [Download PDF]
    @Misc{Fluigi_huang_SBB_2014,
    Title = {Fluigi: Microfluidic Device Synthesis for Synthetic Biology},
    Author = {Huang, Haiyao and Densmore, Douglas},
    HowPublished = {poster presented at Synthetic Biology: Boston},
    Year = {2014},
    Journal = {Synthetic Biology: Boston},
    URL = {http://cidarlab.org/wp-content/uploads/2014/12/sb2_poster.pdf}
    }

  • H. Huang and D. Densmore, “Fluigi: Microfluidic Device Synthesis for Synthetic Biology,” J. Emerg. Technol. Comput. Syst. Special Issue on Synthetic Biology, vol. 11, iss. 3, p. 26:1–26:19, 2014. doi:10.1145/2660773
    [BibTeX] [Download PDF]
    @Article{Huang:2014:FMD:2711453.2660773,
    Title = {Fluigi: Microfluidic Device Synthesis for Synthetic Biology},
    Author = {Huang, Haiyao and Densmore, Douglas},
    Journal = {J. Emerg. Technol. Comput. Syst. Special Issue on Synthetic Biology},
    Year = {2014},
    Month = dec,
    Number = {3},
    Pages = {26:1--26:19},
    Volume = {11},
    Acmid = {2660773},
    Address = {New York, NY, USA},
    Articleno = {26},
    DOI = {10.1145/2660773},
    ISSN = {1550-4832},
    Issue_date = {December 2014},
    Keywords = {Synthetic biology, genetic circuits, microfluidics},
    Numpages = {19},
    Owner = {Aaron},
    Publisher = {ACM},
    Timestamp = {2015.01.28},
    URL = {http://doi.acm.org/10.1145/2660773}
    }

  • M. Galdzicki, K. P. Clancy, E. Oberortner, M. Pocock, J. Y. Quinn, C. A. Rodriguez, N. Roehner, M. L. Wilson, L. Adam, C. J. Anderson, B. A. Bartley, J. Beal, D. Chandran, J. Chen, D. Densmore, D. Endy, R. Grunberg, J. Hallinan, N. J. Hillson, J. D. Johnson, A. Kuchinsky, M. Lux, G. Misirli, J. Peccoud, H. A. Plahar, E. Sirin, G. Stan, A. Villalobos, A. Wipat, J. H. Gennari, C. J. Myers, and H. M. Sauro, “The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology,” Nature Biotechnology, vol. 32, iss. 6, pp. 545-550, 2014.
    [BibTeX] [Abstract] [Download PDF]
    The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.

    @Article{Galdzicki2014,
    Title = {The Synthetic Biology Open Language (SBOL) provides a community standard for communicating designs in synthetic biology},
    Author = {Galdzicki, Michal and Clancy, Kevin P and Oberortner, Ernst and Pocock, Matthew and Quinn, Jacqueline Y and Rodriguez, Cesar A and Roehner, Nicholas and Wilson, Mandy L and Adam, Laura and Anderson, J Christopher and Bartley, Bryan A and Beal, Jacob and Chandran, Deepak and Chen, Joanna and Densmore, Douglas and Endy, Drew and Grunberg, Raik and Hallinan, Jennifer and Hillson, Nathan J and Johnson, Jeffrey D and Kuchinsky, Allan and Lux, Matthew and Misirli, Goksel and Peccoud, Jean and Plahar, Hector A and Sirin, Evren and Stan, Guy-Bart and Villalobos, Alan and Wipat, Anil and Gennari, John H and Myers, Chris J and Sauro, Herbert M},
    Journal = {Nature Biotechnology},
    Year = {2014},
    Month = jun,
    Number = {6},
    Pages = {545--550},
    Volume = {32},
    __markedentry = {[Kirrei:6]},
    Abstract = {The re-use of previously validated designs is critical to the evolution of synthetic biology from a research discipline to an engineering practice. Here we describe the Synthetic Biology Open Language (SBOL), a proposed data standard for exchanging designs within the synthetic biology community. SBOL represents synthetic biology designs in a community-driven, formalized format for exchange between software tools, research groups and commercial service providers. The SBOL Developers Group has implemented SBOL as an XML/RDF serialization and provides software libraries and specification documentation to help developers implement SBOL in their own software. We describe early successes, including a demonstration of the utility of SBOL for information exchange between several different software tools and repositories from both academic and industrial partners. As a community-driven standard, SBOL will be updated as synthetic biology evolves to provide specific capabilities for different aspects of the synthetic biology workflow.},
    ISSN = {1087-0156},
    Publisher = {Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.},
    Timestamp = {2014.08.25},
    URL = {http://dx.doi.org/10.1038/nbt.2891}
    }

  • E. Appleton, J. Tao, T. Haddock, and D. Densmore, “Interactive assembly algorithms for molecular cloning,” Nature Methods, 2014. doi:10.1038/nmeth.2939
    [BibTeX] [Download PDF]
    @Article{Appleton1038,
    Title = {Interactive assembly algorithms for molecular cloning},
    Author = {E Appleton and J Tao and T Haddock and D Densmore},
    Journal = {Nature Methods},
    Year = {2014},
    DOI = {10.1038/nmeth.2939},
    Keywords = {Raven, Synthetic Biology, Assembly, Design Automation},
    Timestamp = {2014.04.29},
    URL = {http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.2939.html}
    }

2013

  • S. B. Carr, E. Appleton, E. A. Gol, C. Belta, and D. M. Densmore, Transcriptional Inverters as Tools for Engineering Principle Formulation, poster presented at SynBERC 2013 Fall Retreat, Massachusetts Institute of Technology, Cambridge MA , September, 2013.
    [BibTeX] [Download PDF]
    @Misc{CarrSynBERCFall2013,
    Title = {Transcriptional Inverters as Tools for Engineering Principle Formulation},
    Author = {Swati B. Carr and Evan Appleton and Ebru Aydin Gol and Calin Belta and Douglas M. Densmore},
    HowPublished = {poster presented at SynBERC 2013 Fall Retreat, Massachusetts Institute of Technology, Cambridge MA},
    Month = {September},
    Year = {2013},
    Timestamp = {2013.11.08},
    URL = {http://cidarlab.org/wp-content/uploads/2013/11/CarrSynBERCFall2013.pdf}
    }

  • S. B. Carr and D. Densmore, Compositional Genetic Inverter Circuits for Complex Logic Functions, poster presented at the UK-US Partnerships in Synthetic Biology Poster Session, Boston University , September, 2013.
    [BibTeX] [Download PDF]
    @Misc{CarrUKUS2013,
    Title = {Compositional Genetic Inverter Circuits for Complex Logic Functions},
    Author = {Carr, Swati B. and Densmore, Douglas},
    HowPublished = {poster presented at the UK-US Partnerships in Synthetic Biology Poster Session, Boston University},
    Month = {September},
    Year = {2013},
    Timestamp = {2013.11.08},
    URL = {http://cidarlab.org/wp-content/uploads/2013/11/CarrUKUS2013.pdf}
    }

  • S. Iverson, T. Haddock, and D. Densmore, Multiplex Modular Assembly and Protein Engineering, poster presented at the SynBERC Spring Retreat, University of California-Berkeley , March, 2013.
    [BibTeX] [Download PDF]
    @Misc{IversonSynBERC2013,
    Title = {Multiplex Modular Assembly and Protein Engineering},
    Author = {Iverson, Sonya and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at the SynBERC Spring Retreat, University of California-Berkeley},
    Month = {March},
    Year = {2013},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/IversonSynBERC2013.pdf}
    }

  • H. Huang, S. Bhatia, A. Khalil, and D. Densmore, Fluigi: a computer aided design framework for combining microfluidics and synthetic biology, poster presented at the 6th International Meeting on Synthetic Biology (SB6.0) , July, 2013.
    [BibTeX] [Download PDF]
    @Misc{HuangSB62013,
    Title = {Fluigi: a computer aided design framework for combining microfluidics and synthetic biology},
    Author = {Huang, Haiyao and Bhatia, Swapnil and Khalil, Ahmad and Densmore, Douglas},
    HowPublished = {poster presented at the 6th International Meeting on Synthetic Biology (SB6.0)},
    Month = {July},
    Year = {2013},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/HuangSB62013.pdf}
    }

  • S. Iverson, T. Haddock, and D. Densmore, Development of a Multiplex Modular Cloning Assembly System, poster presented at the 6th International Meeting on Synthetic Biology (SB6.0) , July, 2013.
    [BibTeX] [Download PDF]
    @Misc{IversonSB62013,
    Title = {Development of a Multiplex Modular Cloning Assembly System},
    Author = {Iverson, Sonya and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at the 6th International Meeting on Synthetic Biology (SB6.0)},
    Month = {July},
    Year = {2013},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/IversonSB62013.pdf}
    }

  • J. Quinn, S. Bhatia, R. S. Cox, C. Rodriguez, L. Soldatova, J. Beal, K. Clancy, and D. Endy, Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology, talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England , July, 2013.
    [BibTeX]
    @Misc{quinnIWBDA2013,
    Title = {Synthetic Biology Open Language Visual: An Open-Source Graphical Notation for Synthetic Biology},
    Author = {Quinn, Jacqueline and Bhatia, Swapnil and Cox, Robert Sidney and Rodriguez, Cesar and Soldatova, Larisa and Beal, Jacob and Clancy, Kevin and Endy, Drew},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England},
    Month = {July},
    Year = {2013},
    Keywords = {synthetic biology},
    Timestamp = {2013.08.13}
    }

