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24th international conference on Architectural Support for programming Languages and Operating Systems (ASPLOS)

作者： Willsey, Max Stephenson, Ashley P. Takahashi, Chris Vaid, Pranav Nguyen, Bichlien H. Piszczek, Michal Betts, Christine Newman, Sharon Joshi, Sarang Strauss, Karin Ceze, Luis Univ Washington Seattle WA 98195 USA Microsoft Redmond WA USA Stanford Univ Stanford CA 94305 USA

ISBN: (纸本)9781450362405

Microfluidic devices promise to automate wetlab procedures by manipulating small chemical or biological samples. this technology comes in many varieties, all of which aim to save time, labor, and supplies by performing lab protocol steps typically done by a technician. However, existing microfluidic platforms remain some combination of inflexible, error-prone, prohibitively expensive, and difficult to program. We address these concerns with a full-stack digital microfluidic automation platform. Our main contribution is a runtime system that provides a high-level API for microfluidic manipulations. It manages fluidic resources dynamically, allowing programmers to freely mix regular computation with microfluidics, which results in more expressive programs than previous work. It also provides real-time error correction through a computer vision system, allowing robust execution on cheaper microfluidic hardware. We implement our stack on top of a low-cost droplet microfluidic device that we have developed. We evaluate our system with the fully-automated execution of polymerase chain reaction (PCR) and a dna sequencing preparation protocol. these protocols demonstrate high-level programs that combine computational and fluidic operations such as input/output of reagents, heating of samples, and data analysis. We also evaluate the impact of automatic error correction on our system's reliability.

关键词： runtime systems digital microfluidics molecular computing microfluidics

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Abstract modelling of tethered dna circuits

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20th international conference on dna computing and molecular programming, dna 2014

作者： Lakin, Matthew R. Petersen, Rasmus Gray, Kathryn E. Phillips, Andrew Department of Computer Science University of New Mexico AlbuquerqueNM United States Microsoft Research Cambridge United Kingdom Computer Laboratory University of Cambridge Cambridge United Kingdom

ISBN: (纸本)9783319112947

Sequence-specific dna interactions are a powerful means of programming nanoscale locomotion. these systems typically use a dna track that is tethered to a surface, and molecular interactions enable a signal or cargo to traverse this track. Such low copy number systems are highly amenable to mechanized analyses such as probabilistic model checking, which requires a formal encoding. In this paper we present the first general encoding of tethered dna species into a formal language, which allows the interactions between tethered species to be derived automatically using standard reaction rules. We apply this encoding to a previously published tethered dna circuit architecture based on hairpin assembly reactions. this work enables automated analysis of large-scale tethered dna circuits and, potentially, synthesis of optimized track layouts to implement specific logic functions. © Springer international Publishing Switzerland 2014.

关键词： Encoding (symbols)

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An Inverse QSAR Method Based on Decision Tree and Integer programming 17th

An Inverse QSAR Method Based on Decision Tree and Integer Pr...

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17th international conference on Intelligent computing, ICIC 2021

作者： Tanaka, Kouki Zhu, Jianshen Azam, Naveed Ahmed Haraguchi, Kazuya Zhao, Liang Nagamochi, Hiroshi Akutsu, Tatsuya Department of Applied Mathematics and Physics Kyoto University Kyoto606-8501 Japan Kyoto University Kyoto606-8306 Japan Bioinformatics Center Institute for Chemical Research Kyoto University Uji611-0011 Japan

ISBN: (纸本)9783030845285

Recently a novel framework has been proposed for designing the molecular structure of chemical compounds using both artificial neural networks (ANNs) and mixed integer linear programming (MILP). In the framework, we first define a feature vector f(C ) of a chemical graph C and construct an ANN that maps x = f(C ) to a predicted value η(x) of a chemical property π to C. After this, we formulate an MILP that simulates the computation process of f(C ) from C and that of η(x) from x. Given a target value y∗ of the chemical property π, we infer a chemical graph C † such that η(f(C †)) = y∗ by solving the MILP. In this paper, in pursuit of alternative learning models, we design an original decision tree that is based on a set of separating hyperplanes in the feature space which is then used to construct a prediction function η instead of ANNs. For this, we derive an MILP formulation that simulates the computation process of the proposed decision tree. the results of computational experiments suggest our method can infer chemical graphs with around up to 50 non-hydrogen atoms and that the prediction function based on a decision tree outperforms that with ANNs for several chemical properties. © 2021, Springer Nature Switzerland AG.

