95 results on '"Densmore D"'
Search Results
2. CO96 Evidence Gap Analysis of the Burden of Illness and Treatment of Thyroid Eye Disease
- Author
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Gildea, L., Arvin-Berod, C.., Heyes, A., Heyerick, A., Urdaniz, E., Vainilovich, Y., Trainor, L., and Densmore, D.
- Published
- 2024
- Full Text
- View/download PDF
3. Rapid prototyping and parametric optimization of plastic acoustofluidic devices for blood–bacteria separation
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Silva, R., Dow, P., Dubay, R., Lissandrello, C., Holder, J., Densmore, D., and Fiering, J.
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- 2017
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4. Biosimilars: The Challenge to Overcome Financial Incentives in a US Payer Market
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Kuehn, M, primary and Densmore, D, additional
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- 2018
- Full Text
- View/download PDF
5. Reproducibility of fluorescent expression from engineered biological constructs in E. coli
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Beal, J, Haddock-Angelli, T, Gershater, M, De Mora, K, Lizarazo, M, Hollenhorst, J, Rettberg, R, Demling, P, Hanke, R, Osthege, M, Schechtel, A, Sudarsan, S, Zimmermann, A, Gabryelczyk, B, Ikonen, M, Salmela, M, Acar, M, Aktas, MF, Bestepe, F, Ceylan, FS, Cigdem, S, Dohan, M, Elitok, M, Gunduz, M, Gunduz, E, Hatipoglu, OF, Kaya, T, Sayin, O, Tapan, S, Tereci, OF, Uçar, A, Yilmaz, M, Barrick, J, Gutierrez, A, Mishler, D, Monk, J, Mortensen, K, Shin, N, Watkins, E, Chen, Y, Jin, Y, Shi, Y, Zhang, HM, Ono, B, Paino, IMM, Ribovski, L, Silva, I, Zampronio, DK, Birkholz, N, Busche, RF, Konzock, O, Lippold, S, Ludwig, C, Philippi, M, Platz, L, Sigismund, C, Weber, S, Wehrs, M, Werchau, N, Wronska, A, Yen, ZZ, Agarwal, Y, Appleton, E, Densmore, D, Esmurria, A, Lewis, K, Pacheco, A, Bruchez, M, Peters, D, Telmer, C, Wang, L, Canas-Duarte, S, Giraldo-Perez, D, Gomez-Garzon, C, Madrid-Wolff, J, Marin-Medina, N, Mazzanti, V, Rodriguez-Forero, L, Scher, E, Dowell, R, O'Hara, S, Pogoda, CS, Shattuck, K, Altintas, A, Bali, AP, Bech, R, Egholm, A, Hansen, ASL, Jensen, K, Karlsen, KB, Mosbech, C, Belkhelfa, S, Berenger, N, Bodinier, R, and Jacry, C
- Abstract
© 2016 Beal et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. We present results of the first large-scale interlaboratory study carried out in synthetic biology, as part of the 2014 and 2015 International Genetically Engineered Machine (iGEM) competitions. Participants at 88 institutions around the world measured fluorescence from three engineered constitutive constructs in E. coli. Few participants were able to measure absolute fluorescence, so data was analyzed in terms of ratios. Precision was strongly related to fluorescent strength, ranging from 1.54-fold standard deviation for the ratio between strong promoters to 5.75-fold for the ratio between the strongest and weakest promoter, and while host strain did not affect expression ratios, choice of instrument did. This result shows that high quantitative precision and reproducibility of results is possible, while at the same time indicating areas needing improved laboratory practices.
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- 2016
6. Genetic circuit design automation
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Nielsen, A. A. K., primary, Der, B. S., additional, Shin, J., additional, Vaidyanathan, P., additional, Paralanov, V., additional, Strychalski, E. A., additional, Ross, D., additional, Densmore, D., additional, and Voigt, C. A., additional
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- 2016
- Full Text
- View/download PDF
7. PHP189 - Biosimilars: The Challenge to Overcome Financial Incentives in a US Payer Market
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Kuehn, M and Densmore, D
- Published
- 2018
- Full Text
- View/download PDF
8. Experimentally driven verification of synthetic biological circuits
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Yordanov, B., Appleton, E., Ganguly, R., Gol, E. A., Carr, S. B., Swapnil Bhatia, Haddock, T., Belta, C., and Densmore, D.
- Published
- 2012
9. Design and Analysis of Biomolecular Circuits
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Koeppl, H., Densmore, D., Setti, G., and Di Bernardo, M.
- Published
- 2011
10. UMTS MPSoC design evaluation using a system level design framework
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Densmore, D., Simalatsar, A., Davare, A., Passerone, R., and Alberto Sangiovanni-Vincentelli
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- 2009
11. State-specific prevalence of obesity among adults--United States, 2005
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Blanck, H.M., Dietz, W.H., Galuska, D.A., Gillespie, C., Hamre, R., Khan, L. Kettel, Serdula, M.K., Ford, E.S., Garvin, W.S., Mokdad, A.H., and Densmore, D.
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Adults -- Surveys ,Adults -- Health aspects ,Obesity -- Surveys - Abstract
Obesity, one of the 10 leading U.S. health indicators (1), is associated with increased risk for hypertension, dyslipidemia, type 2 diabetes, coronary heart disease, stroke, and certain cancers (2). A [...]