  • E. Appleton, J. Tao, and D. Densmore, Interactive Experimentally Driven Algorithms for Optimized DNA Assembly, talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England London, England: , July, 2013.
    [BibTeX] [Abstract] [Download PDF]
    Synthetic biologists build genetic devices from DNA parts. Once a device is designed, the problem of how to assemble it has a complex solution. Selection of the best assembly plan is error-prone and un-optimized when performed manually. Automated assembly is a key component of high-throughput cloning and can help biologists construct devices more effi- ciently and build part libraries with great modularity. DNA assembly algorithms exist to optimize the speed of assembly [2] but are agnostic to experimental constraints and only consider binary assembly methods. <br><br> We present a method that uses experimental data and dynamic programming op- timization algorithms in a computer-aided design tool called Raven that supports ‘binary’ and ‘multi-way’ (‘one pot’) DNA assemblies. Raven returns a hierarchical assembly plan optimized for time, modularity and efficiency, complete with assembly intermediates and their part junctions. For any cloning-based DNA assembly method [3, 6, 5], Raven automatically finds an optimized way to reuse existing parts and utilize experimental outcomes to inform future assembly optimizations to increase the speed and efficiency of assembly. <br><br> <a href="http://cidarlab.org/wp-content/uploads/2013/09/appleIWBDA2013_abs.pdf ">A detailed abstract for this IWBDA presentation is available here.</a>

    @Misc{appleIWBDA2013,
    Title = {Interactive Experimentally Driven Algorithms for Optimized DNA Assembly},
    Author = {Appleton, Evan and Tao, Jenhan and Densmore, Doug},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England},
    Month = {July},
    Year = {2013},
    Abstract = {Synthetic biologists build genetic devices from DNA parts. Once a device is designed, the problem of how to assemble it has a complex solution. Selection of the best assembly plan is error-prone and un-optimized when performed manually. Automated assembly is a key component of high-throughput cloning and can help biologists construct devices more effi- ciently and build part libraries with great modularity. DNA assembly algorithms exist to optimize the speed of assembly [2] but are agnostic to experimental constraints and only consider binary assembly methods. <br><br>
    We present a method that uses experimental data and dynamic programming op- timization algorithms in a computer-aided design tool called Raven that supports 'binary' and 'multi-way' ('one pot') DNA assemblies. Raven returns a hierarchical assembly plan optimized for time, modularity and efficiency, complete with assembly intermediates and their part junctions. For any cloning-based DNA assembly method [3, 6, 5], Raven automatically finds an optimized way to reuse existing parts and utilize experimental outcomes to inform future assembly optimizations to increase the speed and efficiency of assembly. <br><br>
    <a href="http://cidarlab.org/wp-content/uploads/2013/09/appleIWBDA2013_abs.pdf
    ">A detailed abstract for this IWBDA presentation is available here.</a>},
    Address = {London, England},
    Booktitle = {5th International Workshop for BioDesign Automation},
    Keywords = {raven, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/appleIWBDA2013.pdf}
    }

  • T. Haddock, M. D. Freitas, S. Jin, and D. Densmore, The Design, Assembly, and Characterization of a New Library of Standardized Modular DNA Parts, poster presented at the 6th International Meeting on Synthetic Biology (SB6.0) , July, 2013.
    [BibTeX] [Download PDF]
    @Misc{HaddockSB62013,
    Title = {The Design, Assembly, and Characterization of a New Library of Standardized Modular DNA Parts},
    Author = {Haddock, Traci and Freitas, Monique De and Jin, Shawn and Densmore, Douglas},
    HowPublished = {poster presented at the 6th International Meeting on Synthetic Biology (SB6.0)},
    Month = {July},
    Year = {2013},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/HaddockSB62013.pdf}
    }

  • S. B. Carr and D. Densmore, Compositional Genetic Inverter Circuits for Complex Logic Functions" Abstract for SB 6.0 (accepted), poster presented at the 6th International Meeting on Synthetic Biology (SB6.0), London, England , July, 2013.
    [BibTeX] [Abstract] [Download PDF]
    Inverters (NOT-gates) are elementary Boolean logic circuits, where the output is absent when the input is present. Inverters mimic the inverse relationships between molecules in natural systems that are responsible for maintaining steady state, and as such form an essential tool in the synthetic biologist’s toolkit.

    @Misc{CarrSB62013,
    Title = {Compositional Genetic Inverter Circuits for Complex Logic Functions" Abstract for SB 6.0 (accepted)},
    Author = {Carr, Swati B. and Densmore, Douglas},
    HowPublished = {poster presented at the 6th International Meeting on Synthetic Biology (SB6.0), London, England},
    Month = {July},
    Year = {2013},
    Abstract = {Inverters (NOT-gates) are elementary Boolean logic circuits, where the output is absent when the input is present. Inverters mimic the inverse relationships between molecules in natural systems that are responsible for maintaining steady state, and as such form an essential tool in the synthetic biologist's toolkit.},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/CarrSB62013.pdf}
    }

  • M. Galdzicki, E. Oberortner, M. Pocock, J. Quinn, M. Wilson, E. Appleton, B. Bartley, J. Beal, S. Bhatia, R. Cox, R. Grunberg, G. Misirli, H. Plahar, N. Roehner, L. Soldotova, G. Stan, D. Densmore, C. Myers, H. Sauro, and A. Wipat, Recent Advances in the Synthetic Biology Open Language, talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England , July, 2013.
    [BibTeX] [Download PDF]
    @Misc{galdzickiIWBDA2013,
    Title = {Recent Advances in the Synthetic Biology Open Language},
    Author = {Galdzicki, Michal and Oberortner, Ernst and Pocock, Mathew and Quinn, Jacqueline and Wilson, Mandy and Appleton, Evan and Bartley, Bryan and Beal, Jacob and Bhatia, Swapnil and Cox, Robert and Grunberg, Raik and Misirli, Goskel and Plahar, Hector and Roehner, Nicholas and Soldotova, Larisa and Stan, Guy-Bart and Densmore, Doug and Myers, Chris and Sauro, Herbert and Wipat, Anil},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA), London, England},
    Month = {July},
    Year = {2013},
    Keywords = {synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/galdzickiIWBDA2013.pdf}
    }

  • S. Bhatia and D. Densmore, “Pigeon: A Design Visualizer for Synthetic Biology,” ACS Synth Biol, vol. 2, iss. 6, pp. 348-350, 2013. doi:10.1021/sb400024s
    [BibTeX] [Download PDF]
    @Article{pmid23654259,
    Title = {{{P}igeon: {A} {D}esign {V}isualizer for {S}ynthetic {B}iology}},
    Author = {Bhatia, S. and Densmore, D.},
    Journal = {ACS Synth Biol},
    Year = {2013},
    Month = {Apr},
    Number = {6},
    Pages = {348--350},
    Volume = {2},
    DOI = {10.1021/sb400024s},
    Eprint = {http://pubs.acs.org/doi/pdf/10.1021/sb400024s},
    Keywords = {design, pigeon, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://pubs.acs.org/doi/full/10.1021/sb400024s}
    }

  • O. Shaer, C. Valdes, S. Liu, K. Lu, K. Chang, W. Xu, T. Haddock, S. Bhatia, D. Densmore, and R. Kincaid, “Designing reality-based interfaces for experiential bio-design,” Personal and Ubiquitous Computing, pp. 1-18, 2013. doi:10.1007/s00779-013-0752-1
    [BibTeX] [Download PDF]
    @Article{ShaerReality2013,
    Title = {Designing reality-based interfaces for experiential bio-design},
    Author = {Shaer, Orit and Valdes, Consuelo and Liu, Sirui and Lu, Kara and Chang, Kimberly and Xu, Wendy and Haddock, TraciL. and Bhatia, Swapnil and Densmore, Douglas and Kincaid, Robert},
    Journal = {Personal and Ubiquitous Computing},
    Year = {2013},
    Pages = {1-18},
    DOI = {10.1007/s00779-013-0752-1},
    ISSN = {1617-4909},
    Keywords = {Reality-based interaction; Multi-touch; Bioinformatics; Collaborative learning; Synthetic biology},
    Language = {English},
    Publisher = {Springer London},
    URL = {http://dx.doi.org/10.1007/s00779-013-0752-1}
    }

  • O. Shaer, C. Valdes, S. Liu, K. Lu, T. Haddock, S. Bhatia, D. Densmore, and R. Kincaid, “MoClo Planner: Interactive Visualization for Modular Cloning Bio-Design,” in IEEE Symposium on Biological Data Visualization (BioVis), 2013, pp. 57-64.
    [BibTeX] [Download PDF]
    @InProceedings{Shaer2013,
    Title = {MoClo Planner: Interactive Visualization for Modular Cloning Bio-Design},
    Author = {Shaer, O. and Valdes, C. and Liu, S. and Lu, K. and Haddock, T. and Bhatia, S. and Densmore, D. and Kincaid, R.},
    Booktitle = {IEEE Symposium on Biological Data Visualization (BioVis)},
    Year = {2013},
    Pages = {57-64},
    Timestamp = {2014.08.25},
    URL = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6664347}
    }

  • M. Leguia, J. A. Brophy, D. Densmore, A. Asante, and J. C. Anderson, “2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts,” J Biol Eng, vol. 7, iss. 1, p. 2, 2013.
    [BibTeX] [Download PDF]
    @Article{pmid23305072,
    Title = {{2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts}},
    Author = {Leguia, M. and Brophy, J. A. and Densmore, D. and Asante, A. and Anderson, J. C.},
    Journal = {J Biol Eng},
    Year = {2013},
    Number = {1},
    Pages = {2},
    Volume = {7},
    Keywords = {assembly, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/23305072}
    }