关键词： Decision trees

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the topology of scaffold routings on non-spherical mesh wireframes 26

The topology of scaffold routings on non-spherical mesh wire...

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26th international conference on dna computing and molecular programming, dna 2020

作者： Mohammed, Abdulmelik Jonoska, Nataa Saito, Masahico Department of Mathematics and Statistics University of South Florida TampaFL United States

ISBN: (纸本)9783959771634

the routing of a dna-origami scaffold strand is often modelled as an Eulerian circuit of an Eulerian graph in combinatorial models of dna origami design. the knot type of the scaffold strand dictates the feasibility of an Eulerian circuit to be used as the scaffold route in the design. Motivated by the topology of scaffold routings in 3D dna origami, we investigate the knottedness of Eulerian circuits on surface-embedded graphs. We show that certain graph embeddings, checkerboard colorable, always admit unknotted Eulerian circuits. On the other hand, we prove that if a graph admits an embedding in a torus that is not checkerboard colorable, then it can be re-embedded so that all its non-intersecting Eulerian circuits are knotted. For surfaces of genus greater than one, we present an infinite family of checkerboard-colorable graph embeddings where there exist knotted Eulerian circuits. © Abdulmelik Mohammed, Nataa Jonoska, and Masahico Saito;licensed under Creative Commons License CC-BY.

关键词： dna

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dna computing and molecular programming: Preface

Lecture Notes in Computer Science (including subseries Lectu...

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Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 2009年 5877 LNCS卷

作者： Deaton, Russell Suyama, Akira Dept. of Computer Science and Computer Engineering JBHT - CSCE 504 1 University of Arkansas Fayetteville AR 72701 United States Department of Life Science Graduate School of Arts and Sciences University of Tokyo 3-8-1 Komaba Meguro-ku Tokyo 153-8902 Japan

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Synthesizing minimal tile sets for complex patterns in the framework of patterned dna self-assembly

Synthesizing minimal tile sets for complex patterns in the f...

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18th international conference on dna computing and molecular programming, dna 18

作者： Czeizler, Eugen Popa, Alexandru Department of Information and Computer Science School of Science Aalto University Aalto FI-00076 Finland Department of Communications and Networking School of Electrical Engineering Aalto University P.O. Box 15400 Aalto FI-00076 Finland

ISBN: (纸本)9783642322075

Ma and Lombardi (2009) introduce and study the Pattern self-Assembly Tile set Synthesis (PATS) problem. In particular they show that the optimization version of the PATS problem is NP-hard. However, their NP-hardness proof turns out to be incorrect. Our main result is to give a correct NP-hardness proof via a reduction from the 3SAT. By definition, the PATS problem assumes that the assembly of a pattern starts always from an "L"-shaped seed structure, fixing the borders of the pattern. In this context, we study the assembly complexity of various pattern families and we show how to construct families of patterns which require a non-constant number of tiles to be assembled. © 2012 Springer-Verlag.

关键词： Self assembly

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Implementation of short read alignment algorithm in OpenCL on Xeon Phi coprocessor

Implementation of short read alignment algorithm in OpenCL o...

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IEEE international Symposium on Cyberspace Safety and Security

作者： Xiquan Zhao Chuang Liu Guangming Tan High Performance Comput. Res. Center Inst. of Comput. Technol. Beijing China

ISBN: (纸本)9781479989386

Aligning sequencing reads to a reference genome is often essential in many comparative genomics pipelines. With the maturation of next-generation dna sequencing (NGS) technologies, an enormous amount of sequence data has been generated, this calls for the development of faster read alignment programs. In this paper we present an OpenCL implementation of the short read aligner BarraCUDA [1], which is based on BWA software package [2] and utilises NVIDIAs GPGPU implementation, namely Compute Unified Device Architecture (CUDA) to parallelise the alignment of sequence reads. We re-implemented BarraCUDA aligner in OpenCL and test it on Intel's MIC architecture device - Xeon Phi 5110P coprocessor. Experiment results show that our OpenCL aligner performs better than its CPU-based software counterpart, with a 4 times performance boost compared to 8-thread BWA.

