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A Review of CADs, Languages and Data Models for Synthetic Biology

Narjeskhatoon Habibi, Siti Zaiton Mohd Hashim, Cesar A. Rodriguez, Mohd Razip Samian
2013 Jurnal Teknologi  
In this review, existing CADs, languages and data models for synthetic biology are explored.  ...  Synthetic biology is to apply engineering standards to the biology.  ...  -Visual combinatorial library design. -Integration with DNA assembly automation. -Including a GUI for the creation of design specification rules.  ... 
doi:10.11113/jt.v63.1644 fatcat:gmxwhokaqfgnfhgfijiukty3wa

Agent-based modelling in synthetic biology

Thomas E. Gorochowski
2016 Essays in Biochemistry  
Agent-based modelling aims to tackle this problem, offering a framework in which to simulate such systems and explore cellular design rules.  ...  Synthetic biology aims to make the engineering of biology easier, offering an opportunity to control natural systems and develop new synthetic systems with useful prescribed behaviours.  ...  Acknowledgements I thank Antoni Matyjaszkiewicz for discussions about agent-based modelling tools.  ... 
doi:10.1042/ebc20160037 pmid:27903820 pmcid:PMC5264505 fatcat:p6dvqojfarfezh33t74lz5dbxu

Eugene – A Domain Specific Language for Specifying and Constraining Synthetic Biological Parts, Devices, and Systems

Lesia Bilitchenko, Adam Liu, Sherine Cheung, Emma Weeding, Bing Xia, Mariana Leguia, J. Christopher Anderson, Douglas Densmore, Diego Di Bernardo
2011 PLoS ONE  
We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive  ...  Conclusions: Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology.  ...  Eugene based synthetic biology design flow. Shown here is the role that Specification, Design, Assembly, and Data can play in synthetic biology.  ... 
doi:10.1371/journal.pone.0018882 pmid:21559524 pmcid:PMC3084710 fatcat:lfo3vjvrozdrhlwwlxe4a6jnhu

Specifications of Standards in Systems and Synthetic Biology: Status and Developments in 2019

Falk Schreiber, Björn Sommer, Gary D. Bader, Padraig Gleeson, Martin Golebiewski, Michael Hucka, Sarah M. Keating, Matthias König, Chris Myers, David Nickerson, Dagmar Waltemath
2019 Journal of Integrative Bioinformatics  
The standards cover representation formats for computational modeling in synthetic and systems biology and include BioPAX, CellML, NeuroML, SBML, SBGN, SBOL and SED-ML.  ...  This special issue of the Journal of Integrative Bioinformatics presents an overview of COMBINE standards and their latest specifications.  ...  SBGN (Systems Biology Graphical Notation) SBGN (Systems Biology Graphical Notation) [ SBOL (Synthetic Biology Open Language) SBOL (Synthetic Biology Open Language) [29] , specifications are -*NEW  ... 
doi:10.1515/jib-2019-0035 pmid:31301675 pmcid:PMC6798822 fatcat:rzfr2orbfjgwpfz4ei72tpi53i

Eugenie

Casey Grote, Evan Segreto, Johanna Okerlund, Robert Kincaid, Orit Shaer
2015 Proceedings of the Ninth International Conference on Tangible, Embedded, and Embodied Interaction - TEI '14  
We describe our two-year-long effort and design iterations of Eugenie, an interface for helping synthetic biologists through the collaborative and intricate process of biodesign.  ...  We present a case study of applying TEI research to a dataintense scientific workflow that requires the exploration of large datasets through the construction of complex queries.  ...  We use the synthetic biology domain-specific languages Eugene [3] and SBOL for validating new designs (G2).  ... 
doi:10.1145/2677199.2680605 dblp:conf/tei/GroteSOKS15 fatcat:j5xy2m7pgnctzcuijzcnimbcyu

Towards an Aspect-Oriented Design and Modelling Framework for Synthetic Biology

Philipp Boeing, Miriam Leon, Darren Nesbeth, Anthony Finkelstein, Chris Barnes
2018 Processes  
Work on synthetic biology has largely used a component-based metaphor for system construction.  ...  of rule, logic and reaction models from synthetic circuit designs.  ...  In rule-based modelling, a model is created as a collection of reaction rules in a rule-based modelling language such as Kappa [55, 56] .  ... 
doi:10.3390/pr6090167 pmid:30568914 pmcid:PMC6296438 fatcat:iwkylnw7u5cnhd7db6fhvku4li

GUBS, a Behaviour-Based Language for Design in Synthetic Biology

Adrien Basso-Blandin, Franck Delaplace
2013 Scientific Annals of Computer Science  
Gubs is a rule-based declarative language. In contrast to a closed system, a program is always a partial description of the behaviour of the system.  ...  In this article, we propose a domain specific language, Gubs (Genomic Unified Behaviour Specification), dedicated to the behavioural specification of synthetic biological devices, viewed as discrete open  ...  Cerrito and Amelie David for their helpful comments.  ... 
doi:10.7561/sacs.2013.1.1 fatcat:64kqze6enne43lq6wsp7mwa42a

Towards a Behavioral-Matching Based Compilation of Synthetic Biology Functions

Adrien Basso-Blandin, Franck Delaplace
2015 Acta Biotheoretica  
The field of synthetic biology is looking forward engineering framework for safely designing reliable de-novo biological functions.  ...  More specifically the Gubs (Genomic Unified Behavioural Specification) language is a specification language used to describe the observations of the expected behaviour.  ...  Acknowledgments The funding for most this work is granted by the ANR SYNBIOTIC (030701).  ... 
doi:10.1007/s10441-015-9265-9 pmid:26141968 pmcid:PMC4531147 fatcat:whso5tz2vrd73c54vngtwgeh5q

Genetic design automation: engineering fantasy or scientific renewal?