  • A. Davare, D. Densmore, L. Guo, R. Passerone, A. L. Sangiovanni-Vincentelli, A. Simalatsar, and Q. Zhu, “MetroII: A design environment for cyber-physical systems,” ACM Trans. Embed. Comput. Syst., vol. 12, iss. 1, p. 49:1–49:31, 2013. doi:10.1145/2435227.2435245
    [BibTeX] [Download PDF]
    @Article{Davare:2013:MID:2435227.2435245,
    Title = {MetroII: A design environment for cyber-physical systems},
    Author = {Davare, Abhijit and Densmore, Douglas and Guo, Liangpeng and Passerone, Roberto and Sangiovanni-Vincentelli, Alberto L. and Simalatsar, Alena and Zhu, Qi},
    Journal = {ACM Trans. Embed. Comput. Syst.},
    Year = {2013},
    Month = mar,
    Number = {1},
    Pages = {49:1--49:31},
    Volume = {12},
    Acmid = {2435245},
    Address = {New York, NY, USA},
    Articleno = {49},
    DOI = {10.1145/2435227.2435245},
    ISSN = {1539-9087},
    Issue_date = {March 2013},
    Keywords = {Cyber-Physical Systems, Heterogeneous Embedded Systems, Modeling, Multiprocessor, Platform-Based Design, System-on-Chip; electronic design automation;},
    Numpages = {31},
    Publisher = {ACM},
    Timestamp = {2013.09.16},
    URL = {http://doi.acm.org/10.1145/2435227.2435245}
    }

  • E. A. Gol, D. Densmore, and C. Belta, “Data-driven Verification of Synthetic Gene Networks,” in 52nd IEEE Conference on Decision and Control (CDC), Firenze, Italy, 2013.
    [BibTeX]
    @InProceedings{Goldata2013,
    Title = {Data-driven Verification of Synthetic Gene Networks},
    Author = {Ebru Aydin Gol and Douglas Densmore and Calin Belta},
    Booktitle = {52nd IEEE Conference on Decision and Control (CDC)},
    Year = {2013},
    Address = {Firenze, Italy},
    Timestamp = {2013.12.13}
    }

2012

  • E. Oberortner, H. Huang, S. Bhatia, and D. Densmore, Eugene 2.0: A Domain-specific Language to Specify Constraint Synthetic Biological Devices, poster presented at the SynBERC Spring Retreat, University of California-Berkeley , March, 2012.
    [BibTeX] [Download PDF]
    @Misc{OberortnerSynBERC2012,
    Title = {Eugene 2.0: A Domain-specific Language to Specify Constraint Synthetic Biological Devices},
    Author = {Oberortner, Ernst and Huang, Haiyao and Bhatia, Swapnil and Densmore, Douglas},
    HowPublished = {poster presented at the SynBERC Spring Retreat, University of California-Berkeley},
    Month = {March},
    Year = {2012},
    Keywords = {eugene, posters, synthetic biology},
    Location = {SynBERC},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/OberortnerSynBERC2012.pdf}
    }

  • S. Bhatia, A. Nielsen, M. Smanski, D. Densmore, and C. Voigt, How to build an n-input circuit library, poster presented at the SynBERC Spring Retreat, University of California-Berkeley , March, 2012.
    [BibTeX] [Download PDF]
    @Misc{BhatiaSynBERCSpring2013,
    Title = {How to build an n-input circuit library},
    Author = {Bhatia, Swapnil and Nielsen, Alec and Smanski, Michael and Densmore, Douglas and Voigt, Christopher},
    HowPublished = {poster presented at the SynBERC Spring Retreat, University of California-Berkeley},
    Month = {March},
    Year = {2012},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/BhatiaSynBERCSpring2013.pdf}
    }

  • E. Appleton, V. Vasilev, S. Bhatia, T. Haddock, and D. Densmore, Testing-Optimized DNA Assembly Algorithms, poster presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2012.
    [BibTeX] [Abstract] [Download PDF]
    Recent work has been done to develop algorithms that op- timize binary assembly [2]. These algorithms do not, how- ever, account for what is being built or the utility of assem- bly intermediates. This is particularly problematic because each step of DNA assembly is prone to multiple sources of error. Frequent errors occur in PCR, ligation, and gel ex- traction, and furthermore, parts with correct sequence sometimes do not function as expected. Thus, it is advantageous to construct assembly intermediates that are easily testable and reusable.<br><br> By accounting for the biological features of parts, an assembly plan can be devised that maximizes the formation of intermediates with the best biological qualities. Based upon prior optimization algorithms [2], here we present algorithms that select an assembly plan optimized for structural and functional testability. Before calculating the optimal plan, an algorithm identifies the most common part-order motifs within a selected database to maximize future reusability of intermediates. These additions to the state-of-the-art can considerably change the optimal assembly plan, even for small parts.<br><br> <a href="http://cidarlab.org/wp-content/uploads/2013/09/appleIWBDA2012_abs.pdf ">A detailed abstract for this IWBDA presentation is available here.</a>`

    @Misc{appleIWBDA2012,
    Title = {Testing-Optimized DNA Assembly Algorithms},
    Author = {Appleton, Evan and Vasilev, Viktor and Bhatia, Swapnil and Haddock, Traci and Densmore, Douglas},
    HowPublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {June},
    Year = {2012},
    Abstract = {Recent work has been done to develop algorithms that op- timize binary assembly [2]. These algorithms do not, how- ever, account for what is being built or the utility of assem- bly intermediates. This is particularly problematic because each step of DNA assembly is prone to multiple sources of error. Frequent errors occur in PCR, ligation, and gel ex- traction, and furthermore, parts with correct sequence sometimes do not function as expected. Thus, it is advantageous to construct assembly intermediates that are easily testable and reusable.<br><br>
    By accounting for the biological features of parts, an assembly plan can be devised that maximizes the formation of intermediates with the best biological qualities. Based upon prior optimization algorithms [2], here we present algorithms that select an assembly plan optimized for structural and functional testability. Before calculating the optimal plan, an algorithm identifies the most common part-order motifs within a selected database to maximize future reusability of intermediates. These additions to the state-of-the-art can considerably change the optimal assembly plan, even for small parts.<br><br>
    <a href="http://cidarlab.org/wp-content/uploads/2013/09/appleIWBDA2012_abs.pdf
    ">A detailed abstract for this IWBDA presentation is available here.</a>`},
    Keywords = {posters, raven, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/appleIWBDA2012.pdf}
    }

  • J. Beal, R. Weiss, D. Densmore, A. Adler, E. Appleton, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, J. Loyall, R. Schantz, V. Vasilev, and F. Yaman, Results from TASBE, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2012.
    [BibTeX]
    @Misc{bealIWBDA2012,
    Title = {Results from TASBE},
    Author = {Beal, Jacob and Weiss, Ron and Densmore, Douglas and Adler, Aaron and Appleton, Evan and Babb, Jonathan and Bhatia, Swapnil and Davidsohn, Noah and Haddock, Traci and Loyall, Joseph and Schantz, Rick and Vasilev, Viktor and Yaman, Fusun},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {June},
    Year = {2012},
    Keywords = {synthetic biology},
    Timestamp = {2013.08.13}
    }

  • H. Huang, E. Oberortner, D. Densmore, and A. Kuchinsky, Eugene’s Enriched Set of Features to Design Synthetic Biological Devices, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2012.
    [BibTeX] [Abstract] [Download PDF]
    Eugene is a design language to support synthetic biologist in order to construct large and complex biological devices more accurately. Compared to its original version, Eugene provides now an enriched set of functionalities to specify and constrain synthetic biological devices and their design synthesis. This work highlights (1) the declaration of devices at various abstraction levels, (2) the control-flow management of design synthesis, (3) a design space exploration to generate devices, and (4) the prototyping of functions. Eugene allows synthetic biologists to specify, design, and constrain a large number of biological devices in a few lines of code, without having to specify every single device manually. <a href="http://cidarlab.org/wp-content/uploads/2013/09/OberortnerSynBERC2012.pdf ">A detailed abstract for this IWBDA presentation is available here.</a>

    @Misc{HuangIWBDA2012,
    Title = {Eugene's Enriched Set of Features to Design Synthetic Biological Devices},
    Author = {Huang, Haiyao and Oberortner, Ernst and Densmore, Douglas and Kuchinsky, Allan},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {June},
    Year = {2012},
    Abstract = {Eugene is a design language to support synthetic biologist in order to construct large and complex biological devices more accurately. Compared to its original version, Eugene provides now an enriched set of functionalities to specify and constrain synthetic biological devices and their design synthesis. This work highlights (1) the declaration of devices at various abstraction levels, (2) the control-flow management of design synthesis, (3) a design space exploration to generate devices, and (4) the prototyping of functions. Eugene allows synthetic biologists to specify, design, and constrain a large number of biological devices in a few lines of code, without having to specify every single device manually.
    <a href="http://cidarlab.org/wp-content/uploads/2013/09/OberortnerSynBERC2012.pdf
    ">A detailed abstract for this IWBDA presentation is available here.</a>},
    Keywords = {eugene, synthetic biology, talk},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/HuangIWBDA2012.pdf}
    }