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- 2006
12. Stochastic simulation for spatial modelling of dynamic processes in a living cell
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Setti, G, Koeppl, H, Densmore, D, di Bernardo, M, Burrage, Kevin, Burrage, Pamela, Leier, Andre, Marquez-Lago, Tatiana, Nicolau Jr., Dan, Setti, G, Koeppl, H, Densmore, D, di Bernardo, M, Burrage, Kevin, Burrage, Pamela, Leier, Andre, Marquez-Lago, Tatiana, and Nicolau Jr., Dan
- Abstract
One of the fundamental motivations underlying computational cell biology is to gain insight into the complicated dynamical processes taking place, for example, on the plasma membrane or in the cytosol of a cell. These processes are often so complicated that purely temporal mathematical models cannot adequately capture the complex chemical kinetics and transport processes of, for example, proteins or vesicles. On the other hand, spatial models such as Monte Carlo approaches can have very large computational overheads. This chapter gives an overview of the state of the art in the development of stochastic simulation techniques for the spatial modelling of dynamic processes in a living cell.
- Published
- 2011
13. Fluorescent-Based Quantitative Measurements of Signal Transduction in Single Cells
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Koeppl, Heinz, Densmore, Douglas, Setti, Gianluca, di Bernardo, Mario, Koeppl, H ( Heinz ), Densmore, D ( Douglas ), Setti, G ( Gianluca ), di Bernardo, M ( Mario ), Pelet, Serge, Peter, Matthias, Koeppl, Heinz, Densmore, Douglas, Setti, Gianluca, di Bernardo, Mario, Koeppl, H ( Heinz ), Densmore, D ( Douglas ), Setti, G ( Gianluca ), di Bernardo, M ( Mario ), Pelet, Serge, and Peter, Matthias
- Abstract
Budding yeast (Saccharomyces cerevisiae) has been widely used as a model system to study fundamental biological processes. Genetic and biochemical approaches have allowed in the last decades to uncover the key components involved in many signaling pathways. Generally, most techniques measure the average behavior of a population of cells, and thus missed important cell-to-cell variations. With the recent progress with fluorescent proteins, new avenues have been opened to quantitatively study the dynamics of signaling in single living cells. In this chapter, we describe several techniques based on fluorescence measurements to quantify the activation of biological pathways. Flow cytometry allows for rapid quantification of the total fluorescence of a large number of single cells. In contrast, microscopy offers a lower throughput but allows to follow with a high temporal resolution the localization of proteins at sub-cellular resolution. Finally, advanced functional imaging techniques such as FRET and FCS offer the possibility to directly visualize the formation of protein complexes or to quantify the activity of proteins in vivo. Together these techniques present powerful new approaches to study cellular signaling and will greatly increase our understanding of the regulation of signaling networks in budding yeast and beyond.
- Published
- 2011
14. A Platform-Based Taxonomy for ESL Design
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Densmore, D., primary and Passerone, R., additional
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- 2006
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15. FPGA Architecture Characterization for System Level Performance Analysis
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Densmore, D., primary, Donlin, A., additional, and Sangiovanni-Vincentelli, A., additional
- Published
- 2006
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16. State-Specific Prevalence of Obesity Among Adults - United States, 2005
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Blanck, H. M., primary, Dietz, W. H., additional, Galuska, D. A., additional, Gillespie, C., additional, Hamre, R., additional, Khan, L. Kettel, additional, Serdula, M. K., additional, Ford, E. S., additional, Garvin, W. S., additional, Mokdad, A. H., additional, and Densmore, D., additional
- Published
- 2006
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17. Rule based constraints for the construction of genetic devices.
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Densmore, D., Kittleson, J.T., Bilitchenko, L., Liu, A., and Anderson, J.C.
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- 2010
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18. Combinational logic design in Synthetic Biology.
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Densmore, D. and Anderson, J.C.
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- 2009
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19. A methodology for architecture exploration and performance analysis using system level design languages and rapid architecture profiling.
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Simalatsar, A., Passerone, R., and Densmore, D.
- Published
- 2008
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20. Functional Model Exploration for Multimedia Applications via Algebraic Operators.
- Author
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Kakita, S., Watanabe, Y., Densmore, D., Davare, A., and Sangiovanni-Vincentelli, A.
- Published
- 2006
- Full Text
- View/download PDF
21. The Ballad of Whoi Bob: a tale of the IGY or the Briny Deep Discovered, with many particulars of the extraordinary adventures and the heroic tasks of science at sea
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Densmore, D. and Neumann, C.
- Subjects
Sociology ,poem ,ComputingMethodologies_DOCUMENTANDTEXTPROCESSING ,international geophysical year ,Oceanography ,poetry - Abstract
PDF contains 19 pages
- Published
- 1961
22. Functional Model Exploration for Multimedia Applications via Algebraic Operators
- Author
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Kakita, S., primary, Watanabe, Y., additional, Densmore, D., additional, Davare, A., additional, and Sangiovanni-Vincentelli, A., additional
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23. Reproducibility of Plasma Catecholamine Metabolites in Normal Subjects
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Amin, F., Hashmi, A., Stroe, A. E., Adebogun, O., Densmore, D., and Knott, P. J.
