跳到主要內容

臺灣博碩士論文加值系統

(35.175.191.36) 您好!臺灣時間:2021/07/30 19:24
字體大小: 字級放大   字級縮小   預設字形  
回查詢結果 :::

詳目顯示

我願授權國圖
: 
twitterline
研究生:張榆源
研究生(外文):Yu-Yuan Chang
論文名稱:生物資訊分子邏輯系統基礎架構:生物資訊資料庫
論文名稱(外文):Bioinformatics Logic Computing: Constructing Bio-molecular Databases
指導教授:何善輝
指導教授(外文):Shan-Hui Ho
學位類別:碩士
校院名稱:銘傳大學
系所名稱:資訊管理學系碩士班
學門:電算機學門
學類:電算機一般學類
論文種類:學術論文
論文出版年:2008
畢業學年度:96
語文別:英文
論文頁數:121
中文關鍵詞:生物分子關聯式計算關聯式資料庫生物分子關聯式資料庫關聯式計算
外文關鍵詞:Bio-molecular Relational DatabasesRelational Algebra (Calculus)Bio-molecular Relational Algebra (Calculus)Relational Databases
相關次數:
  • 被引用被引用:0
  • 點閱點閱:222
  • 評分評分:
  • 下載下載:0
  • 收藏至我的研究室書目清單書目收藏:0
近年來因為數位應用的興盛,找尋足夠的儲存空間存放膨脹的數位資料儼然成為一項重要的挑戰。Codd.是首位針對資料儲存方式提出關聯式資料庫概念的人,而Adleman也是首位將DNA計算應用於解決漢彌爾敦路徑問題的學者。透過DNA序列儲存資料的方式,可以將資料儲存的密集度提高至1.25 × 1026 Bytes/m3。
本研究將生物邏輯操作應用於關聯式資料庫上,來建構分子生物資訊資料庫。目的是以DNA序列的儲存方式來實踐關聯式資料庫的架構,並且解決目前大量資料儲存的問題。為了架構分子生物資訊資料庫,我們以分子生物和生物邏輯平行基礎架構演算法來完成關聯式資料庫的基本操作和函數。
It is one of great challenges to find enough storage to handle rapidly growing data in recent years. Codd proposed the first conception about the model of a relational database. Adleman wrote the first paper in which DNA strands in the test tube were used to solve an instance of the Hamiltonian path problem. It is obviously indicated that for storing information in molecules of DNA allows for an information density of approximately 1 bit per cubic nm (nanometer). This article demonstrates that bio-logical operations can be applied to construct bio-molecular databases where data records in the relational tables are encoded as DNA strands. In this research, DNA algorithms are proposed to perform eight operations of relational algebra (calculus) on bio-molecular relational databases and database functions.
List of Contents
Chinese Abstract i
Abstract ii
List of Contents iii
List of Table v
List of Algorithm vi
List of Figure viii
1. Introduction 1
1.1Background 1
1.2Motivation 2
2. Literature Review 4
2.1. The Structure of DNA 4
2.2. Adleman’s Experiment for Solving the Hamiltonian Path Problem 6
2.3 The Sticker Based Model 7
2.4 DNA Manipulations 8
2.5 Other research about DNA Model of Computation 9
3. Constructing Bio-Molecular Relational Databases and Basic Boolean Bio-circuit Operations with Bio-molecular Computing 12
3.1. The Introduction to a Relational View of Data 12
3.2. DNA Algorithms for the Cartesian Product on Bio-molecular Databases 13
3.3 DNA Algorithms for Set Operations on Bio-molecular Databases 16
3.3.1 A DNA Algorithm for Union Operator on Bio-molecular Databases 17
3.3.2. A DNA Algorithm for Intersection Operator on Bio-molecular Databases 19
3.3.3. A DNA Algorithm for Different Operator on Bio-molecular Databases 22
3.4 DNA Algorithms for Projection Operator on Bio-molecular Databases 25
3.5 DNA Algorithms for Selection Operator on Bio-molecular Databases 31
3.6 DNA Algorithms for Theta-Join Operator on Bio-molecular Databases 36
3.7 DNA Algorithms for Division Operator on Bio-molecular Databases 40
3.8 The Power of DNA Algorithms on Bio-molecular Databases 42
3.9 Basic Boolean Bio-circuit Operations with Bio-molecular Computing 44
3.9.1 NOT Operation on Bio-molecular Computing 44
3.9.2 AND Operation on Bio-molecular Computing 47
3.9.3 Construction of a Parallel OR 51
3.9.4 Construction of a Parallel NOR 55
3.9.5 Construction of a Parallel NAND 58
3.9.6 Construction of a Parallel XOR 62
3.9.7 Construction of a Parallel XNOR 66
4. DNA Algorithms Based on the DNA Model for 70
4.1.Construction of Parallel Adder 70
4.1.1 Construction of the Parallel One-bit Adder 70
4.1.2 Construction of a N-bits Parallel Adder 72
4.2 Construction of Parallel Multiplier 73
4.2.1 Construction of One-bit Parallel Multiplier 73
4.2.2 Construction of a N-bit Parallel Multiplier 75