  • D. Densmore and S. Hassoun, “Design Automation for Synthetic Biological Systems,” IEEE Design & Test of Computers, vol. 29, iss. 3, pp. 7-20, 2012. doi:10.1109/MDT.2012.2193370
    [BibTeX] [Download PDF]
    @Article{Densmore2012,
    Title = {Design Automation for Synthetic Biological Systems},
    Author = {Densmore, Douglas and Hassoun, Soha},
    Journal = {IEEE Design \& Test of Computers},
    Year = {2012},
    Month = {Jun},
    Number = {3},
    Pages = {7-20},
    Volume = {29},
    DOI = {10.1109/MDT.2012.2193370},
    Keywords = {synthetic biology; design},
    Publisher = {Institute of Electrical and Electronics Engineers},
    Timestamp = {2013.08.09},
    URL = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=6178303}
    }

  • F. Yaman, S. Bhatia, A. Adler, D. Densmore, and J. Beal, “Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks,” ACS Synth Biol, vol. 1, iss. 8, pp. 332-344, 2012. doi:doi:10.1021/sb300032y
    [BibTeX] [Download PDF]
    @Article{pmid23651287,
    Title = {Automated Selection of Synthetic Biology Parts for Genetic Regulatory Networks},
    Author = {Yaman, F. and Bhatia, S. and Adler, A. and Densmore, D. and Beal, J.},
    Journal = {ACS Synth Biol},
    Year = {2012},
    Month = {Aug},
    Number = {8},
    Pages = {332--344},
    Volume = {1},
    DOI = {doi:10.1021/sb300032y},
    Eprint = {http://pubs.acs.org/doi/pdf/10.1021/sb300032y},
    Keywords = {design, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/23651286}
    }

  • J. Beal, R. Weiss, D. Densmore, A. Adler, E. Appleton, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, J. Loyall, R. Schantz, V. Vasilev, and F. Yaman, “An end-to-end workflow for engineering of biological networks from high-level specifications,” ACS Synth Biol, vol. 1, iss. 8, pp. 317-331, 2012.
    [BibTeX] [Download PDF]
    @Article{pmid23651286,
    Title = {{{A}n end-to-end workflow for engineering of biological networks from high-level specifications}},
    Author = {Beal, J. and Weiss, R. and Densmore, D. and Adler, A. and Appleton, E. and Babb, J. and Bhatia, S. and Davidsohn, N. and Haddock, T. and Loyall, J. and Schantz, R. and Vasilev, V. and Yaman, F.},
    Journal = {ACS Synth Biol},
    Year = {2012},
    Month = {Aug},
    Number = {8},
    Pages = {317--331},
    Volume = {1},
    Keywords = {specification, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/23651286}
    }

  • B. Yordanov, E. Appleton, R. Ganguly, E. A. Gol, S. B. Carr, S. Bhatia, T. Haddock, C. Belta, and D. Densmore, “Experimentally driven verification of synthetic biological circuits,” in Proceedings of the Conference on Design, Automation and Test in Europe, Dresden, Germany, 2012, pp. 236-241.
    [BibTeX] [Abstract] [Download PDF]
    We present a framework that allows us to construct and formally analyze the behavior of synthetic gene circuits from specifications in a high level language used in describing electronic circuits. Our back-end synthesis tool automatically generates genetic-regulatory network (GRN) topology realizing the specifications with assigned biological parts from a database. We describe experimental procedures to acquire characterization data for the assigned parts and construct mathematical models capturing all possible behaviors of the generated GRN. We delineate algorithms to create finite abstractions of these models, and novel analysis techniques inspired from model-checking to verify behavioral specifications using Linear Temporal Logic (LTL) formulae.

    @InProceedings{Yordanov:2012:EDV:2492708.2492767,
    Title = {Experimentally driven verification of synthetic biological circuits},
    Author = {Yordanov, Boyan and Appleton, Evan and Ganguly, Rishi and Gol, Ebru Aydin and Carr, Swati Banerjee and Bhatia, Swapnil and Haddock, Traci and Belta, Calin and Densmore, Douglas},
    Booktitle = {Proceedings of the Conference on Design, Automation and Test in Europe},
    Year = {2012},
    Address = {Dresden, Germany},
    Pages = {236--241},
    Publisher = {EDA Consortium},
    Series = {DATE '12},
    Abstract = {We present a framework that allows us to construct and formally analyze the behavior of synthetic gene circuits from specifications in a high level language used in describing electronic circuits. Our back-end synthesis tool automatically generates genetic-regulatory network (GRN) topology realizing the specifications with assigned biological parts from a database. We describe experimental procedures to acquire characterization data for the assigned parts and construct mathematical models capturing all possible behaviors of the generated GRN. We delineate algorithms to create finite abstractions of these models, and novel analysis techniques inspired from model-checking to verify behavioral specifications using Linear Temporal Logic (LTL) formulae.},
    Acmid = {2492767},
    ISBN = {978-3-9810801-8-6},
    Keywords = {synthetic biology; verification},
    Location = {Dresden, Germany},
    Numpages = {6},
    Timestamp = {2013.09.16},
    URL = {http://dl.acm.org/citation.cfm?id=2492708.2492767}
    }

  • D. Densmore and S. Hassoun, “Guest Editors’ Introduction: Synthetic Biology,” Design Test of Computers, IEEE, vol. 29, iss. 3, pp. 5-6, 2012. doi:10.1109/MDT.2012.2194609
    [BibTeX] [Download PDF]
    @Article{IEEE_6327729,
    Title = {Guest Editors' Introduction: Synthetic Biology},
    Author = {Densmore, D. and Hassoun, S.},
    Journal = {Design Test of Computers, IEEE},
    Year = {2012},
    Number = {3},
    Pages = {5-6},
    Volume = {29},
    DOI = {10.1109/MDT.2012.2194609},
    ISSN = {0740-7475},
    Keywords = {Biological information theory, DNA, Molecular biophysics, Special issues and sbiology, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=6327729&tag=1}
    }

  • D. Densmore, “Bio-Design Automation: Nobody Said It Would Be Easy,” ACS Synthetic Biology, vol. 1, iss. 8, pp. 296-296, 2012. doi:10.1021/sb300062c
    [BibTeX] [Download PDF]
    @Article{doi:10.1021/sb300062c,
    Title = {Bio-Design Automation: Nobody Said It Would Be Easy},
    Author = {Densmore, Douglas},
    Journal = {ACS Synthetic Biology},
    Year = {2012},
    Number = {8},
    Pages = {296-296},
    Volume = {1},
    DOI = {10.1021/sb300062c},
    Eprint = {http://pubs.acs.org/doi/pdf/10.1021/sb300062c},
    Keywords = {bio-design automation, design, design automation, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://pubs.acs.org/doi/abs/10.1021/sb300062c}
    }

  • E. Oberortner, D. Densmore, and J. C. Anderson, “An Interactive Pattern Story on Designing the Architecture of Clotho,” in 19th Conference on Pattern Languages of Programs (PLoP), 2012, cidarlab_conference_papers.
    [BibTeX] [Download PDF]
    @InProceedings{oberortnerClothoPattern2012,
    Title = {An Interactive Pattern Story on Designing the Architecture of Clotho},
    Author = {Oberortner, Ernst and Densmore, Dougls and Anderson, J. C.},
    Booktitle = {19th Conference on Pattern Languages of Programs (PLoP)},
    Year = {2012},
    Note = {cidarlab_conference_papers},
    Keywords = {clotho, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/oberortnerClothoPattern2012.pdf}
    }

  • J. Chen, D. Densmore, T. S. Ham, J. D. Keasling, and N. J. Hillson, “DeviceEditor visual biological CAD canvas,” J Biol Eng, vol. 6, iss. 1, p. 1, 2012.
    [BibTeX] [Download PDF]
    @Article{pmid22373390,
    Title = {{{D}evice{E}ditor visual biological {C}{A}{D} canvas}},
    Author = {Chen, J. and Densmore, D. and Ham, T. S. and Keasling, J. D. and Hillson, N. J. },
    Journal = {J Biol Eng},
    Year = {2012},
    Number = {1},
    Pages = {1},
    Volume = {6},
    Keywords = {device editor, eugene, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/22373390}
    }

2011

  • R. Ganguly, R. Ghamari, E. Appleton, S. P. Bhatia, B. Yordanov, E. AydinGol, C. Belta, and D. Densmore, Computational Design and Verification of Genetic Regulatory Circuits, poster presented at the SynBERC Fall Retreat, Harvard University , September, 2011.
    [BibTeX] [Download PDF]
    @Misc{GangulySynBERC2011,
    Title = {Computational Design and Verification of Genetic Regulatory Circuits},
    Author = {Ganguly, Rishi and Ghamari, Roza and Appleton, Evan and Bhatia, Swapnil P. and Yordanov, Boyan and Ebru AydinGol and Belta, Calin and Densmore, Douglas},
    HowPublished = {poster presented at the SynBERC Fall Retreat, Harvard University},
    Month = {September},
    Year = {2011},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/GangulySynBERC2011.pdf}
    }

  • V. Vasilev, C. Liu, J. Fernandes, E. Orozco, T. Haddock, S. Bhatia, A. Adler, F. Yaman, J. Beal, J. Babb, R. Weiss, and D. Densmore, A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering, poster presented at the SynBERC Fall Retreat, Harvard University , September, 2011.
    [BibTeX]
    @Misc{VasilevSynBERC2011,
    Title = {A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering},
    Author = {Vasilev, Viktor and Liu, Chenkai and Fernandes, Janoo and Orozco, Evelyn and Haddock, Traci and Bhatia, Swapnil and Adler, Aaron and Yaman, Fusun and Beal, Jacob and Babb, Jonathan and Weiss, Ron and Densmore, Douglas},
    HowPublished = {poster presented at the SynBERC Fall Retreat, Harvard University},
    Month = {September},
    Year = {2011},
    Keywords = {posters, puppeteer, synthetic biology},
    Timestamp = {2013.08.13}
    }