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- 1998
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24. Diurnal Variation in Plasma Homovanillic Acid: Not a Renal Phenomenon
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Stroe, A. E., Amin, F., Hashmi, A., Densmore, D., Kahn, T., and Knott, P. J.
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- 1997
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25. State-Specific Prevalence of Obesity Among Adults--United States, 2005.
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Blanck, H. M., Dietz, W. H., Caluska, D. A., Gillespie, C., Hamre, R., Khan, L. Kettle, Serdula, M. K., Ford, E. S., Garvin, W. S., Mokdad, A. H., and Densmore, D.
- Subjects
OBESITY ,PUBLIC health ,TELEPHONE surveys ,OVERWEIGHT persons - Abstract
The article describes a study on adult obesity in the United States undertaken by the U.S. Centers for Disease Control and Prevention. The study assessed the prevalence of obesity by state and demographic characteristics by using data from the Behavioral Risk Factor Surveillance System. There was a significant increase in state-level prevalence of obesity from 1995-2005. Limitations to the study include the fact that the data was self-reported and that people without land-line telephones were not included in the study. Public health initiatives are needed to combat the prevalence of obesity in the United States.
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- 2006
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26. 2ab assembly: a methodology for automatable, high-throughput assembly of standard biological parts
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Leguia Mariana, Brophy Jennifer AN, Densmore Douglas, Asante Angel, and Anderson J Christopher
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2ab reaction ,Automated assembly ,DNA fabrication ,Synthetic biology ,Biology (General) ,QH301-705.5 - Abstract
Abstract There is growing demand for robust DNA assembly strategies to quickly and accurately fabricate genetic circuits for synthetic biology. One application of this technology is reconstitution of multi-gene assemblies. Here, we integrate a new software tool chain with 2ab assembly and show that it is robust enough to generate 528 distinct composite parts with an error-free success rate of 96%. Finally, we discuss our findings in the context of its implications for biosafety and biosecurity.
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- 2013
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27. DeviceEditor visual biological CAD canvas
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Chen Joanna, Densmore Douglas, Ham Timothy S, Keasling Jay D, and Hillson Nathan J
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bioCAD ,Visual design abstraction ,Correct-by-construction design ,Design specification rules ,Combinatorial library ,DNA assembly ,Biology (General) ,QH301-705.5 - Abstract
Abstract Background Biological Computer Aided Design (bioCAD) assists the de novo design and selection of existing genetic components to achieve a desired biological activity, as part of an integrated design-build-test cycle. To meet the emerging needs of Synthetic Biology, bioCAD tools must address the increasing prevalence of combinatorial library design, design rule specification, and scar-less multi-part DNA assembly. Results We report the development and deployment of web-based bioCAD software, DeviceEditor, which provides a graphical design environment that mimics the intuitive visual whiteboard design process practiced in biological laboratories. The key innovations of DeviceEditor include visual combinatorial library design, direct integration with scar-less multi-part DNA assembly design automation, and a graphical user interface for the creation and modification of design specification rules. We demonstrate how biological designs are rendered on the DeviceEditor canvas, and we present effective visualizations of genetic component ordering and combinatorial variations within complex designs. Conclusions DeviceEditor liberates researchers from DNA base-pair manipulation, and enables users to create successful prototypes using standardized, functional, and visual abstractions. Open and documented software interfaces support further integration of DeviceEditor with other bioCAD tools and software platforms. DeviceEditor saves researcher time and institutional resources through correct-by-construction design, the automation of tedious tasks, design reuse, and the minimization of DNA assembly costs.
- Published
- 2012
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28. Microarchitecture development via metropolis successive platform refinement.
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Densmore, D., Rekhi, S., and Sangiovanni-Vincentelli, A.
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- 2004
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29. A New Monthly Spiritual Paper.
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Densmore, D. C.
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- 1876
30. THE PRACTICAL GOOD ACCOMPLISHED BY SPIRIT COMMUNION.
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DENSMORE, D. C.
- Published
- 1874
31. Stochastic simulation for spatial modelling of dynamic process in a living cell
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André Leier, Pamela Burrage, Tatiana T. Marquez-Lago, Kevin Burrage, Dan V. Nicolau, Koeppl, H., Densmore, D., Setti, G., and di Bernardo, M.
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Stochastic simulators ,Mathematical model ,Stochastic simulation algorithm ,Multiscale stochastic modelling ,Computer science ,Monte Carlo method ,Living cell ,090300 BIOMEDICAL ENGINEERING ,Delayed reactions ,Quantitative Biology::Cell Behavior ,Gene regulation ,Chemical kinetics ,Diffusion ,Stochastic simulation ,Statistical physics ,Plasma membrane - Abstract
One of the fundamental motivations underlying computational cell biology is to gain insight into the complicated dynamical processes taking place, for example, on the plasma membrane or in the cytosol of a cell. These processes are often so complicated that purely temporal mathematical models cannot adequately capture the complex chemical kinetics and transport processes of, for example, proteins or vesicles. On the other hand, spatial models such as Monte Carlo approaches can have very large computational overheads. This chapter gives an overview of the state of the art in the development of stochastic simulation techniques for the spatial modelling of dynamic processes in a living cell.