4.3 Construction of Parallel Subtractor 78
4.3.1 Construction of One-bit Parallel Subtractor 78
4.3.2 Construction of a Parallel N-bit Subtractor 80
4.4 Construction of a Parallel Divider 83
4.4.1 Construction of a N-bit Parallel Divider 83
4.5 Construction of Parallel Comparator 87
4.5.1 Construction of the Parallel One-bit Comparator 88
4.5.2 Construction of a N-bit Parallel Comparator 92
4.6 Construction of Parallel Modular 93
4.6.1 The Construction of the Parallel One-bit Modular 94
5.1 Bio-logical Algorithm for the Average Function on Bio-molecular 100
5.2 Bio-logical Algorithm for the Summation Function on Bio-molecular Databases 101
5.3 Bio-logical algorithm for the Maximum function on Bio-molecular 103
5.4 Bio-logical algorithm for the Minimum function on Bio-molecular 104
5.5 Bio-logical Algorithm for the Variance Function on Bio-molecular Databases 106
6. Conclusions 108
Adleman, L. (1994). "Molecular computation of solutions to combinatorial problems." Science 266(Nov): 1021-1024.
Adleman, L., P. W. K. Rothemund, et al. (1999). On applying molecular computation to the Data Encryption Standard. The 2nd annual workshop on DNA Computing, Princeton University, American Mathematical Society.
Adleman, L. M. (1996). "On Constructing a Molecular Computer." DNA Based Computers, Eds. R. Lipton and E. Baum, DIMACS: series in Discrete Mathematics and Theoretical Computer Science, American Mathematical Society: 1-21.
Amos, M. (1997). DNA Computation. computer science, Warwick. Ph.D.
Amos, M. and P. E. Dunne (1997). DNA Simulation of Boolean Circuits. Technical Report CTAG-97009, University of Liverpool.
Arita, M., A. Suyama, et al. (1997). A heuristic approach for the Hamiltonian path problem with molecules. 2nd Genetic Programming Conf.
Atanasiu, A. (2000). Arithmetic with Membrames. Workshop on Mutiset Processing.
Bach, E., A.Condon, et al. (1996). DNA Models and Algorithms for NP-complete Problems. the 11th Annual Conference on Structure in Complexity Theory.
Barua, R. and J. Misra (2002). Binary arithmetic for DNA computers. 8th Int. Workshop DNA Based Computers.
Boneh, D., C. Dunworth, et al. (1996). Breaking DES using a molecular computer. 1st DIMACS Workshop on DNA Based Computers, American Mathematical Society.
Boneh, D., C. Dunworth, et al. (1996). "On the Computational Power of DNA." Discrete Applied Mathematics 71: 79-94.
Braich, R. S., C. Johnson, et al. Solution of a satisfiability problem on a gel-based DNA computer. 6th International Conference on DNA Computation in the Springer-Verlag Lecture Notes in Computer Science series.
Braich, R. S., C. Johnson, et al. (2002). "Solution of a 20-variable 3-SAT problem on a DNA computer." Science 296(5567): 499-502.
Chang, W.-L. and M. Guo (2002c). Resolving the 3-Dimensional Matching Problem and the Set-packing Problem in Adleman-Lipton’s Model. IASTED International Conference, Networks, Parallel and Distributed Processing, and Applications. Japan.
Chang, W.-L. and M. Guo (2002b). Solving NP-Complete Problem in the Adleman-Lipton Model. International Conference on Computer and Information Technology.
Chang, W.-L. and M. Guo (2002a). Solving the Clique Problem and the Vertex Cover Problem in Adleman-Lipton''s Model. IASTED International Conference, Networks, Parallel and Distributed Processing, and Applications. Japan.
Chang, W.-L. and M. Guo (2002). Solving the Dominating-set Problem in Adleman-Lipton''s Model. The Third International Conference on Parallel and Distributed Computing, Applications and Technologies, Japan. Japan.
Chang, W.-L. and M. Guo (2003). "Solving the Set-cover Problem and the Problem of Exact Cover by 3-Sets in the Adleman-Lipton''s Model." BioSystems 72(3): 263-275.