  • J. Beal, R. Weiss, D. Densmore, A. Adler, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, E. Appleton, F. Yaman, R. Schantz, and J. Loyall, TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering, poster presented at the Cold Springs Harbor Asia Series 2011 Symposium: Design & Synthesis of Biological Systems , November, 2011.
    [BibTeX]
    @Misc{BealColdspring2011,
    Title = {TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering},
    Author = {Beal, Jacob and Weiss, Ron and Densmore, Douglas and Adler, Aaron and Babb, Jonathan and Bhatia, Swapnil and Davidsohn, Noah and Haddock, Traci and Appleton, Evan and Yaman, Fusun and Schantz, Rick and Loyall, Joseph},
    HowPublished = {poster presented at the Cold Springs Harbor Asia Series 2011 Symposium: Design \& Synthesis of Biological Systems},
    Month = {November},
    Year = {2011},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13}
    }

  • E. Appleton, S. Bhatia, T. Haddock, V. Vasilev, R. Ghamari, R. Ganguly, and D. Densmore., Specify, Design, and Assemble: A Top-Down Design Flow Using Clotho, talk presented at Cold Springs Harbor Asia Series 2011 Symposium: Design & Synthesis of Biological Systems , November, 2011.
    [BibTeX] [Download PDF]
    @Misc{appletonColdSpring2011,
    Title = {Specify, Design, and Assemble: A Top-Down Design Flow Using Clotho},
    Author = {Appleton, Evan and Bhatia, Swapnil and Haddock, Traci and Vasilev, Viktor and Ghamari, Roza and Ganguly, Rishi and Douglas Densmore.},
    HowPublished = {talk presented at Cold Springs Harbor Asia Series 2011 Symposium: Design \& Synthesis of Biological Systems},
    Month = {November},
    Year = {2011},
    Keywords = {clotho, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/appletonColdSpring2011.pdf}
    }

  • R. Ghamari, B. Stanton, T. Haddock, S. Bhatia, K. Clancy, T. Peterson, C. Voigt, and D. Densmore, “Applying Hardware Description Languages to Genetic Circuit Design,” , 2011.
    [BibTeX] [Download PDF]
    @MastersThesis{GhamariIWBDA2011,
    Title = {Applying Hardware Description Languages to Genetic Circuit Design},
    Author = {Ghamari, Roza and Stanton, Brynne and Haddock, Traci and Bhatia, Swapnil and Clancy, Kevin and Peterson, Todd and Voigt, Christopher and Densmore, Douglas},
    Year = {2011},
    Month = {June},
    HowPublished = {poster presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/11/GhamariIWBDS2011.pdf}
    }

  • V. Vasilev, C. Liu, T. Haddock, S. Bhatia, A. Adler, F. Yaman, J. Beal, J. Babb, R. Weiss, and D. Densmore, A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2011.
    [BibTeX]
    @Misc{VasilevIWBDA2011,
    Title = {A Software Stack for Specification and Robotic Execution of Protocols for Synthetic Biological Engineering},
    Author = {Vasilev, Viktor and Liu, Chenkai and Haddock, Traci and Bhatia, Swapnil and Adler, Aaron and Yaman, Fusun and Beal, Jacob and Babb, Jonathan and Weiss, Ron and Densmore, Douglas},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {June},
    Year = {2011},
    Keywords = {puppeteer, synthetic biology, talks},
    Timestamp = {2013.08.13}
    }

  • T. Haddock, S. Bhatia, V. Vasilev, C. Liu, A. Adler, J. Beal, J. Babb, R. Weiss, and D. Densmore, A Novel Automated Assembly Approach for Use in Synthetic Circuit Construction, poster presented at the 5th International Meeting on Synthetic Biology (SB5.0), Palo Alto, CA , June, 2011.
    [BibTeX] [Download PDF]
    @Misc{HaddockSB52011,
    Title = {A Novel Automated Assembly Approach for Use in Synthetic Circuit Construction},
    Author = {Haddock, Traci and Bhatia, Swapnil and Vasilev, Viktor and Liu, Chenkai and Adler, Aaron and Beal, Jacob and Babb, Jonathan and Weiss, Ron and Densmore, Douglas},
    HowPublished = {poster presented at the 5th International Meeting on Synthetic Biology (SB5.0), Palo Alto, CA},
    Month = {June},
    Year = {2011},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/HaddockSB52011.pdf}
    }

  • A. Adler, J. Beal, S. Bhatia, N. Davidsohn, D. Densmore, T. Haddock, J. Loyall, R. Schantz, R. Weiss, and F. Yaman, Towards automated selection of parts for genetic regulatory networks, poster presented at the 5th International Meeting on Synthetic Biology (SB5.0), Palo Alto, CA , June, 2011.
    [BibTeX]
    @Misc{AdlerSB52011,
    Title = {Towards automated selection of parts for genetic regulatory networks},
    Author = {Adler, Aaron and Beal, Jacob and Bhatia, Swapnil and Davidsohn, Noah and Densmore, Douglas and Haddock, Traci and Loyall, Joseph and Schantz, Rick and Weiss, Ron and Yaman, Fusun},
    HowPublished = {poster presented at the 5th International Meeting on Synthetic Biology (SB5.0), Palo Alto, CA},
    Month = {June},
    Year = {2011},
    Keywords = {posters, synthetic biology},
    Timestamp = {2013.08.13}
    }

  • J. Beal, R. Weiss, D. Densmore, A. Adler, J. Babb, S. Bhatia, N. Davidsohn, T. Haddock, F. Yaman, R. Schantz, and J. Loyall, TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering, talk presented at the International Workshop on Bio-Design Automation (IWBDA) , June, 2011.
    [BibTeX]
    @Misc{BealIWBDA2011,
    Title = {TASBE: A Tool-Chain to Accelerate Synthetic Biological Engineering},
    Author = {Beal, Jacob and Weiss, Ron and Densmore, Douglas and Adler, Aaron and Babb, Jonathan and Bhatia, Swapnil and Davidsohn, Noah and Haddock, Traci and Yaman, Fusun and Schantz, Rick and Loyall, Joseph},
    HowPublished = {talk presented at the International Workshop on Bio-Design Automation (IWBDA)},
    Month = {June},
    Year = {2011},
    Keywords = {synthetic biology},
    Timestamp = {2013.08.13}
    }

  • J. Peccoud, C. J. Anderson, D. Chandran, D. Densmore, M. Galdzicki, M. W. Lux, C. A. Rodriguez, G. Stan, and H. M. Sauro, “Essential information for synthetic DNA sequences,” Nature Biotechnology, vol. 29, iss. 1, pp. 22-22, 2011. doi:10.1038/nbt.1753
    [BibTeX] [Download PDF]
    @Article{Peccoud2011,
    Title = {Essential information for synthetic {DNA} sequences},
    Author = {Peccoud, Jean and Anderson, J Christopher and Chandran, Deepak and Densmore, Douglas and Galdzicki, Michal and Lux, Matthew W and Rodriguez, Cesar A and Stan, Guy-Bart and Sauro, Herbert M},
    Journal = {Nature Biotechnology},
    Year = {2011},
    Month = {Jan},
    Number = {1},
    Pages = {22-22},
    Volume = {29},
    DOI = {10.1038/nbt.1753},
    Keywords = {design, synthetic biology},
    Publisher = {Nature Publishing Group},
    Timestamp = {2013.08.09},
    URL = {http://dx.doi.org/10.1038/nbt.1753}
    }

  • M. Leguia, J. Brophy, D. Densmore, and J. C. Anderson, “Automated assembly of standard biological parts,” Meth. Enzymol., vol. 498, pp. 363-397, 2011.
    [BibTeX] [Download PDF]
    @Article{pmid21601686,
    Title = {{{A}utomated assembly of standard biological parts}},
    Author = {Leguia, M. and Brophy, J. and Densmore, D. and Anderson, J. C. },
    Journal = {Meth. Enzymol.},
    Year = {2011},
    Pages = {363--397},
    Volume = {498},
    Keywords = {assembly, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/21601686}
    }

  • L. Bilitchenko, A. Liu, and D. Densmore, “The Eugene language for synthetic biology,” Meth. Enzymol., vol. 498, pp. 153-172, 2011.
    [BibTeX] [Download PDF]
    @Article{pmid21601677,
    Title = {{{T}he {E}ugene language for synthetic biology}},
    Author = {Bilitchenko, L. and Liu, A. and Densmore, D. },
    Journal = {Meth. Enzymol.},
    Year = {2011},
    Pages = {153--172},
    Volume = {498},
    Keywords = {design, eugene, specification, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/21601677}
    }

  • B. Xia, S. Bhatia, B. Bubenheim, M. Dadgar, D. Densmore, and J. C. Anderson, “Developer’s and user’s guide to Clotho v2.0 A software platform for the creation of synthetic biological systems,” Meth. Enzymol., vol. 498, pp. 97-135, 2011.
    [BibTeX] [Download PDF]
    @Article{pmid21601675,
    Title = {{{D}eveloper's and user's guide to {C}lotho v2.0 {A} software platform for the creation of synthetic biological systems}},
    Author = {Xia, B. and Bhatia, S. and Bubenheim, B. and Dadgar, M. and Densmore, D. and Anderson, J. C.},
    Journal = {Meth. Enzymol.},
    Year = {2011},
    Pages = {97--135},
    Volume = {498},
    Keywords = {clotho, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/21601675}
    }