- Published
- 2011
32. Rational design of robust biomolecular circuits: from specification to parameters
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James Lu, Tatjana Petrov, Marc Hafner, Heinz Koeppl, Köppl, Heinz, Densmore, D., di Bernardo, M., and Setti, Gianluca
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model ,Circuit design ,robustness ,Inverse problem ,Parameter space ,Optimal control ,Linear temporal logic ,Large deviations theory ,Robust control ,parameter space ,Formal verification ,Algorithm ,Mathematics ,LTL - Abstract
Despite the early success stories synthetic biology, the development of larger, more complex synthetic systems necessitates the use of appropriate design methodologies. In particular, the integration of smaller circuits in order to perform complex tasks remains one of the most important challenges faced in synthetic biology. We propose here a methodology to determine the region in the parameter space where a given dynamical model works as desired. It is based on the inverse problem of finding parameter sets that exhibit the specified behavior for a defined topology. The main issue we face is that such inverse mapping is highly expansive and suffers from instability: small changes in the specified dynamic property could lead to large deviations in the parameters for the identified models. To solve this issue, we discuss regularized maps complemented by local analysis. With a stabilized inversion map, small neighborhoods in the property space are mapped to small neighborhoods in the parameter space, thereby finding parameter vectors that are robust to the problem specification. To specify dynamic circuit properties we discuss Linear Temporal Logic (LTL). We apply these concepts to two models of the cyanobacterial circadian oscillation.
33. Partitioning of a 2-bit hash function across 66 communicating cells.
- Author
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Padmakumar JP, Sun JJ, Cho W, Zhou Y, Krenz C, Han WZ, Densmore D, Sontag ED, and Voigt CA
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Powerful distributed computing can be achieved by communicating cells that individually perform simple operations. Here, we report design software to divide a large genetic circuit across cells as well as the genetic parts to implement the subcircuits in their genomes. These tools were demonstrated using a 2-bit version of the MD5 hashing algorithm, which is an early predecessor to the cryptographic functions underlying cryptocurrency. One iteration requires 110 logic gates, which were partitioned across 66 Escherichia coli strains, requiring the introduction of a total of 1.1 Mb of recombinant DNA into their genomes. The strains were individually experimentally verified to integrate their assigned input signals, process this information correctly and propagate the result to the cell in the next layer. This work demonstrates the potential to obtain programable control of multicellular biological processes., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)
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- 2024
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34. GOLDBAR: A Framework for Combinatorial Biological Design.
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Roehner N, Roberts J, Lapets A, Gould D, Akavoor V, Qin L, Gordon DB, Voigt C, and Densmore D
- Subjects
- Machine Learning, Multigene Family, Gene Library, DNA genetics, DNA chemistry, Gene Regulatory Networks, Synthetic Biology methods
- Abstract
With the rise of new DNA part libraries and technologies for assembling DNA, synthetic biologists are increasingly constructing and screening combinatorial libraries to optimize their biological designs. As combinatorial libraries are used to generate data on design performance, new rules for composing biological designs will emerge. Most formal frameworks for combinatorial design, however, do not yet support formal comparison of design composition, which is needed to facilitate automated analysis and machine learning in massive biological design spaces. To address this need, we introduce a combinatorial design framework called GOLDBAR. Compared with existing frameworks, GOLDBAR enables synthetic biologists to intersect and merge the rules for entire classes of biological designs to extract common design motifs and infer new ones. Here, we demonstrate the application of GOLDBAR to refine/validate design spaces for TetR-homologue transcriptional logic circuits, verify the assembly of a partial nif gene cluster, and infer novel gene clusters for the biosynthesis of rebeccamycin. We also discuss how GOLDBAR could be used to facilitate grammar-based machine learning in synthetic biology.
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- 2024
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35. Ten simple rules for managing laboratory information.
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Berezin CT, Aguilera LU, Billerbeck S, Bourne PE, Densmore D, Freemont P, Gorochowski TE, Hernandez SI, Hillson NJ, King CR, Köpke M, Ma S, Miller KM, Moon TS, Moore JH, Munsky B, Myers CJ, Nicholas DA, Peccoud SJ, Zhou W, and Peccoud J
- Abstract
Information is the cornerstone of research, from experimental (meta)data and computational processes to complex inventories of reagents and equipment. These 10 simple rules discuss best practices for leveraging laboratory information management systems to transform this large information load into useful scientific findings., Competing Interests: I have read the journal’s policy and the authors of this manuscript have the following competing interests:J.P., S.P., and K.M. have a financial interest in GenoFAB, Inc., M.K. is an employee of LanzaTech. N.J.H. has a financial interest in TeselaGen Biotechnology, Inc. and Ansa Biotechnologies, Inc. GenoFAB Inc. and TeselaGen Biotechnology, Inc. provide research information management systems. These companies may benefit or be perceived as benefiting from this publication., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)
- Published
- 2023
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36. Versatility and stability optimization of flow-focusing droplet generators via quality metric-driven design automation.
- Author
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McIntyre D, Lashkaripour A, Arguijo D, Fordyce P, and Densmore D
- Abstract
Droplet generation is a fundamental component of droplet microfluidics, compartmentalizing biological or chemical systems within a water-in-oil emulsion. As adoption of droplet microfluidics expands beyond expert labs or integrated devices, quality metrics are needed to contextualize the performance capabilities, improving the reproducibility and efficiency of operation. Here, we present two quality metrics for droplet generation: performance versatility, the operating range of a single device, and stability, the distance of a single operating point from a regime change. Both metrics were characterized in silico and validated experimentally using machine learning and rapid prototyping. These metrics were integrated into a design automation workflow, DAFD 2.0, which provides users with droplet generators of a desired performance that are versatile or flow stable. Versatile droplet generators with stable operating points accelerate the development of sophisticated devices by facilitating integration of other microfluidic components and improving the accuracy of design automation tools.
