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A platform-based design environment for synthetic biological systems

Douglas Densmore, Anne Van Devender, Matthew Johnson, Nade Sritanyaratana
2009 The Fifth Richard Tapia Celebration of Diversity in Computing Conference on Intellect, Initiatives, Insight, and Innovations - TAPIA '09  
Specifically this paper presents the Clotho toolset which uses these concepts to create a complete design environment for standardized biological parts.  ...  A Platform-Based Design approach views genetic information as having a particular functionality and assembles platforms (collections of DNA elements) to perform this functionality.  ...  Ryan Owen, Ethan Mirsky, and Josh Kittleson for their valuable input on the paper and related discussions.  ... 
doi:10.1145/1565799.1565806 dblp:conf/tapia/DensmoreDJS09 fatcat:73wgnrvbnvda3ov56na37453iy

Cell-Free Synthetic Biology Platform for Engineering Synthetic Biological Circuits and Systems

Jeong, Klocke, Agarwal, Kim, Choi, Franco, Kim
2019 Methods and Protocols  
Synthetic biology brings engineering disciplines to create novel biological systems for biomedical and technological applications.  ...  Here, we review the capabilities of the current cell-free platforms, focusing on nucleic acid-based molecular programs and circuit construction.  ...  This suggests toehold switches can provide a novel, high-performance platform for synthetic biological circuits.  ... 
doi:10.3390/mps2020039 pmid:31164618 pmcid:PMC6632179 fatcat:tuoyrfi5bnespmmmkip5xec4ti

Synthetic biology - the state of play

Richard Kitney, Paul Freemont
2012 FEBS Letters  
It first considers the current background to synthetic biology, whether it is a legitimate field and how it relates to foundational biological sciences.  ...  The evidence for this statement can be found in a number of sources. For example the bcc report [2] which predicts that: The global value of the synthetic biology market reached $1.  ...  Acknowledgements We wish to acknowledge the support of the Engineering and Physical Science Research Council in the Work and that of our colleagues in the Centre for Synthetic Biology and Innovation at  ... 
doi:10.1016/j.febslet.2012.06.002 pmid:22704968 fatcat:p2dyuav5pzdnpdzldfbavaz3jq

A living foundry for Synthetic Biological Materials: A synthetic biology roadmap to new advanced materials

Rosalind A. Le Feuvre, Nigel S. Scrutton
2018 Synthetic and Systems Biotechnology  
It considers requirements, early understanding and foresight of the challenges faced in delivering a Discovery to Manufacturing Pipeline for synthetic biological materials using synthetic biology approaches  ...  This challenge spans the complete production cycle from intelligent and predictive design, fabrication, evaluation and production of synthetic biological materials to new ways of bringing these products  ...  the potential to develop sustainable and affordable bio-production platforms and distributed manufacture in challenging environments for both small molecule and biopolymer-based materials.  ... 
doi:10.1016/j.synbio.2018.04.002 pmid:29900423 pmcid:PMC5995479 fatcat:iswszk6myfg77payg3qmvd6k7e

Moving forward with molecular communication: from theory to human health applications [point of view]

Ian F. Akyildiz, Massimiliano Pierobon, Sasitharan Balasubramaniam
2019 Proceedings of the IEEE  
(a) Cellular communication using microfluidic platform. (b) System level for in vivo nervous system information transfer. (c) Optical-to-chemical modulator for biological interfaces.  ...  designed for electrical communication systems. 1) Engineered Cell Communication: The engineering of cell communications based on the aforementioned programming of DNA biological circuits is one of the  ... 
doi:10.1109/jproc.2019.2913890 fatcat:7sdms62ii5bt7g2hizvkrq4jg4

Cell-free synthetic biology: Engineering in an open world

Yuan Lu
2017 Synthetic and Systems Biotechnology  
Cell-free synthetic biology emerges as a powerful and flexible enabling technology that can engineer biological parts and systems for life science applications without using living cells.  ...  Buildup of artificial cells based on cell-free systems will improve our understanding of life and use them for environmental and biomedical applications.  ...  Cell-free system can be a powerful platform for design, synthesis and high-throughput screening of novel proteins.  ... 
doi:10.1016/j.synbio.2017.02.003 pmid:29062958 pmcid:PMC5625795 fatcat:n4x4hna7ojcnjdb22wew73kjcq

Looking into the Crystal Ball: From Transistors to the Smart Earth

Alberto Vincentelli, Donatella Sciuto
2014 IEEE design & test  
Figure 5 The Swarm as a Platform (courtesy of Jan Rabaey) Similarly, the principles of platform--based design can be used for designing synthetic biological systems, in which standardized biological parts  ...  Platform--Based Design as a Paradigm for System Design Platform--based design has been advocated since the end of the 80's for electronic design, and used today for cyber--physical systems.  ... 
doi:10.1109/mdat.2014.2316209 fatcat:jiki2eqo3zda3f6y3cdrd3ebpe

Microfluidic Technologies for Synthetic Biology

Parisutham Vinuselvi, Seongyong Park, Minseok Kim, Jung Min Park, Taesung Kim, Sung Kuk Lee
2011 International Journal of Molecular Sciences  
Synthetic biology is an emerging field of biology and has drawn much attraction due to its potential to create novel, functional biological parts and systems for special purposes.  ...  Microfluidic technologies have shown powerful abilities for reducing cost, time, and labor, and at the same time, for increasing accuracy, throughput, and performance in the analysis of biological and  ...  Understanding the overall behavior of the natural system is a prerequisite for the successful design of a synthetic biological system.  ... 
doi:10.3390/ijms12063576 pmid:21747695 pmcid:PMC3131579 fatcat:lg5ycqfhhzbe7d42ffmvizaizm