  • H. Koeppl, D. Densmore, M. di Bernardo, and G. Setti, Design and Analysis of Biomolecular Circuits, Springer Books, 2011.
    [BibTeX] [Download PDF]
    @Book{Koeppl2011,
    Title = {Design and Analysis of Biomolecular Circuits},
    Author = {Koeppl, Heinz and Densmore, Douglas and Mario di Bernardo and Setti, Gianluca},
    Publisher = {Springer Books},
    Year = {2011},
    Keywords = {synthetic biology},
    Timestamp = {2013.08.09},
    URL = {http://www.springer.com/engineering/circuits+%26+systems/book/978-1-4419-6765-7}
    }

  • L. Bilitchenko, A. Liu, S. Cheung, E. Weeding, B. Xia, M. Leguia, J. C. Anderson, and D. Densmore, “Eugene–a domain specific language for specifying and constraining synthetic biological parts, devices, and systems,” PLoS ONE, vol. 6, iss. 4, p. e18882, 2011.
    [BibTeX] [Download PDF]
    @Article{pmid21559524,
    Title = {{{E}ugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems}},
    Author = {Bilitchenko, L. and Liu, A. and Cheung, S. and Weeding, E. and Xia, B. and Leguia, M. and Anderson, J. C. and Densmore, D. },
    Journal = {PLoS ONE},
    Year = {2011},
    Number = {4},
    Pages = {e18882},
    Volume = {6},
    Keywords = {design, eugene, specification, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/21559524}
    }

  • A. Adler, J. Beal, S. Bhatia, N. Davidsohn, D. Densmore, T. Haddock, J. Loyall, R. Schantz, R. Weiss, and F. Yaman, Towards automated selection of parts for genetic regulatory networks, talks presented at the International Workshop on Bio-Design Automation (IWBDA), San Diego, CA and at the Annual Conference of the Institute of Biological Engineering, Atlanta, GA , 2011.
    [BibTeX]
    @Misc{AdlerIWBDA2011,
    Title = {Towards automated selection of parts for genetic regulatory networks},
    Author = {Adler, Aaron and Beal, Jacob and Bhatia, Swapnil and Davidsohn, Noah and Densmore, Douglas and Haddock, Traci and Loyall, Joseph and Schantz, Rick and Weiss, Ron and Yaman, Fusun},
    HowPublished = {talks presented at the International Workshop on Bio-Design Automation (IWBDA), San Diego, CA and at the Annual Conference of the Institute of Biological Engineering, Atlanta, GA},
    Year = {2011},
    Keywords = {synthetic biology},
    Timestamp = {2013.08.13}
    }

2010

  • D. Densmore, T. H. Hsiau, J. T. Kittleson, W. DeLoache, C. Batten, and J. C. Anderson, “Algorithms for automated DNA assembly,” Nucleic Acids Res., vol. 38, iss. 8, pp. 2607-2616, 2010.
    [BibTeX] [Download PDF]
    @Article{pmid20335162,
    Title = {{{A}lgorithms for automated {D}{N}{A} assembly}},
    Author = {Densmore, D. and Hsiau, T. H. and Kittleson, J. T. and DeLoache, W. and Batten, C. and Anderson, J. C. },
    Journal = {Nucleic Acids Res.},
    Year = {2010},
    Month = {May},
    Number = {8},
    Pages = {2607--2616},
    Volume = {38},
    Keywords = {assembly, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://www.ncbi.nlm.nih.gov/pubmed/20335162}
    }

  • D. Densmore, “Method and apparatus for precharacterizing systems for use in system level design of integrated circuits,” , iss. 7788625, 2010.
    [BibTeX] [Download PDF]
    @Patent{DensmorePatent2010,
    Title = {Method and apparatus for precharacterizing systems for use in system level design of integrated circuits},
    Nationality = {United States of America},
    Number = {7788625},
    Year = {2010},
    Yearfiled = {2005},
    Author = {Densmore, Douglas},
    Day = {31},
    Dayfiled = {14},
    Month = {August},
    Monthfiled = {April},
    URL = {http://www.google.com/patents/US7788625},
    Keywords = {electronic design automation;},
    Timestamp = {2013.08.12}
    }

  • D. Densmore, J. T. Kittleson, L. Bilitchenko, A. Liu, and J. C. Anderson, “Rule based constraints for the construction of genetic devices,” in Circuits and Systems (ISCAS), Proceedings of 2010 IEEE International Symposium on, 2010, pp. 557-560. doi:10.1109/ISCAS.2010.5537540
    [BibTeX] [Download PDF]
    @InProceedings{IEEE_5537540,
    Title = {Rule based constraints for the construction of genetic devices},
    Author = {Densmore, D. and Kittleson, J.T. and Bilitchenko, L. and Liu, A. and Anderson, J.C.},
    Booktitle = {Circuits and Systems (ISCAS), Proceedings of 2010 IEEE International Symposium on},
    Year = {2010},
    Pages = {557-560},
    DOI = {10.1109/ISCAS.2010.5537540},
    Keywords = {Assembly, Automation, Computer science, Design engineering, Domain specific languages, Electronic circuits, Eugene, Genetic engineering, Laboratories, Process design, Synthetic biology, application specific integrated circuits, automated design, eugene, genetic devices construction, hardware description languages, integrated circuit design, laboratory creation, logic design, phagemid, rule based constraints, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://ieeexplore.ieee.org/xpl/abstractReferences.jsp?arnumber=5537540&tag=1}
    }

2009

  • F. Balarin, M. DAngelo, A. Davare, D. Densmore, T. Meyerowitz, R. Passerone, A. Pinto, A. Sangiovanni-Vincentelli, A. Simalatsar, Y. Watanabe, G. Yang, and Q. Zhu, “Platform-Based Design and Frameworks: Metropolis and Metro II,” in Model-Based Design for Embedded Systems (Computational Analysis, Synthesis, and Design of Dynamic Systems), G. Nicolescu and P. J. Mosterman, Eds., CRC Press, 2009.
    [BibTeX] [Download PDF]
    @InCollection{Nicolescu2009,
    Title = {Platform-Based Design and Frameworks: Metropolis and Metro II},
    Author = {Balarin, Felice and Massimiliano DAngelo and Davare, Abhijit and Densmore, Douglas and Meyerowitz, Trevor and Passerone, Roberto and Pinto, Alessandro and Alberto Sangiovanni-Vincentelli and Simalatsar, Alena and Watanabe, Yosinori and Yang, Guang and Zhu, Qi},
    Booktitle = {Model-Based Design for Embedded Systems (Computational Analysis, Synthesis, and Design of Dynamic Systems)},
    Publisher = {CRC Press},
    Year = {2009},
    Editor = {Gabriela Nicolescu and Pieter J. Mosterman},
    ISBN = {1420067842},
    Keywords = {electronic design automation;},
    Timestamp = {2013.08.12},
    URL = {http://www.amazon.com/Model-Based-Embedded-Computational-Analysis-Synthesis/dp/1420067842%3FSubscriptionId%3D0JYN1NVW651KCA56C102%26tag%3Dtechkie-20%26linkCode%3Dxm2%26camp%3D2025%26creative%3D165953%26creativeASIN%3D1420067842}
    }

  • D. Densmore and J. C. Anderson, “Combinational logic design in Synthetic Biology,” in Circuits and Systems, 2009. ISCAS 2009. IEEE International Symposium on, 2009, pp. 301-304. doi:10.1109/ISCAS.2009.5117745
    [BibTeX] [Download PDF]
    @InProceedings{IEEE_5117745,
    Title = {Combinational logic design in Synthetic Biology},
    Author = {Densmore, D. and Anderson, J.C.},
    Booktitle = {Circuits and Systems, 2009. ISCAS 2009. IEEE International Symposium on},
    Year = {2009},
    Pages = {301-304},
    DOI = {10.1109/ISCAS.2009.5117745},
    Keywords = {Biological systems, Biology computing, CMOS logic circuits, Chemical technology, Logic design, Logic devices, Logic gates, Switches, Synthetic biology, VLSI, Very large scale integration, automatic VLSI synthesis, biocomputing, biomolecular electronics, combinational circuits, combinational logic circuits, combinational logic design, digital electronics, synthetic biology},
    Timestamp = {2013.09.16},
    URL = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=5117745}
    }

  • D. Densmore, A. Van Devender, M. Johnson, and N. Sritanyaratana, “A platform-based design environment for synthetic biological systems,” in The Fifth Richard Tapia Celebration of Diversity in Computing Conference: Intellect, Initiatives, Insight, and Innovations, New York, NY, USA, 2009, pp. 24-29. doi:10.1145/1565799.1565806
    [BibTeX] [Download PDF]
    @InProceedings{Densmore:2009:PDE:1565799.1565806,
    Title = {A platform-based design environment for synthetic biological systems},
    Author = {Densmore, Douglas and Van Devender, Anne and Johnson, Matthew and Sritanyaratana, Nade},
    Booktitle = {The Fifth Richard Tapia Celebration of Diversity in Computing Conference: Intellect, Initiatives, Insight, and Innovations},
    Year = {2009},
    Address = {New York, NY, USA},
    Pages = {24--29},
    Publisher = {ACM},
    Series = {TAPIA '09},
    Acmid = {1565806},
    DOI = {10.1145/1565799.1565806},
    ISBN = {978-1-60558-217-7},
    Keywords = {clotho, design, platform-based design, synthetic bclotho, synthetic biology},
    Location = {Portland, Oregon},
    Numpages = {6},
    Timestamp = {2013.09.16},
    URL = {http://doi.acm.org/10.1145/1565799.1565806}
    }

