生物資料庫越來越龐大也越複雜，這結果致使科學家必須有效率的去與各個基因序列作比對。而一些生物資訊的相關軟體，例如NCBI的Blast、FASTA與ClustalW證實可被用來快速的處理序列比對的問題。這些比對中，不管是結構特徵或蛋白質序列的搜尋都是生物資訊學的重點核心。當在這些龐大序列作搜尋時，所有的動作皆需要高速、高效的計算能力。而近年來電腦運算處理的速度以指數攀升，配置上透過新興的Grid(網格)與既有的PC Cluster(個人電腦叢集)技術做整合，便可以與超級電腦相較勁，提高了生物資訊的普遍性。由於現在發展生物資訊的各個研究單位可能使用不同的平台，不同的資料庫來存放他們的研究資料。因此存放資料的格式，便會有所差異。這會造成在資源共享上有所困難。為了改善這個問題，我們將生物軟體的比對結果，如Blast、FastA的比對結果，轉換成XML的方式來儲存。利用XML的跨平台特性，增加生物資訊的流通性與一致性。在本論文中，我們實作一個生物資訊應用平台:包含底層的高效能計算環境(Grid 與PC Cluster 系統)，多重介面的入口網站來操控此生物資訊系統，簡化使用的複雜度，讓不屬於IT(Information Technology)產業界的人士能有效的利用這高效環境，以及一個將生物資料轉換成XML格式的轉換工具。 Biology databases are diversified and massive. As a result, researchers must compare each sequence with vast numbers of other sequences. Programs such as BLAST, FASTA, ClustalW, etc., were written to enable rapid database searches for query sequences. Comparison, whether of structural features or protein sequences, lies at the heart of bioinformatics. These activities require high-speed, high-performance computing power to search through and analyze huge amounts of data, and industrial-strength databases to perform a wide range of data-intensive computing functions. Grid computing and Cluster computing provide ways to meet these requirements. Biological data exist all over the world in various web services that help biologists search for and extract useful information. The data formats produced by the various biology tools are heterogeneous. Thus, powerful tools are needed to handle the complex and difficult task of integrating these heterogeneous biological data. This paper describes an approach to solving this problem using XML technologies. We report on implementing an experimental distributed computing application for bioinformatics consisting of basic high-performance computing environments (Grid and PC Cluster systems), multiple interfaces at user portals that provide useful graphical interfaces to enable biologists who are not IT specialists to benefit directly from the use of high-performance technology, and a translation tool for converting biology data into XML format.