Synthetic biology platform technologies for antimicrobial applications

Dana Braff, David Shis, James J. Collins
2016 Advanced Drug Delivery Reviews  
Lobritz for critical review of the manuscript. This work was supported by the Defense Threat Reduction Agency grants HDTRA1-14-1-0006 and HDTRA1-15-1-0051.  ...  In vitro cell free expression systems that contain transcription and translation machinery provide the environment necessary for biologically-based technologies to function independently of living cells  ...  To mitigate these constraints, Pardee et al. recently developed a paper-based system for cellfree gene expression, providing a simple platform for the real-world application of engineered genetic systems  ... 
doi:10.1016/j.addr.2016.04.006 pmid:27089812 fatcat:wygnxux6andhjjpps6hmvxmmtm

Basic research opportunities focused on bio-based and bio-inspired materials and potential applications

Stephanie A. Nick McElhinny, Jennifer J. Becker
2014 Frontiers in Chemistry  
material, (iii) Integrating biology with synthetic materials, and (iv) Imparting properties inherent in biological systems to materials.  ...  Keywords: bio-based materials, bio-inspired materials, hybrid materials, biomimetic systems, basic research The U.S.  ...  Biological synthetic platforms are also conducive to the design and production of hybrid products that contain both biological and non-biological elements.  ... 
doi:10.3389/fchem.2014.00024 pmid:24860801 pmcid:PMC4026725 fatcat:ggxoj4bhwzgmpcapimpeagsifi

Constructing synthetic biology workflows in the cloud

Göksel Mısırlı, Curtis Madsen, Iñaki Sainz de Murieta, Matthieu Bultelle, Keith Flanagan, Matthew Pocock, Jennifer Hallinan, James Alastair McLaughlin, Justin Clark-Casey, Mike Lyne, Gos Micklem, Guy-Bart Stan (+2 others)
2017 Engineering Biology  
and ultimately to facilitate the synthetic biology life cycle for designing and implementing biological systems.  ...  Here, the authors present the Protocol for Linking External Nodes (POLEN), a Cloud-based system that facilitates synthetic biology design workflows that operate asynchronously.  ...  The POLEN system facilitates the development of workflows for the design of complex genetic circuits using a message-based system.  ... 
doi:10.1049/enb.2017.0001 fatcat:qi5dsmxnz5ggbg274o7ogjgufe

Next-generation synthetic gene networks

Timothy K Lu, Ahmad S Khalil, James J Collins
2009 Nature Biotechnology  
As a result, the design cycle for engineering synthetic gene networks remains slow and error prone.  ...  information flow through engineered gene networks and test platforms for rapidly designing and constructing synthetic circuits.  ...  We also thank the reviewers for their insights and suggestions.  ... 
doi:10.1038/nbt.1591 pmid:20010597 pmcid:PMC2796205 fatcat:ydulznd2nneofhi2hlg5epswku

Next generation tools to accelerate the synthetic biology process

Steve C. C. Shih, Christopher Moraes
2016 Integrative Biology  
We highlight recently developed microfluidic tools that can be used to automate the synthetic biology workflow with the goal of advancing the likelihood of producing desired functionalities.  ...  Engineering a new biological system starts with the ''design'' phase. It can be thought of as developing the initial specifications for a system to achieve a certain task.  ...  The main goal of synthetic biology is to rapidly design biological systems following the DBTL workflow.  ... 
doi:10.1039/c6ib90017h pmid:27146265 fatcat:ofy3xwif7vghxlndq7zdtyse3m

Cell-Free Approaches in Synthetic Biology Utilizing Microfluidics

Samar Damiati, Rami Mhanna, Rimantas Kodzius, Eva-Kathrin Ehmoser
2018 Genes  
Synthetic biology is a rapidly growing multidisciplinary branch of science which aims to mimic complex biological systems by creating similar forms.  ...  This review highlights the recent evolution of cell-free gene design, proteins, and cells integrated with microfluidic platforms as a promising technology, which has allowed for the transformation of the  ...  An alternate, versatile platform for synthetic biology, paper-based synthetic gene networks were developed by Pardee et al.  ... 
doi:10.3390/genes9030144 pmid:29509709 pmcid:PMC5867865 fatcat:irrk7pdg25e47ief2q5o7g4i5i

Engineering Living Functional Materials

Allen Y. Chen, Chao Zhong, Timothy K. Lu
2015 ACS Synthetic Biology  
Thus, tools from synthetic biology, such as those for artificial gene regulation, can be used to engineer the spatiotemporal characteristics of living systems and to interface living systems with inorganic  ...  As a proof-of-concept, we recently demonstrated that synthetic gene circuits in Escherichia coli enabled biofilms to be both a functional material in its own right and a materialssynthesis platform.  ...  The authors declare the following competing financial interest(s): T.K.L. and A.Y.C. have filed a patent application with the U.S. Patent and Trademark Office.  ... 
doi:10.1021/sb500113b pmid:25592034 pmcid:PMC4304442 fatcat:qccbq32fsbd3nnqxrj24riwvpm
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