  • D. Densmore, A. Simalatsar, A. Davare, R. Passerone, and A. Sangiovanni-Vincentelli, “UMTS MPSoC design evaluation using a system level design framework,” in Design, Automation Test in Europe Conference Exhibition, 2009. DATE ’09., Nice, France, 2009, pp. 478-483. doi:10.1109/DATE.2009.5090712
    [BibTeX] [Download PDF]
    @InProceedings{DATE_5090712,
    Title = {UMTS MPSoC design evaluation using a system level design framework},
    Author = {Densmore, D. and Simalatsar, A. and Davare, A. and Passerone, R. and Sangiovanni-Vincentelli, A.},
    Booktitle = {Design, Automation Test in Europe Conference Exhibition, 2009. DATE '09.},
    Year = {2009},
    Address = {Nice, France},
    Pages = {478-483},
    DOI = {10.1109/DATE.2009.5090712},
    ISSN = {1530-1591},
    Keywords = {3G mobile communication;integrated circuit design;system-on-chip;MPSoC;UMTS;data link layer design;design evaluation;designer productivity;electronic system level;space exploration;system level design;3G mobile communication;Computational modeling;Computer architecture;Design methodology;Discrete event simulation;Process design;Productivity;Software design;Space exploration;System-level design; electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=5090712}
    }

2008

  • D. Densmore, T. Meyerowitz, A. Davare, Q. Zhu, and G. Yang, “Metro II Execution Semantics for Mapping,” University of California, Berkeley, UCB/EECS-2008-16, , 2008.
    [BibTeX] [Abstract] [Download PDF]
    This document presents three proposals for the execution semantics of mapping in Metro II. Mapping is the relationship between what a system does (functionality) and how it does it (architecture). The main concern is whether the functionality and architecture models should execute concurrently or sequentially during simulation. Proposal \#1 presents sequential execution with the functionality being executed before the architecture. Proposal \#2 also presents sequential execution, but with the architecture executing before the functionality. Finally, Proposal \#3 presents concurrent execution. Processes are present in the architecture to execute simultaneously with the events mapped to them in the functionality. Each of these three proposals is demonstrated on a set of design scenarios with hand traces illustrating their execution. Additionally general assumptions, glossary terms, and proposal-specific assumptions made regarding the execution semantics are discussed. Finally, the proposals are compared and contrasted, especially regarding how they can properly implement the examples and the general semantic assumptions.

    @TechReport{MetroIITech2008,
    Title = {Metro II Execution Semantics for Mapping},
    Author = {Douglas Densmore and Trevor Meyerowitz and Abhijit Davare and Qi Zhu and Guang Yang},
    Institution = {University of California, Berkeley},
    Year = {2008},
    Month = {February},
    Number = {UCB/EECS-2008-16},
    Abstract = {This document presents three proposals for the execution semantics of mapping in Metro II. Mapping is the relationship between what a system does (functionality) and how it does it (architecture). The main concern is whether the functionality and architecture models should execute concurrently or sequentially during simulation. Proposal \#1 presents sequential execution with the functionality being executed before the architecture. Proposal \#2 also presents sequential execution, but with the architecture executing before the functionality. Finally, Proposal \#3 presents concurrent execution. Processes are present in the architecture to execute simultaneously with the events mapped to them in the functionality. Each of these three proposals is demonstrated on a set of design scenarios with hand traces illustrating their execution. Additionally general assumptions, glossary terms, and proposal-specific assumptions made regarding the execution semantics are discussed. Finally, the proposals are compared and contrasted, especially regarding how they can properly implement the examples and the general semantic assumptions.},
    Keywords = {electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/MetroIITech2008.pdf}
    }

  • A. Simalatsar, R. Passerone, and D. Densmore, “A methodology for architecture exploration and performance analysis using system level design languages and rapid architecture profiling,” in Industrial Embedded Systems, 2008. SIES 2008. International Symposium on, La Grande Motte, France, 2008, pp. 95-102. doi:10.1109/SIES.2008.4577686
    [BibTeX] [Download PDF]
    @InProceedings{IEEE_4577686,
    Title = {A methodology for architecture exploration and performance analysis using system level design languages and rapid architecture profiling},
    Author = {Simalatsar, A. and Passerone, R. and Densmore, D.},
    Booktitle = {Industrial Embedded Systems, 2008. SIES 2008. International Symposium on},
    Year = {2008},
    Address = {La Grande Motte, France},
    Pages = {95-102},
    DOI = {10.1109/SIES.2008.4577686},
    Keywords = {3G mobile communication;middleware;software architecture;software performance evaluation;software radio;specification languages;UMTS protocol;architecture exploration;middleware;performance analysis;performance evaluation;rapid architecture profiling;rapid exploration;software defined radio oriented architectures;system level design languages;system level specification languages;traditional sequential programming model;Computational modeling;Computer architecture;Costs;High performance computing;LAN interconnection;Middleware;Performance analysis;Real time systems;Specification languages;System-level design; electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=4577686}
    }

  • D. Densmore, A Platform-Based Design Methodology for the Electronic System Level: Frameworks, Designs Flows, and Case Studies, VDM Verlag, 2008.
    [BibTeX] [Download PDF]
    @Book{DensmorePlatform2008,
    Title = {A Platform-Based Design Methodology for the Electronic System Level: Frameworks, Designs Flows, and Case Studies},
    Author = {Densmore, D.},
    Publisher = {VDM Verlag},
    Year = {2008},
    ISBN = {3836473143},
    Keywords = {electronic design automation;},
    Timestamp = {2013.08.12},
    URL = {http://www.amazon.com/Platform-Based-Design-Methodology-Electronic-System/dp/3836473143%3FSubscriptionId%3D0JYN1NVW651KCA56C102%26tag%3Dtechkie-20%26linkCode%3Dxm2%26camp%3D2025%26creative%3D165953%26creativeASIN%3D3836473143}
    }

2007

  • D. Densmore, “A Design Flow for the Development, Characterization, and Refinement of System Level Architectural Services,” PhD Thesis, University of California, Berkeley, 2007.
    [BibTeX] [Download PDF]
    @PhdThesis{DensmoreThesis2007,
    Title = {A Design Flow for the Development, Characterization, and Refinement of System Level Architectural Services},
    Author = {Densmore, Douglas},
    School = {University of California, Berkeley},
    Year = {2007},
    Month = {May},
    Keywords = {electronic design automation;},
    Timestamp = {2013.08.12},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/DensmoreThesis2007.pdf}
    }

  • A. Davare, D. Densmore, T. Meyerowitz, A. Pinto, A. Sangiovanni-Vincentelli, G. Yang, H. Zeng, and Q. Zhu, “A Next-Generation Design Framework for Platform-Based Design,” in Conference on Using Hardware Design and Verification Languages (DVCon), San Jose, CA, 2007.
    [BibTeX] [Download PDF]
    @InProceedings{DVCON2007,
    Title = {A Next-Generation Design Framework for Platform-Based Design},
    Author = {Davare, Abhijit and Densmore, Douglas and Meyerowitz, Trevor and Pinto, Alessandro and Alberto Sangiovanni-Vincentelli and Yang, Guang and Zeng, Haibo and Zhu, Qi},
    Booktitle = {Conference on Using Hardware Design and Verification Languages (DVCon)},
    Year = {2007},
    Address = {San Jose, CA},
    Month = {February},
    Keywords = {electronic design automation},
    Timestamp = {2013.08.12},
    URL = {http://sws.bu.edu/dougd/Papers/DVCON.pdf}
    }

2006

  • D. Densmore, A. Sangiovanni-Vincentelli, and A. Donlin, “Leveraging Programmability in Electronic System Level Designs,” Xcell Journal, vol. 56, pp. 29-31, 2006.
    [BibTeX] [Download PDF]
    @Article{DensmoreXcell2006,
    Title = {Leveraging Programmability in Electronic System Level Designs},
    Author = {Densmore, Douglas and Alberto Sangiovanni-Vincentelli and Donlin, Adam},
    Journal = {Xcell Journal},
    Year = {2006},
    Month = {Q1},
    Pages = {29-31},
    Volume = {56},
    Keywords = {electronic design automation;},
    Timestamp = {2013.08.12},
    URL = {http://www.xilinx.com/publications/archives/xcell/Xcell56.pdf}
    }

  • A. Davare, J. Chong, Q. Zhu, D. M. Densmore, and A. L. Sangiovanni-Vincentelli, “Classification, Customization, and Characterization: Using MILP for Task Allocation and Scheduling,” EECS Department, University of California, Berkeley, UCB/EECS-2006-166, , 2006.
    [BibTeX] [Abstract] [Download PDF]
    Task allocation and scheduling for heterogeneous multi-core platforms must be automated for such platforms to be successful. Techniques such as Mixed Integer Linear Programming (MILP) provide the ability to easily customize the allocation and scheduling problem to application or platform-specific peculiarities. The representation of the core problem in a MILP form has a large impact on the solution time required. In this paper, we investigate a variety of such representations and propose a taxonomy for them. A promising representation is chosen with extensive computational characterization. The MILP formulation is customized for a multimedia case study involving the deployment of a Motion JPEG encoder application onto a Xilinx Virtex II Pro FPGA platform. We demonstrate that our approach can produce solutions that are competitive with manual designs.

