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6th IEEE international conference on Smart computing (SMARTCOMP)

作者： Tricomi, Giuseppe Giosa, Domenico Merlino, Giovanni Romeo, Orazio Longo, Francesco Univ Messina Dipartimento Ingn Messina Italy Univ Messina Dipartimento Med Clin & Sperimentale Messina Italy Univ Messina Dipartimento Sci Chim Biol Farmaceut & Ambientali Messina Italy

ISBN: (数字)9781728169972

ISBN: (纸本)9781728169972

Nowadays, the study of nucleic acids (dna/RNA) has become a digital science thanks to the advent of modern massive parallel sequencing technologies, better known with the acronym NGS standing for next-generation sequencing, and to the availability of a vast amount of genetic data easily accessible from publicly available databases. Due to the quantity and complexity of such data, its processing requires strong computer science knowledge and skills. this background includes topics such as programming and scripting languages, command-line interfaces, low-level data management tools, which are not always part of the toolbox of molecular biologists and geneticists. the need to adapt to entirely new IT tools and workflows slow down even the more experienced researchers, thus dedicated and customizable GUIs would be much more preferable and conducive. In this paper, we tackle this issue by proposing a preliminary architecture for a framework providing the following benefits: i) it supports the post-NGS analysis process definition phase (commonly called pipeline definition) via a graphical dashboard designed with NodeRED;ii) it automatically deploys the workflows on top of a cluster of computational resources, according to the Function-as-a-Service paradigm, i.e., treating each step of the pipeline as a function to be executed within Linux-based containers, pre-configured with all the necessary dependencies;iii) it runs such containers taking care automatically of resource load balancing. Finally, the framework is thought to include human feedback in the loop, thanks to the availability of a smart notification system, allowing the researcher to monitor the workflows and make any decision needed for its continuation.

关键词： FaaS Serverless dna sequence alignment string matching Next Generation Sequencing NodeRED flow editor

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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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ALCH: An imperative language for chemical reaction network-controlled tile assembly 26

ALCH: An imperative language for chemical reaction network-c...

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

作者： Klinge, Titus H. Lathrop, James I. Moreno, Sonia Potter, Hugh D. Raman, Narun K. Riley, Matthew R. Department of Mathematics and Computer Science Drake University Des MoinesIA United States Department of Computer Science Iowa State University AmesIA United States Department of Computer Science Carleton College NorthfieldMN United States

ISBN: (纸本)9783959771634

In 2015 Schiefer and Winfree introduced the chemical reaction network-controlled tile assembly model (CRN-TAM), a variant of the abstract tile assembly model (aTAM), where tile reactions are mediated via non-local chemical signals. In this paper, we introduce ALCH, an imperative programming language for specifying CRN-TAM programs. ALCH contains common features like Boolean variables, conditionals, and loops. It also supports CRN-TAM-specific features such as adding and removing tiles. A unique feature of the language is the branch statement, a nondeterministic control structure that allows us to query the current state of tile assemblies. We also developed a compiler that translates ALCH to the CRN-TAM, and a simulator that simulates and visualizes the self-assembly of a CRN-TAM program. Using this language, we show that the discrete Sierpinski triangle can be strictly self-assembled in the CRN-TAM. this solves an open problem that the CRN-TAM is capable of self-assembling infinite shapes at scale one that the aTAM cannot. ALCH allows us to present this construction at a high level, abstracting species and reactions into C-like code that is simpler to understand. Our construction utilizes two new CRN-TAM techniques that allow us to tackle this open problem. First, it employs the branching feature of ALCH to probe the previously placed tiles of the assembly and detect the presence and absence of tiles. Second, it uses scaffolding tiles to precisely control tile placement by occluding any undesired binding sites. © Titus H. Klinge, James I. Lathrop, Sonia Moreno, Hugh D. Potter, Narun K. Raman, and Matthew R. Riley

关键词： C (programming language)

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23rd international conference on dna computing and molecular programming, dna 2017

23rd International Conference on DNA Computing and Molecular...

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23rd international conference on dna computing and molecular programming, dna 2017

ISBN: (纸本)9783319667980

the proceedings contain 16 papers. the special focus in this conference is on dna computing and molecular programming. the topics include: Automated, constraint-based analysis of tethered dna nanostructures;dna-templated synthesis optimization;ruleset optimization on isomorphic oritatami systems;unknotted strand routings of triangulated meshes;the design space of strand displacement cascades with toehold-size clamps;a stochastic molecular scheme for an artificial cell to infer its environment from partial observations;complexities for high-temperature two-handed tile self-assembly;a dna neural network constructed from molecular variable gain amplifiers;a stochastic approach to shortcut bridging in programmable matter;a minimal requirement for self-assembly of lines in polylogarithmic time;robust detection in leak-prone population protocols;inferring parameters for an elementary step model of dna structure kinetics with locally context-dependent arrhenius rates;simplifying analyses of chemical reaction networks for approximate majority;chemical boltzmann machines;a general-purpose CRN-to-DSD compiler with formal verification, optimization, and simulation capabilities and thermodynamic binding networks.

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An improved molecular computation model of integer power using self-assembly of dna tiles 20

An improved molecular computation model of integer power usi...

