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1. 发明申请

US20110225109A1 Hardware acceleration of DNA codeword searching and fitness determination 审中-公开
标题翻译： DNA码字搜索和适应度确定的硬件加速
公开(公告)号：US20110225109A1
公开(公告)日：2011-09-15
申请号：US13068911
申请日：2011-05-19
申请人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
发明人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
IPC分类号： G06N3/12
CPC分类号： G06N3/126 , G16B30/00
摘要： An apparatus for a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA reverse complement, edit distance codes. Two embodiments are implemented and evaluated, including a code generator that uses a genetic algorithm (GA) to produce nearly locally optimal codes in a few minutes, and a code extender that uses exhaustive search to produce locally optimum codes in about 1.5 hours for the case of length 16 codes. Experimental results demonstrate that the GA embodiment can find ˜99% of the words in locally optimum libraries, and that the hybrid architecture embodiment provides more than 1000 times speed-up compared to a software only implementation.
摘要翻译：一种用于混合架构的装置，由通用微处理器和硬件加速器组成，用于加速DNA反向补码的发现，编辑距离代码。实现和评估两个实施例，包括使用遗传算法（GA）在几分钟内产生几乎局部最佳代码的代码生成器，以及使用穷举搜索以在大约1.5小时内产生局部最佳代码的代码扩展器的长度为16个码。实验结果表明，GA实施例可以在局部优化库中找到约99％的单词，并且混合体系结构实施例与仅软件实现相比提供了超过1000倍的加速。

2. 发明申请

US20110224916A1 Fitness determination for DNA codeword searching 审中-公开
标题翻译： DNA码字搜索的健身测定
公开(公告)号：US20110224916A1
公开(公告)日：2011-09-15
申请号：US13068910
申请日：2011-05-19
申请人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
发明人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
IPC分类号： G06F19/00
CPC分类号： G06N3/126 , G16B30/00
摘要： An apparatus for a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA reverse complement, edit distance codes. Two embodiments are implemented and evaluated, including a code generator that uses a genetic algorithm (GA) to produce nearly locally optimal codes in a few minutes, and a code extender that uses exhaustive search to produce locally optimum codes in about 1.5 hours for the case of length 16 codes. Experimental results demonstrate that the GA embodiment can find ˜99% of the words in locally optimum libraries, and that the hybrid architecture embodiment provides more than 1000 times speed-up compared to a software only implementation.
摘要翻译：一种用于混合架构的装置，由通用微处理器和硬件加速器组成，用于加速DNA反向补码的发现，编辑距离代码。实现和评估两个实施例，包括使用遗传算法（GA）在几分钟内产生几乎局部最佳代码的代码生成器，以及使用穷举搜索以在大约1.5小时内产生局部最佳代码的代码扩展器的长度为16个码。实验结果表明，GA实施例可以在局部优化库中找到约99％的单词，并且混合体系结构实施例与仅软件实现相比提供了超过1000倍的加速。

3. 发明申请

US20090325820A1 Hardware acceleration for thermodynamically constrained DNA code generation 审中-公开
标题翻译：用于热力学约束的DNA代码生成的硬件加速
公开(公告)号：US20090325820A1
公开(公告)日：2009-12-31
申请号：US12455564
申请日：2009-06-03
申请人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre , Morgan A. Bishop
发明人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre , Morgan A. Bishop
IPC分类号： C40B40/08 , C40B60/14
CPC分类号： G16B25/00 , G16B15/00
摘要： An apparatus that accelerates the determination of NN free energy of binding estimates for a large number of DNA oligomers using reconfigurable hardware and applies it to the design of high quality DNA code word libraries. The invention provides a reconfigurable hardware accelerator and method for implementing a nearest-neighbor based free energy calculation. The invention further provides a method to produce the maximum weight of the 2-stem common subsequence of two DNA oligonucleotides. In practice, the present invention comprises a general purpose microprocessor or computer, a hardware accelerator, and a software program.
摘要翻译：一种使用可重配置硬件加速大量DNA寡聚体的结合估计的NN自由能的测定的装置，并将其应用于设计高质量的DNA代码字库。本发明提供了一种用于实现基于最近邻的自由能计算的可重新配置的硬件加速器和方法。本发明还提供了产生两个DNA寡核苷酸的2-茎共同亚序列的最大重量的方法。实际上，本发明包括通用微处理器或计算机，硬件加速器和软件程序。