Chang, W.-L., M. Ho, et al. (2005). "Fast parallel molecular algorithms for DNA-based computation: factoring integers." IEEE Transactions on Nanobioscience 4(2): 149-163.
Codd, E. F. (1970). "A Relational Model of Data for Large Shared Data Banks." Communication of the ACM 13(6): 377-387.
Eckstein, F., Oligonucleotides, et al. (1991). Oxford University Press. U. K.
Feynman, R. P. (1961). In minaturizatio. D. H. Gilbert, Reinhold Publishing Corporation: 282-296.
Frisco, P. (2000). "Parallel Arithmetic with Splicing." Romanian Journal of Information Science and Technology: 113-128.
Fu., B. (1997). Volume Bounded Molecular Computation". Department of Computer Science, Yale University. Ph.D.
Gait, G. M. B. a. M. J. (1990). Nucleic Acids in Chemistry and Biology. Washington. DC: IRL.
Guarneiri, F., M. Fliss, et al. (1996). "Making DNA add." Science 273: 220–223.
Gupta, V., S. Parthasarathy, et al. (1997). Arithmetic and logic operations with DNA. 3rd DIMACS Workshop DNA Based Computers.
Hug, H. and R. Schuler (2001). DNA Based Parallel Computation of Simple Arithmetic. 7th Workshop on DNA Based Computers.
LaBean, M. C., T. H. Reif, et al. "Logical computation using algorithmic self-assembly of DNA triple-crossover molecules." Nature 407: 493-496.
LaBean, T. H., E. Winfree, et al. (2000). "Experimental Progress in Computation by Self-Assembly of DNA Tilings." Theoretical Computer Science 54: 123-140.
Lipton, R. J. (1995). "DNA solution of hard computational problems." Science 268:: 542-545.
Morimoto, N., M. Arita, et al. (1999). Solid phase DNA solution to the Hamiltonian path problem. 3rd DIMACS Workshop DNA Based Computers.
Narayanan, A. and S. Zorbala (1998). DNA Algorithms for Computing Shortest Paths. In Genetic Programming 1998: Proceedings of the Third Annual Conference, R. Koza et al. (Eds).
Ogihara, M. and A. Ray (1996). Simulating Boolean Circuits on a DNA Computer. Technical Report TR631, University of Rochester.
Paun, G., G. Rozenberg, et al. (1998). DNA Computing: New Computing Paradigms. New York.
Perez-Jimenez, M. J. and F. Sancho-Caparrini (2001). Solving knapsack problems in a sticker based model. 7nd Annu.Workshop DNA Computing, DIMACS Series in Discrete Mathematics and Theoretical Computer Science.
Qiu, Z. F. and M. Lu (1998). Arithmetic and logic Operations with DNA computers. 2nd IASTED Int. Conf. Parallel and Distributed Computing and Networks.
Quyang, Q., P. D. Kaplan, et al. (1997). "DNA solution of the maximal clique problem." Science 278: 446-449.
Reif, J. H., T. H. LaBean, et al. (2000). Challenges and Applications for Self-Assembled DNA-Nanostructures. the 6th DIMACS Workshop on DNA Based Computers
Roweis, S., E. Winferr, et al. (1999). A sticker based model for DNA computation. DIMACS series in Discrete Mathematics and Theoretical Computer Science. L. Landweber and E. Baum: 1-29.
Shin, S.-Y., B.-T. Zhang, et al. (1999). Solving traveling salesman problems using molecular programming. in Proc. 1999 Congr. Evolutionary Computation.
Sinden, R. R. (1994). DNA Structure and Function. New York: Academic.
Ullman, J. D. and J. Widom (2008). A FIRST COURSE IN DATABASE SYSTEMS 3/E, Prentice Hall; 3 edition.
Watson, J., M. Gilman, et al. (1992). Recombinant DNA. S. Francisco. CA: Freeman.
Watson, J., N. Hoplins, et al. (1987). Molecular Biology of the Gene. M. Park. CA: Benjamin/Cummings.
QRCODE
 
 
 
 
 
                                                                                                                                                                                                                                                                                                                                                                                                               
第一頁 上一頁 下一頁 最後一頁 top