Matthew W. Lux, Brian W. Bramlett, David A. Ball, Jean Peccoud
2012 Trends in Biotechnology  
Computer-Aided Design tools for synthetic biology Several groups have been developing Computer-Aided Design (CAD) solutions for synthetic biology [1-10] yet the transcriptional complexity of published  ...  Synthetic biology aims to make genetic systems more amenable to engineering, which has naturally led to the development of Computer-Aided Design (CAD) tools.  ...  The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript  ... 
doi:10.1016/j.tibtech.2011.09.001 pmid:22001068 pmcid:PMC3779889 fatcat:7wzubr5ewzgjfgsnwplhpotcda

Design Automation in Synthetic Biology

Evan Appleton, Curtis Madsen, Nicholas Roehner, Douglas Densmore
2017 Cold Spring Harbor Perspectives in Biology  
In synthetic biology, these tools are called bio-design automation (BDA) tools.  ...  Design automation refers to a category of software tools for designing systems that work together in a workflow for designing, building, testing, and analyzing systems with a target behavior.  ...  Formal languages for describing the diverse domains in synthetic biology (e.g., metabolic net- Design Automation in Synthetic Biology Cite this article as Cold Spring Harb Perspect Biol 2017;9:a023978  ... 
doi:10.1101/cshperspect.a023978 pmid:28246188 fatcat:fyds5ow54zcxhfbqpnnwfuxp6u

Synthetic biology: history, challenges and prospects

J. Haseloff, J. Ajioka
2009 Journal of the Royal Society Interface  
Phillips & Cardelli (2009) present a programming language for the design and simulation of DNA computers based on strand displacement, while Pedersen & Phillips (2009) introduce a formal language for  ...  Welch et al. (2009) apply their considerable experience in DNA synthesis to provide a discussion of the main constraints for the design of synthetic genes and outline rules for the optimization of gene  ... 
doi:10.1098/rsif.2009.0176.focus pmid:19493895 pmcid:PMC2843964 fatcat:lffa4zdylzgqbmenqtsdw7mgzi

GUBS, a Behavior-based Language for Open System Dedicated to Synthetic Biology

Adrien Basso-Blandin, Franck Delaplace
2012 Electronic Proceedings in Theoretical Computer Science  
GUBS is a rule-based declarative language. By contrast to a closed system, a program is always a partial description of the behavior of the system.  ...  In this article, we propose a domain specific language, GUBS (Genomic Unified Behavior Specification), dedicated to the behavioral specification of synthetic biological devices, viewed as discrete open  ...  The funding for most of this work is granted by the anr synbiotic (anr blan 0307 01) and we would like to thank the colleagues of this project for their fruitful discussions.  ... 
doi:10.4204/eptcs.100.3 fatcat:vsubd2pexra2djdxf3akwbgro4

Specifications of standards in systems and synthetic biology: status and developments in 2021

Falk Schreiber, Padraig Gleeson, Martin Golebiewski, Thomas E. Gorochowski, Michael Hucka, Sarah M. Keating, Matthias König, Chris J. Myers, David P. Nickerson, Björn Sommer, Dagmar Waltemath
2021 Journal of Integrative Bioinformatics  
The 2021 special issue presents four updates of standards: Synthetic Biology Open Language Visual Version 2.3, Synthetic Biology Open Language Visual Version 3.0, Simulation Experiment Description Markup  ...  This special issue of the Journal of Integrative Bioinformatics contains updated specifications of COMBINE standards in systems and synthetic biology.  ...  Acknowledgements: We thank all members of the COMBINE initiative for their help. DPN is supported by the National Institutes of Health [P41EB023912].  ... 
doi:10.1515/jib-2021-0026 pmid:34674411 pmcid:PMC8573232 fatcat:abs7qckeyfdeddd4x5z6g54ape

A Property-Driven Methodology for Formal Analysis of Synthetic Biology Systems

Savas Konur, Marian Gheorghe
2015 IEEE/ACM Transactions on Computational Biology & Bioinformatics  
This paper proposes a formal methodology to analyse bio-systems, in particular synthetic biology systems.  ...  biology systems.  ...  Fig. 1 : 1 A property-based methodology for model checking synthetic biology systems.  ... 
doi:10.1109/tcbb.2014.2362531 pmid:26357223 fatcat:iljr55mvq5co5jgkx3r3r5jvjq

Joint DAC/IWBDA special session design and synthesis of biological circuits

Douglas Densmore, Mark Horowitz, Smita Krishnaswamy, Xiling Shen, Adam Arkin, Erik Winfree, Chris Voigt
2011 Proceedings of the 48th Design Automation Conference on - DAC '11  
into the next generation of tools for synthetic biology.  ...  With the growing complexity of synthetic biological circuits, robust and systematic methods are needed for design and test.  ...  Gene and Cellular Circuit Design Chris Voigt (Speaker) Univ. of California, San Francisco A genetic compiler for synthetic biology would enable biological systems to be specified in a high-level language  ... 
doi:10.1145/2024724.2024750 dblp:conf/dac/DensmoreHKSAWV11 fatcat:3mh4dsrcn5axrjw6iakveztjzq
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