4. 发明申请

US20120296857A1 Hardware acceleration of DNA codeword searching and fitness determination employing a code extender 审中-公开
标题翻译：使用代码扩展器的DNA码字搜索和适应度确定的硬件加速
公开(公告)号：US20120296857A1
公开(公告)日：2012-11-22
申请号：US13385471
申请日：2012-01-25
申请人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
发明人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
IPC分类号： G06N3/12
CPC分类号： G06N3/126 , G16B30/00
摘要： An apparatus for a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA reverse complement edit distance codes. An embodiment is implemented and evaluated, including a code extender that uses exhaustive search to produce locally optimum codes in about 1.5 hours for the case of length 16 codes.
摘要翻译：一种用于混合架构的装置，其由通用微处理器和用于加速DNA反向补码编码距离码的发现的硬件加速器组成。一个实施例被实现和评估，包括一个代码扩展器，在长度为16个码的情况下，使用穷举搜索来产生大约1.5小时的局部最佳代码。

5. 发明申请

US20110225110A1 Software control of hardware accelerated DNA codeword searching 审中-公开
标题翻译：软件控制硬件加速DNA码字搜索
公开(公告)号：US20110225110A1
公开(公告)日：2011-09-15
申请号：US13068912
申请日：2011-05-19
申请人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
发明人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
IPC分类号： G06N3/12
CPC分类号： G06N3/126 , G16B30/00
摘要： An apparatus for a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA reverse complement, edit distance codes. Two embodiments are implemented and evaluated, including a code generator that uses a genetic algorithm (GA) to produce nearly locally optimal codes in a few minutes, and a code extender that uses exhaustive search to produce locally optimum codes in about 1.5 hours for the case of length 16 codes. Experimental results demonstrate that the GA embodiment can find ˜99% of the words in locally optimum libraries, and that the hybrid architecture embodiment provides more than 1000 times speed-up compared to a software only implementation.
摘要翻译：一种用于混合架构的装置，由通用微处理器和硬件加速器组成，用于加速DNA反向补码的发现，编辑距离代码。实现和评估两个实施例，包括使用遗传算法（GA）在几分钟内产生几乎局部最佳代码的代码生成器，以及使用穷举搜索以在大约1.5小时内产生局部最佳代码的代码扩展器的长度为16个码。实验结果表明，GA实施例可以在局部优化库中找到约99％的单词，并且混合体系结构实施例与仅软件实现相比提供了超过1000倍的加速。

6. 发明申请

US20090248598A1 Hardware acceleration of DNA codeword searching 审中-公开
标题翻译： DNA码字搜索的硬件加速
公开(公告)号：US20090248598A1
公开(公告)日：2009-10-01
申请号：US12378261
申请日：2009-02-12
申请人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
发明人： Daniel J. Burns , Qinru Qiu , Qing Wu , Prakash Mukre
IPC分类号： G06N3/12 , G06N3/08
CPC分类号： G06N3/126 , G16B30/00
摘要： An apparatus for a hybrid architecture that consists of a general purpose microprocessor and a hardware accelerator for accelerating the discovery of DNA reverse complement, edit distance codes. Two embodiments are implemented and evaluated, including a code generator that uses a genetic algorithm (GA) to produce nearly locally optimal codes in a few minutes, and a code extender that uses exhaustive search to produce locally optimum codes in about 1.5 hours for the case of length 16 codes. Experimental results demonstrate that the GA embodiment can find ˜99% of the words in locally optimum libraries, and that the hybrid architecture embodiment provides more than 1000 times speed-up compared to a software only implementation.
摘要翻译：一种用于混合架构的装置，由通用微处理器和硬件加速器组成，用于加速DNA反向补码的发现，编辑距离代码。实现和评估两个实施例，包括使用遗传算法（GA）在几分钟内产生几乎局部最佳代码的代码生成器，以及使用穷举搜索以在大约1.5小时内产生局部最佳代码的代码扩展器的长度为16个码。实验结果表明，GA实施例可以在局部最佳库中找到约99％的字，并且与仅软件实现相比，混合架构实施例提供了超过1000倍的加速。

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