- Published
- 2023
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- View/download PDF
37. ICOR: improving codon optimization with recurrent neural networks.
- Author
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Jain R, Jain A, Mauro E, LeShane K, and Densmore D
- Subjects
- Codon genetics, Escherichia coli genetics, Genomics, Amino Acids genetics
- Abstract
Background: In protein sequences-as there are 61 sense codons but only 20 standard amino acids-most amino acids are encoded by more than one codon. Although such synonymous codons do not alter the encoded amino acid sequence, their selection can dramatically affect the expression of the resulting protein. Codon optimization of synthetic DNA sequences is important for heterologous expression. However, existing solutions are primarily based on choosing high-frequency codons only, neglecting the important effects of rare codons. In this paper, we propose a novel recurrent-neural-network based codon optimization tool, ICOR, that aims to learn codon usage bias on a genomic dataset of Escherichia coli. We compile a dataset of over 7,000 non-redundant, high-expression, robust genes which are used for deep learning. The model uses a bidirectional long short-term memory-based architecture, allowing for the sequential context of codon usage in genes to be learned. Our tool can predict synonymous codons for synthetic genes toward optimal expression in Escherichia coli., Results: We demonstrate that sequential context achieved via RNN may yield codon selection that is more similar to the host genome. Based on computational metrics that predict protein expression, ICOR theoretically optimizes protein expression more than frequency-based approaches. ICOR is evaluated on 1,481 Escherichia coli genes as well as a benchmark set of 40 select DNA sequences whose heterologous expression has been previously characterized. ICOR's performance is measured across five metrics: the Codon Adaptation Index, GC-content, negative repeat elements, negative cis-regulatory elements, and codon frequency distribution., Conclusions: The results, based on in silico metrics, indicate that ICOR codon optimization is theoretically more effective in enhancing recombinant expression of proteins over other established codon optimization techniques. Our tool is provided as an open-source software package that includes the benchmark set of sequences used in this study., (© 2023. The Author(s).)
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- 2023
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38. Safety by design: Biosafety and biosecurity in the age of synthetic genomics.
- Author
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Hoffmann SA, Diggans J, Densmore D, Dai J, Knight T, Leproust E, Boeke JD, Wheeler N, and Cai Y
- Abstract
Technologies to profoundly engineer biology are becoming increasingly affordable, powerful, and accessible to a widening group of actors. While offering tremendous potential to fuel biological research and the bioeconomy, this development also increases the risk of inadvertent or deliberate creation and dissemination of pathogens. Effective regulatory and technological frameworks need to be developed and deployed to manage these emerging biosafety and biosecurity risks. Here, we review digital and biological approaches of a range of technology readiness levels suited to address these challenges. Digital sequence screening technologies already are used to control access to synthetic DNA of concern. We examine the current state of the art of sequence screening, challenges and future directions, and environmental surveillance for the presence of engineered organisms. As biosafety layer on the organism level, we discuss genetic biocontainment systems that can be used to created host organisms with an intrinsic barrier against unchecked environmental proliferation., Competing Interests: D.D. is a co-founder of Lattice Automation, Inc. and Asimov Inc. Both companies create engineered biological systems using software and automation. J.D.B. is a Founder and Director of CDI Labs, Inc., a Founder of and consultant to Neochromosome, Inc, a Founder, SAB member of and consultant to Re-Open Diagnostics, LLC, and serves or served on the Scientific Advisory Board of the following: Sangamo Therapeutics, Inc., Modern Meadow, Inc., Rome Therapeutics, Inc., Sample6, Inc., Tessera Therapeutics, Inc. and the Wyss Institute. T.K. is co-founder of Ginkgo Bioworks, Inc. EL is CEO and co-founder of Twist Bioscience, Inc., and J.D. is an employee of Twist Bioscience, Inc., (© 2023 The Author(s).)
- Published
- 2023
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39. Buildout and integration of an automated high-throughput CLIA laboratory for SARS-CoV-2 testing on a large urban campus.
