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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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Separating repeats in dna sequence assembly 01

Separating repeats in DNA sequence assembly

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5th Annual Internatinal conference on Computational Biology

作者： Kececioglu, J. Yu, J. Department of Computer Science University of Arizona Tucson AZ 85721-0077 United States

ISBN: (纸本)9781581133530

One of the key open problems in large-scale dna sequence assembly is the correct reconstruction of sequences that contain repeats. A long repeat can confound a sequence assembler into falsely overlaying fragments that sample its copies, effectively compressing out the repeat in the reconstructed sequence. We call the task of correcting this compression by separating the overlaid fragments into the distinct copies they sample, the repeat separation problem. We present a rigorous formulation of repeat separation in the general setting without prior knowledge of consensus sequences of repeats or their number of copies. Our formulation decomposes the task into a series of four subproblems, and we design probabilistic tests or combinatorial algorithms that solve each subproblem. the core subproblem separates repeats using the so-called k-median problem in combinatorial optimization, which we solve using integer linear-programming. Experiments with an implementation show we can separate fragments that are over laid at 10 times the coverage with very few mistakes in a few seconds of computation, even when the sequencing error rate and the error rate between copies are identical. To our knowledge this is the first rigorous and fully general approach to separating repeats that directly addresses the problem.

关键词： dna sequences

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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

12th International Conference on Practical Applications of C...

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12th international conference on Practical Applications of Computational Biology and Bioinformatics, PACBB 2018

ISBN: (纸本)9783319987019

the proceedings contain 26 papers. the special focus in this conference is on Practical Applications of Computational Biology and Bioinformatics. the topics include: A bioinformatics protocol for quickly creating large-scale phylogenetic trees;Deep learning analysis of binding behavior of virus displayed peptides to AuNPs;compression of amino acid sequences;NET-ASAR: A tool for dna sequence search based on data compression;Can an integrative SNP approach substitute standard identification in comprehensive case/control analyses?;simple pattern-only heuristics lead to fast subgraph matching strategies on very large networks;in silico predictions for fucoxanthin production by the diatom phaeodactylum tricornutum;EvoPPI: A web application to compare protein-protein interactions (PPIs) from different databases and species;a review on metabolomics data analysis for cancer applications;parameter estimation of essential amino acids in Arabidopsis thaliana using hybrid of bees algorithm and harmony search;a framework for the automatic combination and evaluation of gene selection methods;parallel cellular automaton tumor growth model;MOSCA: An automated pipeline for integrated metagenomics and metatranscriptomics data analysis;metabolite integration pipeline for the improvement of human metabolic models;a genetic programming approach applied to feature selection from medical data;A dna sequence corpus for compression benchmark;17α-ethinylestradiol analysis of endo- and exometabolome of ulva lactuca (chlorophyta) by 1H-NMR spectroscopy and bioinformatics tools;in silico modeling and simulation approach for apoptosis caspase pathways;molecular dynamic simulations suggest that P152R mutation within MeCP2 can lead to higher dna binding affinity and loss of selective binding to methylated dna.

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Solving computational learning problems of boolean formulae on dna computers 1

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6th international Workshop on dna-Based Computers, dna 2000

作者： Sakakibara, Yasubumi Department of Information Sciences Tokyo Denki University Hiki-gunSaitama350-0394 Japan

ISBN: (数字)9783540449928

ISBN: (纸本)3540420762

We apply a dna-based massively parallel exhaustive search to solving the computational learning problems of DNF (disjunctive normal form) Boolean formulae. Learning DNF formulae from examples is one of the most important open problems in computational learning theory and the problem of learning 3-term DNF formulae is known as intractable if RP 6 ≠ NP. We propose new methods to encode any k-term DNF formula to a dna strand, evaluate the encoded DNF formula for a truth-value assignment by using hybridization and PCR, and find a consistent DNF formula with the given examples. By employing these methods, we show that the class of k-term DNF formulae (for any constant k) and the class of general DNF formulae are eficiently learnable on dna computer. © Springer-Verlag Berlin Heidelberg 2001.

关键词： dna

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dna self-assembly and computation studied with a coarse-grained dynamic bonded model

DNA self-assembly and computation studied with a coarse-grai...

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

作者： Svaneborg, Carsten Fellermann, Harold Rasmussen, Steen Center for Fundamental Living Technology Department of Physics Chemistry and Pharmacy University of Southern Denmark Campusvej 55 Odense DK-5320 Denmark Complex Systems Lab. Barcelona Biomedical Research Park Universitat Pompeu Fabra Dr. Aiguadé 88 08003 Barcelona Spain Santa Fe Institute 1399 Hyde Park Road Santa Fe NM 87501 United States

ISBN: (纸本)9783642322075

We study dna self-assembly and dna computation using a coarse-grained dna model within the directional dynamic bonding framework [C. Svaneborg, Comp. Phys. Comm. 183, 1793 (2012)]. In our model, a single nucleotide or domain is represented by a single interaction site. Complementary sites can reversibly hybridize and dehybridize during a simulation. this bond dynamics induces a dynamics of the angular and dihedral bonds, that model the collective effects of chemical structure on the hybridization dynamics. We use the dna model to perform simulations of the self-assembly kinetics of dna tetrahedra, an icosahedron, as well as strand displacement operations used in dna computation. © 2012 Springer-Verlag.

关键词： Dynamics

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A circuit simplification mechanism based on dna combinatorial strands displacement 12th

A circuit simplification mechanism based on DNA combinatoria...