    @TechReport{DavareEECS_2006_166,
    Title = {Classification, Customization, and Characterization: Using MILP for Task Allocation and Scheduling},
    Author = {Davare, Abhijit and Chong, Jike and Zhu, Qi and Densmore, Douglas Michael and Sangiovanni-Vincentelli, Alberto L.},
    Institution = {EECS Department, University of California, Berkeley},
    Year = {2006},
    Month = {Dec},
    Number = {UCB/EECS-2006-166},
    Abstract = {Task allocation and scheduling for heterogeneous multi-core platforms must be automated for such platforms to be successful. Techniques such as Mixed Integer Linear Programming (MILP) provide the ability to easily customize the allocation and scheduling problem to application or platform-specific peculiarities. The representation of the core problem in a MILP form has a large impact on the solution time required. In this paper, we investigate a variety of such representations and propose a taxonomy for them. A promising representation is chosen with extensive computational characterization. The MILP formulation is customized for a multimedia case study involving the deployment of a Motion JPEG encoder application onto a Xilinx Virtex II Pro FPGA platform. We demonstrate that our approach can produce solutions that are competitive with manual designs.},
    Keywords = {electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/DavareEECS_2006_166.pdf}
    }

  • S. Kakita, Y. Watanabe, D. Densmore, A. Davare, and A. Sangiovanni-Vincentelli, “Functional Model Exploration for Multimedia Applications via Algebraic Operators,” in Application of Concurrency to System Design, 2006. ACSD 2006. Sixth International Conference on, Turku Finland, 2006, pp. 229-238. doi:10.1109/ACSD.2006.8
    [BibTeX] [Download PDF]
    @InProceedings{IEEE_1640240,
    Title = {Functional Model Exploration for Multimedia Applications via Algebraic Operators},
    Author = {Kakita, S. and Watanabe, Y. and Densmore, D. and Davare, A. and Sangiovanni-Vincentelli, A.},
    Booktitle = {Application of Concurrency to System Design, 2006. ACSD 2006. Sixth International Conference on},
    Year = {2006},
    Address = {Turku Finland},
    Pages = {229-238},
    DOI = {10.1109/ACSD.2006.8},
    ISSN = {1550-4808},
    Keywords = {concurrency control;embedded systems;field programmable gate arrays;logic design;multimedia systems;parallel architectures;FPGA architecture;algebraic operators;concurrent architecture;functional model exploration;metropolis design framework;multimedia application;optimized functional design space exploration method;Application software;Boolean functions;Concurrent computing;Design methodology;Design optimization;Logic design;Network synthesis;Partitioning algorithms;Process design;Space eautomation; electronic design automation},
    Timestamp = {2013.09.16},
    URL = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1640240}
    }

  • D. Densmore and R. Passerone, “A Platform-Based Taxonomy for ESL Design,” Design Test of Computers, IEEE, vol. 23, iss. 5, pp. 359-374, 2006. doi:10.1109/MDT.2006.112
    [BibTeX] [Download PDF]
    @Article{Densmore1704727,
    Title = {A Platform-Based Taxonomy for ESL Design},
    Author = {Densmore, D. and Passerone, R.},
    Journal = {Design Test of Computers, IEEE},
    Year = {2006},
    Number = {5},
    Pages = {359-374},
    Volume = {23},
    DOI = {10.1109/MDT.2006.112},
    ISSN = {0740-7475},
    Keywords = {electronic design automation;embedded systems;hardware description languages;logic design;ESL design;electronic system-level;platform-based taxonomy;Aerospace industry;Consumer electronics;Information analysis;Packaging;Paints;Process design;System-level design;Taxonomy;Terminology;Web page design;ESL;design flow;electronic system-level design;taxonomy; electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1704727}
    }

  • D. Densmore, A. Donlin, and A. Sangiovanni-Vincentelli, “FPGA architecture characterization for system level performance analysis,” in Proceedings of the conference on Design, automation and test in Europe: Proceedings, Munich, Germany, 2006, pp. 734-739.
    [BibTeX] [Download PDF]
    @InProceedings{Densmore:2006:FAC:1131481.1131691,
    Title = {FPGA architecture characterization for system level performance analysis},
    Author = {Densmore, Douglas and Donlin, Adam and Sangiovanni-Vincentelli, Alberto},
    Booktitle = {Proceedings of the conference on Design, automation and test in Europe: Proceedings},
    Year = {2006},
    Address = {Munich, Germany},
    Pages = {734--739},
    Publisher = {European Design and Automation Association},
    Series = {DATE '06},
    Acmid = {1131691},
    ISBN = {3-9810801-0-6},
    Keywords = {electronic design automation;},
    Numpages = {6},
    Timestamp = {2013.09.16},
    URL = {http://dl.acm.org/citation.cfm?id=1131481.1131691}
    }

  • D. Densmore, A. Donlin, and A. Sangiovanni-Vincentelli, “Programmable Platform Characterization for System Level Performance Analysis,” in Platform Based Design at the Electronic System Level: Industry Perspectives and Experiences, M. Burton and A. Morawiec, Eds., Springer, 2006, pp. 13-30.
    [BibTeX] [Download PDF]
    @InCollection{DensmorePPC2006,
    Title = {Programmable Platform Characterization for System Level Performance Analysis},
    Author = {Densmore, Douglas and Donlin, Adam and Alberto Sangiovanni-Vincentelli},
    Booktitle = {Platform Based Design at the Electronic System Level: Industry Perspectives and Experiences},
    Publisher = {Springer},
    Year = {2006},
    Editor = {Mark Burton and Adam Morawiec},
    Pages = {13--30},
    ISBN = {1402051379},
    Keywords = {electronic design automation;},
    Timestamp = {2013.08.12},
    URL = {http://www.amazon.com/Platform-Based-Design-Electronic-System/dp/1402051379%3FSubscriptionId%3D0JYN1NVW651KCA56C102%26tag%3Dtechkie-20%26linkCode%3Dxm2%26camp%3D2025%26creative%3D165953%26creativeASIN%3D1402051379}
    }

2004

  • H. Zeng, V. Shah, D. Densmore, and A. Davare, “Simple Case Study in Metropolis,” EECS Department, University of California, Berkeley, UCB/ERL M04/37, , 2004.
    [BibTeX] [Download PDF]
    @TechReport{ZengM04_37,
    Title = {Simple Case Study in Metropolis},
    Author = {Zeng, H. and Shah, V. and Densmore, D. and Davare, A.},
    Institution = {EECS Department, University of California, Berkeley},
    Year = {2004},
    Number = {UCB/ERL M04/37},
    Keywords = {electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/ZengM04_37.pdf}
    }

  • D. Densmore, “Platform Based Reconfigurable Architecture Exploration via Boolean Constraints,” , University of California, Berkeley, 2004.
    [BibTeX] [Download PDF]
    @MastersThesis{DensmoreReport2004,
    Title = {Platform Based Reconfigurable Architecture Exploration via Boolean Constraints},
    Author = {Douglas Densmore},
    School = {University of California, Berkeley},
    Year = {2004},
    Keywords = {electronic design automation;},
    Timestamp = {2013.08.12},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/DensmoreReport2004.pdf}
    }

  • D. Densmore, “Metropolis Architecture Refinement Styles nd Methodology,” EECS Department, University of California, Berkeley, UCB/ERL M04/36, , 2004.
    [BibTeX] [Download PDF]
    @TechReport{DensmoreM04_36,
    Title = {Metropolis Architecture Refinement Styles nd Methodology},
    Author = {Densmore, D.},
    Institution = {EECS Department, University of California, Berkeley},
    Year = {2004},
    Number = {UCB/ERL M04/36},
    Keywords = {electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/DensmoreM04_36.pdf}
    }

  • D. Densmore, “Formal Refinement Verification in Metropolis,” EECS Department, University of California, Berkeley, UCB/ERL M04/10, , 2004.
    [BibTeX] [Download PDF]
    @TechReport{DensmoreM04_10,
    Title = {Formal Refinement Verification in Metropolis},
    Author = {Densmore, D.},
    Institution = {EECS Department, University of California, Berkeley},
    Year = {2004},
    Number = {UCB/ERL M04/10},
    Keywords = {electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://cidarlab.org/wp-content/uploads/2013/09/DensmoreM04_10.pdf}
    }

  • D. Densmore, S. Rekhi, and A. Sangiovanni-Vincentelli, “Microarchitecture Development via Metropolis Successive Platform Refinement,” in Proceedings of the conference on Design, automation and test in Europe – Volume 1, Paris, France, 2004, p. 10346–.
    [BibTeX] [Download PDF]
    @InProceedings{Densmore:2004:MDV:968878.968963,
    Title = {Microarchitecture Development via Metropolis Successive Platform Refinement},
    Author = {Densmore, Douglas and Rekhi, Sanjay and Sangiovanni-Vincentelli, Alberto},
    Booktitle = {Proceedings of the conference on Design, automation and test in Europe - Volume 1},
    Year = {2004},
    Address = {Paris, France},
    Pages = {10346--},
    Publisher = {IEEE Computer Society},
    Series = {DATE '04},
    Acmid = {968963},
    ISBN = {0-7695-2085-5},
    Keywords = {electronic design automation;},
    Timestamp = {2013.09.16},
    URL = {http://dl.acm.org/citation.cfm?id=968878.968963}
    }