- Author
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Landaverde L, McIntyre D, Robson J, Fu D, Ortiz L, Chen R, Oliveira SMD, Fan A, Barrett A, Burgay SP, Choate S, Corbett D, Doucette-Stamm L, Gonzales K, Hamer DH, Huang L, Huval S, Knight C, Landa C, Lindquist D, Lockard K, Macdowell TL, Mauro E, McGinty C, Miller C, Monahan M, Moore R, Platt J, Rolles L, Roy J, Schroeder T, Tolan DR, Zaia A, Brown RA, Waters G, Densmore D, and Klapperich CM
- Subjects
- COVID-19 Testing, Humans, Pandemics prevention & control, Real-Time Polymerase Chain Reaction methods, United States, COVID-19 diagnosis, SARS-CoV-2
- Abstract
In 2019, the first cases of SARS-CoV-2 were detected in Wuhan, China, and by early 2020 the first cases were identified in the United States. SARS-CoV-2 infections increased in the US causing many states to implement stay-at-home orders and additional safety precautions to mitigate potential outbreaks. As policies changed throughout the pandemic and restrictions lifted, there was an increase in demand for COVID-19 testing which was costly, difficult to obtain, or had long turn-around times. Some academic institutions, including Boston University (BU), created an on-campus COVID-19 screening protocol as part of a plan for the safe return of students, faculty, and staff to campus with the option for in-person classes. At BU, we put together an automated high-throughput clinical testing laboratory with the capacity to run 45,000 individual tests weekly by Fall of 2020, with a purpose-built clinical testing laboratory, a multiplexed reverse transcription PCR (RT-qPCR) test, robotic instrumentation, and trained staff. There were many challenges including supply chain issues for personal protective equipment and testing materials in addition to equipment that were in high demand. The BU Clinical Testing Laboratory (CTL) was operational at the start of Fall 2020 and performed over 1 million SARS-CoV-2 PCR tests during the 2020-2021 academic year., Competing Interests: Declaration of interests The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Author(s). Published by Elsevier Inc. All rights reserved.)
- Published
- 2022
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40. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology.
- Author
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Oliveira SMD and Densmore D
- Abstract
Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements., Competing Interests: S.M.D.O declares that there is no conflict of interest regarding the publication of this article. D.D. is a cofounder of Asimov, Lattice Automation, and BioSens8. These are companies that use synthetic biology, create biodesign software, and design biosensors., (Copyright © 2022 Samuel M. D. Oliveira and Douglas Densmore.)
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- 2022
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41. Machine learning for microfluidic design and control.
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McIntyre D, Lashkaripour A, Fordyce P, and Densmore D
- Subjects
- High-Throughput Nucleotide Sequencing, Lab-On-A-Chip Devices, Machine Learning, Microfluidic Analytical Techniques, Microfluidics
- Abstract
Microfluidics has developed into a mature field with applications across science and engineering, having particular commercial success in molecular diagnostics, next-generation sequencing, and bench-top analysis. Despite its ubiquity, the complexity of designing and controlling custom microfluidic devices present major barriers to adoption, requiring intuitive knowledge gained from years of experience. If these barriers were overcome, microfluidics could miniaturize biological and chemical research for non-experts through fully-automated platform development and operation. The intuition of microfluidic experts can be captured through machine learning, where complex statistical models are trained for pattern recognition and subsequently used for event prediction. Integration of machine learning with microfluidics could significantly expand its adoption and impact. Here, we present the current state of machine learning for the design and control of microfluidic devices, its possible applications, and current limitations.
- Published
- 2022
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42. Genetic circuit design automation with Cello 2.0.
- Author
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Jones TS, Oliveira SMD, Myers CJ, Voigt CA, and Densmore D
- Subjects
- Automation, DNA genetics, Escherichia coli genetics, Synthetic Biology, Gene Regulatory Networks, Software
- Abstract
Cells interact with their environment, communicate among themselves, track time and make decisions through functions controlled by natural regulatory genetic circuits consisting of interacting biological components. Synthetic programmable circuits used in therapeutics and other applications can be automatically designed by computer-aided tools. The Cello software designs the DNA sequences for programmable circuits based on a high-level software description and a library of characterized DNA parts representing Boolean logic gates. This process allows for design specification reuse, modular DNA part library curation and formalized circuit transformations based on experimental data. This protocol describes Cello 2.0, a freely available cross-platform software written in Java. Cello 2.0 enables flexible descriptions of the logic gates' structure and their mathematical models representing dynamic behavior, new formal rules for describing the placement of gates in a genome, a new graphical user interface, support for Verilog 2005 syntax and a connection to the SynBioHub parts repository software environment. Collectively, these features expand Cello's capabilities beyond Escherichia coli plasmids to new organisms and broader genetic contexts, including the genome. Designing circuits with Cello 2.0 produces an abstract Boolean network from a Verilog file, assigns biological parts to each node in the Boolean network, constructs a DNA sequence and generates highly structured and annotated sequence representations suitable for downstream processing and fabrication, respectively. The result is a sequence implementing the specified Boolean function in the organism and predictions of circuit performance. Depending on the size of the design space and users' expertise, jobs may take minutes or hours to complete., (© 2022. The Author(s), under exclusive licence to Springer Nature Limited.)