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12th international conference on Bio-Inspired computing: theories and Applications, BIC-TA 2017

作者： Zhang, Xuncai Han, Feng Wang, Yanfeng College of Electrical and Electronic Engineering Zhengzhou University of Light Industry Zhengzhou450002 China

ISBN: (纸本)9789811071782

through extensive application of dna strand displacement technology in the field of molecular computing, we know that the dna strand of the toehold domain and the branch migration domain are covalently connected to form logical gates in traditional dna strand displacement circuits. In this paper, we will adopt a composite strand mechanism that the toehold domain and branch migration domain in different single strand form displacing complex, and construct logical gates with combinatorial strand displacement mechanism. After that, a logic gate model is constructed, and the mechanism is verified by the design and simulation of the logical molecular model of the encoder. When the dna signal strand is input, the signal strand molecule can be output by combination of molecular specific hybridization reaction and intermolecular strand displacement reaction. the results of Visual DSD simulation show the feasibility and accuracy of the encoder logic calculation model designed in this article. © Springer Nature Singapore Pte Ltd 2017.

关键词： Timing circuits

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Combined Amplification and molecular Classification for Gene Expression Diagnostics 1

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

作者： Gowri, Gokul Lopez, Randolph Seelig, Georg California Institute of Technology PasadenaCA United States University of Washington SeattleWA United States

ISBN: (数字)9783030268077

ISBN: (纸本)9783030268060

RNA expression profiles contain information about the state of a cell and specific gene expression changes are often associated with disease. Classification of blood or similar samples based on RNA expression can thus be a powerful method for disease diagnosis. However, basing diagnostic decisions on RNA expression remains impractical for most clinical applications because it requires costly and slow gene expression profiling based on microarrays or next generation sequencing followed by often complex in silico analysis. dna-based molecular classifiers that perform a computation over RNA inputs and summarize a diagnostic result in situ have been developed to address this issue, but lack the sensitivity required for use with actual biological samples. To address this limitation, we here propose a dna-based classification system that takes advantage of PCR-based amplification for increased sensitivity. In our initial scheme, the importance of a transcript for a diagnostic decision is proportional to the number of molecular probes bound to that transcript. Although probe concentration is similar to that of the RNA input, subsequent amplification of the probes with PCR can dramatically increase the sensitivity of the assay. However, even slight biases in PCR efficiency can distort weight information encoded by the original probe set. To address this concern, we developed and mathematically analyzed multiple strategies for mitigating the bias associated with PCR-based amplification. We evaluate these amplified molecular classification strategies through simulation using two distinct gene expression data sets and associated disease categories as inputs. through this analysis, we arrive at a novel molecular classifier framework that naturally accommodates PCR bias and also uses a smaller number of molecular probes than required in the initial, naive implementation. © 2019, Springer Nature Switzerland AG.

关键词： RNA

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Multiple sequence alignment a quick tour

Multiple sequence alignment a quick tour

引用

international conference on Advanced computing Technologies (ICACT)

作者： Radha Chintapalli Amit Kumar Laxminarayana Parayitam Research and Training Unit for Navigational Electronics Osmania University Hyderabad Andhra Pradesh India BIOAXIS DNA Research Center Hyderabad Andhra Pradesh India

Sequence alignment has a lot of significance in the field of bioinformatics. Since multiple sequence alignment (MSA) carries more information than pairwise alignment of the sequences, it has more number of applications. In the past few decades many algorithms and tools have been developed for the computation of multiple sequence alignment. However, accuracy of MSA still remains an open problem for further research. As more and more experimental data is being generated through sequencing technologies of second generation, there is an urgent need to develop tools that make use of integrative methods to derive biologically meaningful information from these immense data and use it to improve the accuracy of MSA. MSA tools that can scale upto the full length genome will also find wide applications in the near future.

关键词： Accuracy Hidden Markov models Probabilistic logic Heuristic algorithms Proteins Dynamic programming Matrices

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11th international conference on Parallel Processing and Applied Mathematics, PPAM 2015

11th International Conference on Parallel Processing and App...

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11th international conference on Parallel Processing and Applied Mathematics, PPAM 2015

ISBN: (纸本)9783319321516

the proceedings contain 56 papers. the special focus in this conference is on Models, Algorithms, Energy Aspects of Computation, Scheduling for Parallel computing and Language-Based Parallel programming Models. the topics include: Virtualizing CUDA enabled GPGPUS on arm clusters;a distributed hash table for shared memory;mathematical approach to the performance evaluation of matrix multiply algorithm;a scalable numerical algorithm for solving tikhonov regularization problems;energy performance modeling with TIA and EML;considerations of computational efficiency in volunteer and cluster computing;parallel programs scheduling with architecturally supported regions;adaptive multi-level workflow scheduling with uncertain task estimates;divisible loads scheduling in hierarchical memory systems with time and energy constraints;extending Gustafson-barsis’s law for dual-architecture computing;free scheduling of tiles based on the transitive closure of dependence graphs;multi-threaded construction of neighbour lists for particle systems in openMP;high productivity and high performance;parallel ant brood graph partitioning in Julia;scalability model based on the concept of granularity;performance and power-aware modeling of MPI applications for cluster computing;running time prediction for web search queries;performance analysis of a parallel, multi-node pipeline for dna sequencing;parallelising the computation of minimal absent words;modeling and simulations of edge-emitting broad-area semiconductor lasers and amplifiers;application of the parallel inmost platform to subsurface flow and transport modelling;genetic algorithm and exact diagonalization approach for molecular nanomagnets modelling and parallel Monte Carlo simulations for spin models with distributed lattice.

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