关键词： dna bioinformatics coprocessors genomics molecular biophysics parallel architectures pipeline processing BWA software package Intel MIC architecture device NVIDIA GPGPU implementation OpenCL aligner OpenCL implementation Xeon Phi 5110P coprocessor compute unified device architecture genomic pipelines next-generation dna sequencing technologies read alignment programs reference genome sequence data generation sequencing reads short read aligner BarraCUDA short read alignment algorithm Bioinformatics Coprocessors Genomics Graphics processing units Kernel Message systems Microwave integrated circuits OpenCL Xeon Phi heterogeneous computing short read alignment

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Robustness of dna Strand Displacement Systems

Robustness of DNA Strand Displacement Systems

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5th IFAC conference on Analysis and Control of Chaotic Systems (CHAOS)

作者： Nakakuki, Takashi Imura, Jun-ichi Kawamata, Ibuki Murata, Satoshi Kyushu Inst Technol Sch Comp Sci & Syst Engn Dept Syst Design & Informat 680-4 Kawazu Iizuka Fukuoka 8208502 Japan Tokyo Inst Technol Dept Mech & Environm Informat Meguro Ku 2-12-1-W8 O Okayama Tokyo 1528552 Japan Tohoku Univ Grad Sch Engn Dept Robot Aoba Ward 6-6-1 Aoba Sendai Miyagi 9808579 Japan

How to construct a reliable deoxyribonucleic acid (dna) circuit is one of the most important issues in the field of molecular programming and computing. Such a circuit frequently suffers from various kinds of unintended binding reactions on account of a lower specificity of the molecular interaction emerging from base complementarity between dna strands, which results in low reliability of the molecular circuit. In this study, we propose a method to quantitatively evaluate the robustness of a dna circuit created by dna strand displacement reactions. the highlight of our method is representing the circuit system contaminated by unintended reactions by a standard form of a disturbed nonlinear system and evaluating the robustness with the L-2 gain by solving the Hamilton-Jacobi inequality. (C) 2018, IFAC (international Federation of Automatic Control) Hosting by Elsevier Ltd. All rights reserved.

关键词： Complex systems Nonlinear circuits Uncertainty Differential equations Robustness

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scadnano: A browser-based, scriptable tool for designing dna nanostructures 26

scadnano: A browser-based, scriptable tool for designing DNA...

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26th international conference on dna computing and molecular programming, dna 2020

作者： Doty, David Lee, Benjamin L. Stérin, Tristan University of California DavisCA United States Maynooth University Ireland

ISBN: (纸本)9783959771634

We introduce scadnano (short for "scriptable cadnano"), a computational tool for designing synthetic dna structures. Its design is based heavily on cadnano [24], the most widely-used software for designing dna origami [33], with three main differences: 1. scadnano runs entirely in the browser, with no software installation required. 2. scadnano designs, while they can be edited manually, can also be created and edited by a well-documented Python scripting library, to help automate tedious tasks. 3. the scadnano file format is easily human-readable. this goal is closely aligned with the scripting library, intended to be helpful when debugging scripts or interfacing with other software. the format is also somewhat more expressive than that of cadnano, able to describe a broader range of dna structures than just dna origami. © David Doty, Benjamin L Lee, and Tristan Stérin;licensed under Creative Commons License CC-BY.

关键词： dna

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CRN++: molecular programming language 1

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24th international conference on dna computing and molecular programming, dna 2018

作者： Vasic, Marko Soloveichik, David Khurshid, Sarfraz The University of Texas at Austin Austin United States

ISBN: (数字)9783030000301

ISBN: (纸本)9783030000295

Synthetic biology is a rapidly emerging research area, with expected wide-ranging impact in biology, nanofabrication, and medicine. A key technical challenge lies in embedding computation in molecular contexts where electronic micro-controllers cannot be inserted. this necessitates effective representation of computation using molecular components. While previous work established the Turing-completeness of chemical reactions, defining representations that are faithful, efficient, and practical remains challenging. this paper introduces, CRN++ a new language for programming deterministic (mass-action) chemical kinetics to perform computation. We present its syntax and semantics, and build a compiler CRN++ translating programs into chemical reactions, thereby laying the foundation of a comprehensive framework for molecular programming. Our language addresses the key challenge of embedding familiar imperative constructs into a set of chemical reactions happening simultaneously and manipulating real-valued concentrations. Although some deviation from ideal output value cannot be avoided, we develop methods to minimize the error, and implement error analysis tools. We demonstrate the feasibility of using CRN++ on a suite of well-known algorithms for discrete and real-valued computation. CRN++ can be easily extended to support new commands or chemical reaction implementations, and thus provides a foundation for developing more robust and practical molecular programs. © Springer Nature Switzerland AG 2018.

关键词： Embeddings

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