- Published
- 2022
- Full Text
- View/download PDF
43. Assessment of a COVID-19 Control Plan on an Urban University Campus During a Second Wave of the Pandemic.
- Author
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Hamer DH, White LF, Jenkins HE, Gill CJ, Landsberg HE, Klapperich C, Bulekova K, Platt J, Decarie L, Gilmore W, Pilkington M, MacDowell TL, Faria MA, Densmore D, Landaverde L, Li W, Rose T, Burgay SP, Miller C, Doucette-Stamm L, Lockard K, Elmore K, Schroeder T, Zaia AM, Kolaczyk ED, Waters G, and Brown RA
- Subjects
- Boston epidemiology, COVID-19 epidemiology, COVID-19 transmission, Contact Tracing instrumentation, Contact Tracing methods, Hand Hygiene methods, Humans, Infection Control methods, Infection Control statistics & numerical data, Quarantine methods, Universities organization & administration, COVID-19 prevention & control, Infection Control standards, Universities trends, Urban Population statistics & numerical data
- Abstract
Importance: The COVID-19 pandemic has severely disrupted US educational institutions. Given potential adverse financial and psychosocial effects of campus closures, many institutions developed strategies to reopen campuses in the fall 2020 semester despite the ongoing threat of COVID-19. However, many institutions opted to have limited campus reopening to minimize potential risk of spread of SARS-CoV-2., Objective: To analyze how Boston University (BU) fully reopened its campus in the fall of 2020 and controlled COVID-19 transmission despite worsening transmission in Boston, Massachusetts., Design, Setting, and Participants: This multifaceted intervention case series was conducted at a large urban university campus in Boston, Massachusetts, during the fall 2020 semester. The BU response included a high-throughput SARS-CoV-2 polymerase chain reaction testing facility with capacity to deliver results in less than 24 hours; routine asymptomatic screening for COVID-19; daily health attestations; adherence monitoring and feedback; robust contact tracing, quarantine, and isolation in on-campus facilities; face mask use; enhanced hand hygiene; social distancing recommendations; dedensification of classrooms and public places; and enhancement of all building air systems. Data were analyzed from December 20, 2020, to January 31, 2021., Main Outcomes and Measures: SARS-CoV-2 diagnosis confirmed by reverse transcription-polymerase chain reaction of anterior nares specimens and sources of transmission, as determined through contact tracing., Results: Between August and December 2020, BU conducted more than 500 000 COVID-19 tests and identified 719 individuals with COVID-19, including 496 students (69.0%), 11 faculty (1.5%), and 212 staff (29.5%). Overall, 718 individuals, or 1.8% of the BU community, had test results positive for SARS-CoV-2. Of 837 close contacts traced, 86 individuals (10.3%) had test results positive for COVID-19. BU contact tracers identified a source of transmission for 370 individuals (51.5%), with 206 individuals (55.7%) identifying a non-BU source. Among 5 faculty and 84 staff with SARS-CoV-2 with a known source of infection, most reported a transmission source outside of BU (all 5 faculty members [100%] and 67 staff members [79.8%]). A BU source was identified by 108 of 183 undergraduate students with SARS-CoV-2 (59.0%) and 39 of 98 graduate students with SARS-CoV-2 (39.8%); notably, no transmission was traced to a classroom setting., Conclusions and Relevance: In this case series of COVID-19 transmission, BU used a coordinated strategy of testing, contact tracing, isolation, and quarantine, with robust management and oversight, to control COVID-19 transmission in an urban university setting.
- Published
- 2021
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- View/download PDF
44. Algorithms for the selection of fluorescent reporters.
- Author
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Vaidyanathan P, Appleton E, Tran D, Vahid A, Church G, and Densmore D
- Subjects
- Computational Biology methods, Databases, Chemical, Internet, Software, Algorithms, Fluorescent Dyes metabolism, Genes, Reporter
- Abstract
Molecular biologists rely on the use of fluorescent probes to take measurements of their model systems. These fluorophores fall into various classes (e.g. fluorescent dyes, fluorescent proteins, etc.), but they all share some general properties (such as excitation and emission spectra, brightness) and require similar equipment for data acquisition. Selecting an ideal set of fluorophores for a particular measurement technology or vice versa is a multidimensional problem that is difficult to solve with ad hoc methods due to the enormous solution space of possible fluorophore panels. Choosing sub-optimal fluorophore panels can result in unreliable or erroneous measurements of biochemical properties in model systems. Here, we describe a set of algorithms, implemented in an open-source software tool, for solving these problems efficiently to arrive at fluorophore panels optimized for maximal signal and minimal bleed-through.
- Published
- 2021
- Full Text
- View/download PDF
45. Machine learning enables design automation of microfluidic flow-focusing droplet generation.
- Author
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Lashkaripour A, Rodriguez C, Mehdipour N, Mardian R, McIntyre D, Ortiz L, Campbell J, and Densmore D
- Subjects
- Algorithms, Automation, Databases as Topic, Equipment Design, Lab-On-A-Chip Devices, Neural Networks, Computer, Machine Learning, Microfluidics, Rheology
- Abstract
Droplet-based microfluidic devices hold immense potential in becoming inexpensive alternatives to existing screening platforms across life science applications, such as enzyme discovery and early cancer detection. However, the lack of a predictive understanding of droplet generation makes engineering a droplet-based platform an iterative and resource-intensive process. We present a web-based tool, DAFD, that predicts the performance and enables design automation of flow-focusing droplet generators. We capitalize on machine learning algorithms to predict the droplet diameter and rate with a mean absolute error of less than 10 μm and 20 Hz. This tool delivers a user-specified performance within 4.2% and 11.5% of the desired diameter and rate. We demonstrate that DAFD can be extended by the community to support additional fluid combinations, without requiring extensive machine learning knowledge or large-scale data-sets. This tool will reduce the need for microfluidic expertise and design iterations and facilitate adoption of microfluidics in life sciences.
