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In recent years, as the development of personal computers shows remarkable progress, computers with excessive computational capacity tends to be everywhere.Today a lot of high-performance computers have been emerged. On the other hand, because network technology has made a remarkable progress and the network infrastructure has been well developed.Grid computing is a cutting edge technology that allows to share computational resources geographically distributed on the network to utilize the resources effectively.It is expected to be provided virtual computation capacity comparable to supercomputer.
The potential of the Grid gives rise to accelerarte a hope that the Grid dramatically applies to every field in science. In particular, medical science and drug discovery are good examples of such field. Genome technology has been advanced dramatically, thanks to the recent progress in computer technology. The result of analys is conducted by researchers, such as vast array of data are accumulated and managed separately in each research institute all over the world. Therefore, there is a growing demand that requires high computational capacity to deal with storing such analyzed data into databases, searching gene sequences and homology from experimental results, and simulation of chemical compound.
Grid technology today has large future possibilities. Currently, it is very difficult for researchers not specialized in IT to use Grid technology. IT engineers are therefore playing an important role to improve the research environment. The mission imposed on us is motivated us to provide an interface for researchers who are not specialized in IT to beable to easily make use of the benefit grid technology. We also provide portal application for network environment of Grid computing.
Drug design is the targeted science field for this application. We aim at creating research environment that application and databases on the Grid can be easily operated. BLAST and ClustalW, both of which are commonly used not only in medical services and drug design, but also biotechnology, have been selected applications to be utilized on the Grid interface. We call this Grid interface application GUIDE (A Grid User Interface to the Distributed Environment).
1. User friendliness
In the early stage of Grid computing, most of the system gridified was build for researchers who want a large-scale computational resources. Because those researchers dealing with a large- scale resources had skills and knowledge to operate computers on the Grid, user friendliness was not necessarily a big issue. However, recent Grid computing is expected to be supplied not only IT researchers, but also to a wide variety of people with different backgrounds. For this reason, user friendliness has become an important issue at current stage of development of the Grid.
2. Scalability
Technology always makes a progress, resulting in updating, modification, and replacement of the system components. For the Grid to be an innovative computer, scalability needs to be carefully considered.
3. Ez-to-use Application workflow
The portal should hide the complexity of the Grid for users and provides the functionality that allows users to benefit much from the Grid. To the end, the portal system should be carefully designed from the point of user practical view. In our case, that is, GUIDE which targets on the research field of drug design, two typical software, BLAST and ClustalW commonly used in the field have been selected as most necessary tools for drug design. In it, these two programs are designed so that they interact each other to form a practical application workflow.
In drug discovery, analysis done by computers was used merely for computational purpose or basis for biochemical experimental verification. It did not used to a technology that played a central role in drug discovery. However, followed by rapid advancement of computers, such analysis is getting to play a key role in drug discovery.
In order to figure out complex medicable relationship in vivo under process of drug discovery, techniques with use of computers are considered necessary. In each phase of drug discovery, there are various ways of approach available, and researchers combine tools to accommodate their needs for each technique. Guide is a Grid-portal system that allows bio researchers to easily benefit much from the Grid. Through GUIDE, we can make maximum use of the computational power delivered without being aware of the complex mechanism behind the Grid. In addition, the seamless integration of tools and software which has a central role in the process of drug design is realized with GUIDE, meaning that every bio-researcher can execute his/her own research purpose.
Tools being implemented on GUIDE
On GUIDE, two interfaces of bioinformatics tools used in the early stage of drug discovery are implemented. We introduce the two tools.
These tools is shown following
BLAST : BLAST is the most popular tool in bioinformatics. This tool compares base or amino acid sequences registered into the database with sequences given by user as query. If the sequences registered into database are homologous with the query, these are scored and shown in order.
If you need more information on BLAST , see NCBI or DDBJ site.
ClustalW : Users give some base or amino acid sequences to ClustalW. The given sequences are aligned with reference to similarity of base or amino acid. By aligning the sequences, we can estimate the function of the gene or protein described with the sequences.
In you need more information on ClustalW , see EMBL or DDBJ site.
Currently there are some problems as operating GUIDE. We are going to develop and implement the following features in the near future to overcome the problems.
Improved operationality
Our final goal of GUIDE operationality is as if people use GUIDE without being aware of using it. Currently we let users select host name and search resources, both of which are trouble spots in the GRID environment.
Expansion of Functional Capability
Parameter capacity is a problem that bioinformatics has been living with. Most bioinformatics-related applications provide vast amount of parameter. In the process of drug design, a great deal of parameter is required to use a number of applications. On the other hand, it is too demanding that bioinformatics researchers memorize all of such parameter and make full use of many applications. In GUIDE, we consider creating a mechanism that saves a parameter history and forms workflow accordingly.
More Tools
Currently, interface of only BLAST and ClustalW is implemented on GUIDE. In practice, more tools are used in the process of drug design (ex. FASTA, SSearch and etc.). We will add more tools in future as functions of GUIDE are extended.
Middleware Adaptation
GUIDE adapts only Globus 2.0. Considering future utilization, GUIDE needs to adapt various kinds of middleware such as Globus 2.2 and up, Globus3.0 and Web service.
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