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Rule based constraints for the construction of genetic devices

Douglas Densmore, Joshua T. Kittleson, Lesia Bilitchenko, Adam Liu, J. Christopher Anderson
2010 Proceedings of 2010 IEEE International Symposium on Circuits and Systems  
The construction of composite genetic devices from primitive parts is a key activity in synthetic biology.  ...  Currently there does not exist a formal method to specify constraints on the construction of these devices.  ...  ACKNOWLEDGMENT The authors would like to thank Joanna Chen, Richard Mar, Thien Nguyen, Nina Revko, and Bing Xia for helping to develop tools related to Eugene's development.  ... 
doi:10.1109/iscas.2010.5537540 dblp:conf/iscas/DensmoreKBLA10 fatcat:7nwamc7ktnf3zacdlemxu7bfje

Constraint-Based Genetic Compilation [chapter]

Christophe Ladroue, Sara Kalvala
2015 Lecture Notes in Computer Science  
Through a simple language, the user provides in-house knowledge about their construct (e.g. relative placement of parts, number of restriction enzymes). atgc combines information from established biology  ...  , user knowledge and bioinformatics databases, and maps the problem to a constraint satisfaction setting.  ...  We are grateful for the collaboration within the Roadblock consortia.  ... 
doi:10.1007/978-3-319-21233-3_3 fatcat:6af36gvxujbirdhzyex4fwansm

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  
It has two main aims; first to design and construct biological systems in order to extend the understanding of how they work, and second, to design biological systems for performing valuable tasks like  ...  The goal is to provide an insight for the synthetic biologists to take advantage of the available computational tools and to find out the gaps to work on.  ...  Devices are ordered 5' to 3': Device BBa_1(P1,GFP); - Rule o Declaration: Describing the constraints on devices using rules operators: Rule R1(P1 BEFORE GFP); o Assert and Note:  Assert: Throws  ... 
doi:10.11113/jt.v63.1644 fatcat:gmxwhokaqfgnfhgfijiukty3wa

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  ...  Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime.  ...  Constraint Scope -Currently, rules are based on Part instances but not Part definitions. For example, a rule will be based on Promoter P1 but not across all Promoters.  ... 
doi:10.1371/journal.pone.0018882 pmid:21559524 pmcid:PMC3084710 fatcat:lfo3vjvrozdrhlwwlxe4a6jnhu

High-Level Programming Languages for Biomolecular Systems [chapter]

Jacob Beal, Andrew Phillips, Douglas Densmore, Yizhi Cai
2011 Design and Analysis of Biomolecular Circuits  
of the genetic code that will be used to implement these behaviors.  ...  High level languages for bio-molecular systems aim to achieve a similar level of abstraction, so that a system might be designed on the basis of the behaviors that are desired, rather than the particulars  ...  This has been extended recently with a second syntactic model, designed specifically for BioBrick TM -based constructs [Cai et al., 2010] .  ... 
doi:10.1007/978-1-4419-6766-4_11 fatcat:uggyvcb36zdataiu7yevewglyi

Android Genetic Programming Framework [chapter]

Alban Cotillon, Philip Valencia, Raja Jurdak
2012 Lecture Notes in Computer Science  
This paper introduces the Android Genetic Programming Framework (AGP) as a personalisation method for smart phones.  ...  AGP considers the specific design challenges of smart phones, such as resource limitation and constrained programming environments.  ...  Acknowledgements The authors would like to thank Brano Kusy for his valuable inputs in realising this work.  ... 
doi:10.1007/978-3-642-29139-5_2 fatcat:4grp5goiojcmbbgu54mfrohxpi

Using Genetic Algorithms to solve scheduling problems on flexible manufacturing systems (FMS): a literature survey, classification and analysis

Moacir Godinho Filho, Clarissa Fullin Barco, Roberto Fernandes Tavares Neto
2012 Flexible Services and Manufacturing Journal  
On the basis of this literature review, a classification system is proposed that encompasses 6 main dimensions: FMS type, types of resource constraints, job description, scheduling problem, measure of  ...  This paper reviews the literature regarding Genetic Algorithms (GAs) applied to flexible manufacturing system (FMS) scheduling.  ...  Holland in 1975 and can be understood as a process for optimizing complex functions based on the mechanisms of genetics and natural evolution.  ... 
doi:10.1007/s10696-012-9143-6 fatcat:7vemtmq6wfbhjctbzxokpgccc4

Optimal Coordination and Penetration of Distributed Generation with Multi Shunt FACTS Compensators Using GA/Fuzzy Rules [chapter]