- Published
- 2021
- Full Text
- View/download PDF
46. Genetic circuit design automation for yeast.
- Author
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Chen Y, Zhang S, Young EM, Jones TS, Densmore D, and Voigt CA
- Subjects
- Automation, Base Sequence, DNA genetics, DNA-Binding Proteins metabolism, DNA-Directed RNA Polymerases metabolism, Gene Expression Regulation, Fungal, Promoter Regions, Genetic, RNA, Catalytic, Software, Synthetic Biology, Transcription Factors genetics, Transcription, Genetic, Gene Regulatory Networks, Saccharomyces cerevisiae genetics
- Abstract
Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of transcription and translation. To this end, we have developed gates for yeast (Saccharomyces cerevisiae) that are connected using RNA polymerase flux as the signal carrier and are insulated from each other and host regulation. They are based on minimal constitutive promoters (~120 base pairs), for which rules are developed to insert operators for DNA-binding proteins. Using this approach, we constructed nine NOT/NOR gates with nearly identical response functions and 400-fold dynamic range. In circuits, they are transcriptionally insulated from each other by placing ribozymes downstream of terminators to block nuclear export of messenger RNAs resulting from RNA polymerase readthrough. Based on these gates, Cello 2.0 was used to build circuits with up to 11 regulatory proteins. A simple dynamic model predicts the circuit response over days. Genetic circuit design automation for eukaryotes simplifies the construction of regulatory networks as part of cellular engineering projects, whether it be to stage processes during bioproduction, serve as environmental sentinels or guide living therapeutics.
- Published
- 2020
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- View/download PDF
47. Rapid and inexpensive microfluidic electrode integration with conductive ink.
- Author
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McIntyre D, Lashkaripour A, and Densmore D
- Abstract
Electrode integration significantly increases the versatility of droplet microfluidics, enabling label-free sensing and manipulation at a single-droplet (single-cell) resolution. However, common fabrication techniques for integrating electronics into microfluidics are expensive, time-consuming, and can require cleanroom facilities. Here, we present a simple and cost-effective method for integrating electrodes into thermoplastic microfluidic chips using an off-the-shelf conductive ink. The developed conductive ink electrodes cost less than $10 for an entire chip, have been shown here in channel geometries as small as 75 μm by 50 μm, and can go from fabrication to testing within a day without a cleanroom. The geometric fabrication limits of this technique were explored over time, and proof-of-concept microfluidic devices for capacitance sensing, droplet merging, and droplet sorting were developed. This novel method complements existing rapid prototyping systems for microfluidics such as micromilling, laser cutting, and 3D printing, enabling their wider use and application.
- Published
- 2020
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48. Correction: Repository-based plasmid design.
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Timmons JJ and Densmore D
- Abstract
[This corrects the article DOI: 10.1371/journal.pone.0223935.].
- Published
- 2020
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49. Repository-based plasmid design.
- Author
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Timmons JJ and Densmore D
- Subjects
- DNA genetics, Genetic Vectors classification, Plasmids classification, Software, Databases, Genetic, Genetic Vectors genetics, Plasmids genetics
- Abstract
There was an explosion in the amount of commercially available DNA in sequence repositories over the last decade. The number of such plasmids increased from 12,000 to over 300,000 among three of the largest repositories: iGEM, Addgene, and DNASU. A challenge in biodesign remains how to use these and other repository-based sequences effectively, correctly, and seamlessly. This work describes an approach to plasmid design where a plasmid is specified as simply a DNA sequence or list of features. The proposed software then finds the most cost-effective combination of synthetic and PCR-prepared repository fragments to build the plasmid via Gibson assembly®. It finds existing DNA sequences in both user-specified and public DNA databases: iGEM, Addgene, and DNASU. Such a software application is introduced and characterized against all post-2005 iGEM composite parts and all Addgene vectors submitted in 2018 and found to reduce costs by 34% versus a purely synthetic plasmid design approach. The described software will improve current plasmid assembly workflows by shortening design times, improving build quality, and reducing costs., Competing Interests: J.T. is employed at and D.D. is a shareholder in Lattice Automation, Inc. which makes commercial software for biologists. This does not alter our adherence to PLOS ONE policies on sharing data and materials. All software and data affiliated with this publication is and will remain accessible and open-source.
- Published
- 2020
- Full Text
- View/download PDF
50. A Computational Workflow for the Automated Generation of Models of Genetic Designs.
- Author
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Misirli G, Nguyen T, McLaughlin JA, Vaidyanathan P, Jones TS, Densmore D, Myers C, and Wipat A
- Subjects
- Computer Simulation, Humans, Models, Biological, Programming Languages, Research Design, Software, Workflow, Gene Regulatory Networks genetics, Synthetic Biology methods, Systems Biology methods
- Abstract
Computational models are essential to engineer predictable biological systems and to scale up this process for complex systems. Computational modeling often requires expert knowledge and data to build models. Clearly, manual creation of models is not scalable for large designs. Despite several automated model construction approaches, computational methodologies to bridge knowledge in design repositories and the process of creating computational models have still not been established. This paper describes a workflow for automatic generation of computational models of genetic circuits from data stored in design repositories using existing standards. This workflow leverages the software tool SBOLDesigner to build structural models that are then enriched by the Virtual Parts Repository API using Systems Biology Open Language (SBOL) data fetched from the SynBioHub design repository. The iBioSim software tool is then utilized to convert this SBOL description into a computational model encoded using the Systems Biology Markup Language (SBML). Finally, this SBML model can be simulated using a variety of methods. This workflow provides synthetic biologists with easy to use tools to create predictable biological systems, hiding away the complexity of building computational models. This approach can further be incorporated into other computational workflows for design automation.
- Published
- 2019
- Full Text
- View/download PDF
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