Since the 1990s, increasingly complex nanostructures have been reliably obtained out of self-assembled dna strands: From "simple" 2D shapes to 3D gears and articulated nano-objects, and even computing struct...
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ISBN:
(纸本)9783959772051
Since the 1990s, increasingly complex nanostructures have been reliably obtained out of self-assembled dna strands: From "simple" 2D shapes to 3D gears and articulated nano-objects, and even computing structures. the success of the assembly of these structures relies on a fine tuning of their structure to match the peculiar geometry of dna helices. Various softwares have been developed to help the designer. these softwares provide essentially four kind of tools: An abstract representation of dna helices (e.g. cadnano, scadnano, dnapen, 3dna, Hex-tiles);a 3D view of the design (e.g., vHelix, Adenita, oxdnaviewer);fully automated design (e.g., BScOR, Daedalus, Perdix, Talos, Athena), generally dedicated to a specific kind of design, such as wireframe origami;and coarse grain or thermodynamical physics simulations (e.g., oxdna, Mrdna, SNUPI, Nupack, ViennaRNA,.). Magicdna combines some of these approaches to ease the design of configurable dna origamis. We present our first step in the direction of conciliating all these different approaches and purposes into one single reliable GUI solution: the first fully usable version (design from scratch to export) of our general purpose 3D dna nanostructure design software ENSnano. We believe that its intuitive, swift and yet powerful graphical interface, combining 2D and 3D editable views, allows fast and precise editing of dna nanostructures. It also handles editing of large 2D/3D structures smoothly, and imports from the most common solutions. Our software extends the concept of grids introduced in cadnano. Grids allow to abstract and articulated the different parts of a design. ENSnano also provides new design tools which speeds up considerably the design of complex large 3D structures, most notably: A 2D split view, which allows to edit intricate 3D structures which cannot easily be mapped in a 2D view, and a copy, paste & repeat functionality, which takes advantage of the grids to design swiftly large repetitive chunks of
In today's time, molecular Science is increasingly dependent on Software Engineering Calculations in the department of Research and Development. Aligning sequences of dna, RNA is becoming a major part of present-d...
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ISBN:
(纸本)9789811510847;9789811510830
In today's time, molecular Science is increasingly dependent on Software Engineering Calculations in the department of Research and Development. Aligning sequences of dna, RNA is becoming a major part of present-day natural sciences. A hereditary database holds a large amount of unprocessed data that resides very crucial information. A single pair of chromosomes contains approximately 3 billion dna base pairs. To look through this information, retrieve the connections, and subconnections in it is a very slow procedure. therefore, scientists are looking forward toward computer science algorithms for faster retrieval of information. this paper is focused upon using a parallel programming algorithm than the previous alignment algorithms.
As a new type of cryptography, dna cryptography generally uses dna molecule as the information carrier and biological technology as the implementation tool. Due to its prominent advantages such as large storage capaci...
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In molecularprogramming, the Chemical Reaction Network model is often used to describe real or hypothetical systems. Often, an interesting computational task can be done with a known hypothetical Chemical Reaction Ne...
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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 o...
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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 withthe acronym NGS standing for next-generation seque...
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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 withthe 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.
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 D...
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GPU has emerged as a platform that off-loads computation intensive work from CPU and performs numerical computations in less time. One such mathematical operation is matrix multiplication. Matrix is one of the fundame...
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ISBN:
(纸本)9789811501845;9789811501838
GPU has emerged as a platform that off-loads computation intensive work from CPU and performs numerical computations in less time. One such mathematical operation is matrix multiplication. Matrix is one of the fundamental mathematical objects used in the scientific calculation, with applicability in various fields such as computer graphics, analysis of electrical circuits, computer networks, dna sequence comparison, protein structure prediction, etc. this work presents a comparative analysis of scalar matrix multiplication in three modes, namely: (i) sequential programming in C language (ii) parallel implementations using OpenCL, and (iii) MPI. the testbed comprises of input matrices ranging from small size of 100 x 100 to a higher size of 12,800 x 12,800. We observe that parallel execution in OpenCL outperforms MPI and sequential C for higher dimensional matrices. In contrast, sequential C outperforms both MPI and OpenCL for small dimension matrices. Besides, we analyze that OpenCL program has attained a speedup of 9x. therefore, we conclude that parallel execution of code is more efficient for data of computationally large sizes and hence provides a potentially useful solution to address NP-complete problems.
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 che...
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Withthe rapid development of bidding market, a new type of bidding method-electronic bidding method has been widely used in the bidding market. this new-type of method is a program that the bidding is completed by gr...
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