Belkacem Mahdad, Tarek Bouktir, Kamel Srairi
2010 Distributed Generation  
The proposed approach is based on a combined Genetic/Fuzzy Rules.  ...  GA Solution for the Economic Dispatch GAs are general purpose optimization algorithms based on the mechanics of natural selection and genetics [14] .  ...  Interconnection of these generators will offer a number of benefits such as improved reliability, power quality, efficiency, alleviation of system constraints along with the environmental benefits.  ... 
doi:10.5772/8877 fatcat:vkvmdlbtizcopo6ukroqmyygyi

Study on Ladle Schedule of Steel Making Process Using Heuristic Scheduling Algorithm

Wei Liu, Liangliang Sun, Jinliang Ding, Tianyou Chai
2011 IFAC Proceedings Volumes  
The priorities of the ladle optimization matching are established based on the rules from the experience of the experts, and then proposed a forward heuristic algorithm to solve the crane scheduling problem  ...  crane interference caused between them as well as many restrictions for each device in the production plant.  ...  ACKNOWLEDGEMENT This work was supported by the CNFR Program (2009CB320601),the NSF of China (61020106003, 60821063 and 60904079) and the 111 project (B08015).  ... 
doi:10.3182/20110828-6-it-1002.02306 fatcat:pbnrhrgyfvgd3ief3ruopgz7wi

Page 617 of The Journal of the Operational Research Society Vol. 54, Issue 6 [page]

2003 The Journal of the Operational Research Society  
So there will be, on average, the same number of solutions forward than backward. Finally, the precedence activity list is constructed, based on the mode assignment.  ...  a random device.  ... 

IJIMAI Editor's Note - Vol. 2 Issue 6

Enrique Herrera-Viedma
2014 International Journal of Interactive Multimedia and Artificial Intelligence  
They introduce a framework for combining genetic algorithms with rule-based models. This framework was used for recognizing the position of Ezafe constructions in Persian written texts.  ...  At the first stage, the rule-based model was applied to tag some tokens of an input sentence.  ... 
doi:10.9781/ijimai.2014.260 fatcat:ik3lehj77nf5xhrkkvbwal7qou

Genetic design automation: engineering fantasy or scientific renewal?

Matthew W. Lux, Brian W. Bramlett, David A. Ball, Jean Peccoud
2012 Trends in Biotechnology  
We argue that the real value of efforts to develop CAD tools is the formalization of genetic design rules that determine the complex relationships between genotype and phenotype.  ...  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  ...  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

SMT-Based Analysis of Biological Computation [chapter]

Boyan Yordanov, Christoph M. Wintersteiger, Youssef Hamadi, Hillel Kugler
2013 Lecture Notes in Computer Science  
Synthetic biology focuses on the re-engineering of living organisms for useful purposes while DNA computing targets the construction of therapeutics and computational circuits directly from DNA strands  ...  It provides a step towards the use of such methods in computational design frameworks for biology and is part of a more general effort towards the formalization of biology and the study of biological computation  ...  For the corrected transducers, we show that the additional constraints from Sec. 3.2 allow us to rule out the possibility of "bad" states, even for systems with many copies of the circuit (Fig. 3-right  ... 
doi:10.1007/978-3-642-38088-4_6 fatcat:pwi5a6vgajft5grcrsf4r6a5gm

Artificial life needs a real epistemology [chapter]

H. H. Pattee
1995 Lecture Notes in Computer Science  
Selective evolution began with a description-construction cut, i.e., the genetically coded synthesis of proteins.  ...  Foundational controversies in artificial life and artificial intelligence arise from lack of decidable criteria for defining the epistemic cuts that separate knowledge of reality from reality itself, e.g  ...  Measuring devices are designed and constructed based on theory.  ... 
doi:10.1007/3-540-59496-5_286 fatcat:ifrw5rpvc5hupjmytblc7c2gnu

Optimization for Disassemble Sequence Planning of Electromechanical Products during Recycling Process Based on Genetic Algorithms

Zhang Chunming
2016 International Journal of Multimedia and Ubiquitous Engineering  
The disassemble sequence optimization based on genetic algorithms has been carried out.  ...  Sequence planning is the core issue of disassemble. In this study, disassemble model has been established based on the analysis of disassemble route planning and disassemble sequence.  ...  Optimization for Disassemble Sequence Planning Based on Genetic Algorithms In this paper, the genetic operation after the process of considering the feasibility of crossover and mutation disassemble geometric  ... 
doi:10.14257/ijmue.2016.11.4.11 fatcat:hnpz7haizvdsjkubrvj7jagekm
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