生物資訊計算所需要的計算資源往往相當龐大，在演算法進一步改良的不容易，以
及大型計算主機成本高昂的限制下，許多研究者嘗試採用分散式運算的方式，結合多台
分散的個人電腦的計算能力合作進行計算工作，以縮短曠時費日的計算時間。當將分散
式運算應用於生物資訊計算問題時，由於各計算節點本身計算能力的不同，或是各計算
節點上運行的其它計算工作份量的不同，計算節點之間可用的計算資源可能會有所差
異。而透過計算節點之間的互相協調來求得適當的計算工作分配策略，以避免計算節點
的計算負載過重，並且增加計算工作的效率，是進行分散式運算時的重要任務。
此時，採用代理人進行各計算節點間計算工作分配的協調任務，能夠以較直觀的概
念來設計適當的計算工作分配策略，而達到避免計算節點負載過重和增加計算工作效率
的目的，因此本篇論文試圖利用JADE 此一多重代理人系統為基礎，提出一個以代理人
協調計算節點間計算工作分配、並適合應用於生物資訊計算的分散式運算系統架構。相
較於BOINC 之類的大型專案利用募集網際網路上大量的志願者協助進行Public
Computing 的方式，此系統架構著眼於結合組織內部多臺個人電腦並且利用區域網路連
結的分散式運算方式，在提出實際的代理人分散運算系統架構之後，本篇論文並採用
“Graph Motif Discovery”和“S-System 參數最佳化”二項生物資訊計算問題對系統的效能
進行檢驗。

The process of bioinformatics computing consumes huge computing resources, in
situation of difficulty in improvement of algorithm and high cost of mainframe, many
scholars choice distributed computing as an approach for reducing computing time. When
using distributed computing for bioinformatics, how to find a properly tasks allocation
strategy among different computing nodes to keep load-balancing is an important issue. By
adopting multi-agent system as a tool, system developer can design tasks allocation strategies
through intuitional view and keep load-balancing among computing nodes.
The purpose of our research work is using multi-agent system as an underlying tool to
develop a distributed computing environment and assist scholars in solving bioinformatics
computing problem, In comparison with public computing projects such as BOINC, our
research work focuses on utilizing computing nodes deployed inside organization and
connected by local area network.

摘要.....................................................................Ⅰ
Abstract.................................................................Ⅱ
目錄.....................................................................Ⅲ
第一章 緒論............................................................... 1
1.1 研究背景與動機 .................................................... 1
1.2 研究目的 .......................................................... 3
第二章 文獻探討........................................................... 5
2.1 代理人與多重代理人系統 ............................................ 5
2.2 利用多重代理人於分散式運算環境 .................................... 8
第三章 研究方法與系統架構................................................ 11
3.1 研究方法 ......................................................... 11
3.2 Java Agent DEvelopment Framework, JADE ........................... 12
3.3 系統架構 ......................................................... 19
3.4 驗證問題 ......................................................... 25
3.4.1 Graph motif discovery ...................................... 25
3.4.2 S-system model 參數最佳化 .................................. 27
第四章 實驗結果與討論.................................................... 29
4.1 實驗環境 ......................................................... 29
4.2 實驗結果 ......................................................... 31
4.2.1 Graph motif discovery 問題 ................................. 31
4.2.2 S-system model 參數最佳化................................... 41
第五章 結論.............................................................. 49
5.1 研究結果討論 ..................................................... 49
5.2 未來研究方向..................................................... 51
參考文獻................................................................. 52

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