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This web page is to report our 6 Grid Project activity.
GUIDE utilizes a variety of advanced technologies such as Globus , MyProxy , Tomcat . GT2.0 is used for the Grid infrastructure, and MyProxy is used for a part of authentication system. Tomcat is used for the Web technology. Figure 1 shows an overall image of GUIDE.
GUIDE is implemented as servlet. From servlet GUIDE connects to the Grid network environment composed of Globus by using Java CoG Kit . For user authentication, MyProxy is used. Prior to use GUIDE,the user certification file is registered to MyProxy. A user determines his/her user name and path phrase when he/she registers. What GUIDE users have to do is only enter user name and path phrase.
Fig 1.GUIDE system architecture
Fig 2.GUIDE widow changes
Frame image is shown in figure 1. All frames are created based on JSP that provides html files. No special application is required to be installed, and clients can operate it from web browsers.
Frame transition is shown in figure 2. Each frame is shown in boxes and each frame transition done by users is described as each arrow shows. There is no special frame for log-out function. When you click log-out in the menu, log-out processing is performed, and then log-in frame is shown.
List of frames Name of Frames
Log in For log in. Enter the user name and pass phrase that have been already registered to MyProxy server.
Menu Shows all frames’ menu. Once logged in, the menu frame is always shown on the top.
BLAST Enables to submit BLAST jobs to the Grid environment. A submitted job’s status can be seen in the Job list Frame.
ClustalW Enables to submit ClustalW jobs to the Grid environment. A submitted job’s status can be seen in the Job list Frame.
Joblist Enables to check job status list BLAST result
BLAST result Shows BLAST result
ClustalW result Shows ClustalW result
This web page is to report our 6 Grid Project activity.
Downloading　the software is limited to registered people only.
If you want to download them, please register first.
You will receive a password for downloading within a couple of days.
This web page is to report our 6 Grid Project activity.
System Requierment
GUIDE requires the following systems being installed.
This web page is to report our 6 Grid Project activity.
Login Frame
In Login frame, the following two items are necessary to be entered.
  • user name
  • pass phrase
Once entered these items and click “submit”, you are logged into GUIDE system. Menu frame and BLAST frame are shown thereafter.
Fig 1. Login Frame
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Menu Frame
Once logged in GUIDE, Menu frame is always shown on a top frame.
The menu frame contains the following items.
  • BLAST
  • ClustalW
  • Job list
  • Logout
There is no Logout frame on the screen. Once logged out, Login frame appears again.
Fig 2. Menu Frame
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BLAST Frame
This frame is to submit BLAST jobs. First, a hostname is selected to submit to BLAST parameter. Next, you click “submit”, and Job list frame consequently appears. Because BLAST job is not completed in a short period of time, any transition of the job is displayed on the job status in the frame. Table 1 shows all items of the frame.
Table 1. BLAST frame item Fig 3. BLAST Frame
item name details
HostName Select a host submitted its job
Program Select a program of BLAST
Database Select the database of base sequences or amino acid sequences
Filter Select On/Off of the Filter
Expect Enter the threshold of E-value
Matrix Select Matrix used for determining Score (Score Matrix)
Input Sequence Input sequence data of base sequences or amino acid sequences
Upload Sequence File Input sequence data of base sequences or amino acid sequences. The data is uploaded on GUIDE system.
OpenGap Input initial penalty when a gap occurs
ExtendGap Input penalties corresponding to every increase of gap.
Strand Select a sequence from the pair of base sequence. 1:top 2: bottom 3:both
More Option This item is used to input the other BLAST parameters.
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ClustalW frame
This frame is to submit ClustalW jobs. First a hostname is selected to submit to ClustalW parameter. Next you click "submit", and the Job list frame consequently appears.
Table 2: Items of ClustalW Frame Fig 4. ClustalW Frame
item detail
HostName Select a host submitted its job
Output Format Specify an output data format
Output Order Select an ordering method of sequence data.
Select “Aligned” to order sequences by homology. Select INPUT for entry sequences.
Matrix Select the matrix used for determining Score (Scoring Matrix)
Alignment Select algorithm of Alignment.
Select “full” to compare all base sequences to all base sequences.
Select “fast” for fast accuracy.
Input Sequence Input sequence data for alignment.
Upload Sequence File Input sequence data for alignment.
The data is uploaded on GUIDE system.
Gap Open Specify a Gap penalty at the time when Gap begins. (default 10.0)
End Gap Select whether to ignore end gaps.
Gap Extension Penalty for alignment score when Gap is extended. This parameter is available when Gap setting is selected.
Gap Distances Specify the distance between Gaps. This parameter is available when Gap setting is selected.
KTUP (Word size) Specify the number of words. (default: 1) It is available only when alignment is selected to “fast” algorism.
Score Type Select a display method of scores. It is available only when alignment is selected to “fast” algorism.
Frame Length Specify a frame’s size (default: 5). It is available when alignment is selected to fast algorism.
Topdiag Specify the number of top diagonals (default: 5)
Pair Gap Specify Gap penalty.
(default: 3) It is available only when alignment is selected to fast algorism.
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Job List Frame
This frame displays the list of jobs submitted in BLAST frame or ClustalW frame.
Its status is shown in Chart 3. Because job status is changing every moment, this frame is reloaded every 10 seconds in order to catch up with the status and inform users the latest status. The file name shown in “result” is a result file. When the status is set to be finished, the result file can be shown. If you click “delete”, the job result is deleted.
Table 3 Job status Fig 5. Job List Frame
status detail
running Job is running
transfer Transferring result file
fix Translating result file to html file.
finished Job process is completed. Result file can be seen by clicking anchor in the result item.
fialed Job is ended abnormally.
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BLAST result frame
The frame displays results of BLAST. The list of search results and, on its underneath, details of a hit sequence are shown on the frame. There is an execution button above the list of search results, and the frame can move to ClusutalW frame when the execution button is pressed. Then the sequence that is checked in the boxes under the search results is shown in Input Sequence item in the ClustalW frame (See Figure 7).


Figure 7 BLAST to ClustalW
Fig 6.BLAST result frame
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ClustalW result frame
This frame displays results of ClustalW. Aligned sequence is displayed with “*” mark indicating similarity. In the future we would like to use phylogenetic tree and more to show the results.
Fig 8.ClustalW Result Frame
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