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20th IEEE international conference on High Performance computing and Communications (HPCC) / 16th IEEE international conference on Smart City (SmartCity) / 4th IEEE international conference on Data Science and Systems (DSS)

作者： Li, Yongnan Peoples Publ Secur Univ China Sch Criminal Invest & Counter Terrorism Beijing 100038 Peoples R China

ISBN: (纸本)9781538666142

this paper proposes how to use self-assembly of dna tiles to calculate integer power over finite field GF(2n) with less assembly processing time. Two key functional components accomplish the computing process. One of them computes modular-multiplication and modularsquare in parallel, and the other one calculates modularsquare and transmits intermediate result. It achieves better performance than previous work for its optimized assembly rules. this tile assembly model requires 5316 types of computation tiles and 12 types of boundary tiles.

关键词： Binary finite field Tile assembly model dna computing Integer power

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SIMD||dna: Single Instruction, Multiple Data Computation with dna Strand Displacement Cascades 1

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25th international conference on dna computing and molecular programming, dna 2019

作者： Wang, Boya Chalk, Cameron Soloveichik, David The University of Texas at Austin Austin United States

ISBN: (数字)9783030268077

ISBN: (纸本)9783030268060

Typical dna storage schemes do not allow in-memory computation, and instead transformation of the stored data requires dna sequencing, electronic computation of the transformation, followed by synthesizing new dna. In contrast we propose a model of in-memory computation that avoids the time consuming and expensive sequencing and synthesis steps, with computation carried out by dna strand displacement. We demonstrate the flexibility of our approach by developing schemes for massively parallel binary counting and elementary cellular automaton Rule 110 computation. © 2019, Springer Nature Switzerland AG.

关键词： dna

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Puddle: A Dynamic, Error-Correcting, Full-Stack Microfluidics Platform 19

Puddle: A Dynamic, Error-Correcting, Full-Stack Microfluidic...

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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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Preface

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Leibniz international Proceedings in Informatics, LIPIcs 2021年 205卷

作者： Lakin, Matthew R. Sulc, Petr Department of Computer Science Department of Chemical and Biological Engineering Center for Biomedical Engineering University of New Mexico AlbuquerqueNM United States School of Molecular Sciences Arizona State University TempeAZ United States

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Enriched dna strands classification using CGR images and convolutional neural network 8

Enriched DNA strands classification using CGR images and con...

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8th international conference on Bioinformatics and Biomedical Science, ICBBS 2019

作者： Safoury, Sarah Hussein, Walid Software Engineering Department Faculty of Informatics and Computer Science British University in Egypt Egypt Computer Science Department Faculty of Informatics and Computer Science British University in Egypt Egypt

ISBN: (纸本)9781450372510

Bioinformatics is the biological study which applies programming techniques for more understanding and analysis of living objects such as the study of genome structure. the genome structure could be represented in the form of an image. Chaos Game Representation (CGR) is the practice of converting the dna sequence (i.e., genomes) into images, where each image is a graphical appearance for an individual dna strand's signature. CGR is a method of converting a long one-dimensional dna sequence into a graphical form. this method provides a visual image of a dna sequence different from the traditional manual linear arrangement of nucleotides polymerase chain reaction. In the recent years, CGR was introduced to automatically classify genomes not only by archival references but also through its' unique signature. In this paper, a novel CGR classification approach is developed combining the advances of image processing and pattern recognition approaches. the approach starts by declaring the genome and using the CGR technique to map it to the graphical interface (i.e., 16x16 signature images). then, an image processing procedure is prepared to handle complex geometric shapes, analyze structured and visualized genome sequences and fractal point the included nucleotides of these images. Finally, the convolutional neural network was designed and well-Trained by those signatures to classify each genome tested. © 2019 Association for computing Machinery.

关键词： Genome

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Automated analysis of tethered dna nanostructures using constraint solving

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NATURAL computing 2018年第4期17卷 709-722页

作者： Lakin, Matthew R. Phillips, Andrew Univ New Mexico Dept Comp Sci Ctr Biomed Engn Albuquerque NM 87131 USA Microsoft Res 21 Stn Rd Cambridge CB1 2FB England

Implementing dna computing circuits using components tethered to a surface offers several advantages over using components that freely diffuse in bulk solution. However, automated computational modeling of tethered circuits is far more challenging than for solution-phase circuits, because molecular geometry must be taken into account when deciding whether two tethered species may interact. Here, we tackle this issue by translating a tethered molecular circuit into a constraint problem that encodes the possible physical configurations of the components, using a simple biophysical model. We use a satisfaction modulo theories solver to determine whether the constraint problem associated with a given structure is satisfiable, which corresponds to whether that structure is physically realizable given the constraints imposed by the tether geometry. We apply this technique to example structures from the literature, and discuss how this approach could be integrated with a reaction enumerator to enable fully automated analysis of tethered molecular computing systems. this paper is a significantly revised and extended version of a conference publication: Lakin and Phillips (in Brijder and Qian (eds) Proceedings of the 23rd international conference on dna computing and molecular programming. Lecture Notes in Computer Science, vol 10467, pp 1-16, 2017).

关键词： molecular computing Tethered dna nanostructures molecular geometry dna strand displacement

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