Difference between revisions of "Connecting to SRB BIRN"
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To be able to connect to SRB BIRN from inside MIPAV and open the image files using SRB you need to: | To be able to connect to SRB BIRN from inside MIPAV and open the image files using SRB you need to: | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Obtain a SRB user account and/or NDAR portal user account, see Section | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Obtain a SRB user account and/or NDAR portal user account, see Section "Requesting the SRB account" <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Set up the MIPAV SRB options, see Section "Setting MIPAV SRB options and opening files" <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 Set up the SRB connection parameters, see Section "Setting the SRB connection parameters" <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Upload your files to the SRB BIRN (optional), see Section "Uploading files to SRB BIRN" .<br /></font></div> |
==== Requesting the SRB account ==== | ==== Requesting the SRB account ==== | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Before connecting to SRB BIRN from inside MIPAV, you should obtain the user account to the NDAR portal, first. In order to do that, connect to the portal using the following link:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> https://nih-cit-dev-apps.nbirn.net/gridsphere/gridsphere?cid=ndar-login<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Then, open the Request an Account tab and follow the instructions provided by the tab. Refer to | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Before connecting to SRB BIRN from inside MIPAV, you should obtain the user account to the NDAR portal, first. In order to do that, connect to the portal using the following link:<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> https://nih-cit-dev-apps.nbirn.net/gridsphere/gridsphere?cid=ndar-login<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> Then, open the Request an Account tab and follow the instructions provided by the tab. Refer to Figure 1.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 6pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> After your request has been approved, you should receive the confirmation email from the NIH help desk. This email should contain your username and instructions on how to log in to the NDAR portal. At that time, log in to the NDAR portal, enter your email address that you entered in the account request, and create your password. Once you have done creating your password, you can log in to the NDAR portal using the username provided in the helpdesk email and the password you just created. [#1260786 <sup>1</sup>]<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> |
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 1. NDAR portal, requesting a user account.<br /></font>'''</div> |
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[[Image:NDARSRB_Account.jpg]] | [[Image:NDARSRB_Account.jpg]] | ||
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==== Setting MIPAV SRB options and opening files ==== | ==== Setting MIPAV SRB options and opening files ==== | ||
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To set up the MIPAV SRB options: | To set up the MIPAV SRB options: | ||
− | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Open MIPAV;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Call Help>MIPAV Options menu;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 In the MIPAV options dialog box that appears, navigate to the SRB tab. See | + | <div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 1 Open MIPAV;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 2 Call Help>MIPAV Options menu;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 3 In the MIPAV options dialog box that appears, navigate to the SRB tab. See Figure 2<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 18pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -18pt; text-transform: none; vertical-align: baseline"><font color="#000000"> 4 Complete the following tab options: <br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Jargon version:</font>'''</span> a version of Jargon API library, which should be used to communicate to the SRB server. Select one from the list;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Transfer Mode </font>'''</span>(parallel or sequential) - specify the file transfer protocol. There are SRB parallel transfer protocol and SRB sequential transfer protocol available;<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 36pt; margin-right: 0pt; margin-top: 6pt; text-align: left; text-decoration: none; text-indent: -12pt; text-transform: none; vertical-align: baseline"><font color="#000000"> <span style="font-style: normal; text-decoration: none; text-transform: none; vertical-align: baseline">'''<font color="#000000">Temporary Directory</font>'''</span> is your local directory, where you keep your files which need to be transferred FROM or TO the SRB server.<br /></font></div><div style="font-style: normal; font-weight: normal; margin-bottom: 0pt; margin-left: 0pt; margin-right: 0pt; margin-top: 0pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline"><font color="#000000"> |
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− | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure | + | |+ <div style="font-style: normal; margin-bottom: 3pt; margin-left: 0pt; margin-right: 0pt; margin-top: 9pt; text-align: left; text-decoration: none; text-indent: 0pt; text-transform: none; vertical-align: baseline">'''<font color="#000000"> Figure 2. The MIPAV options dialog - SRB options tab.<br /></font>'''</div> |
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[[Image:MIPAV_optionsSRB_Tab.jpg]] | [[Image:MIPAV_optionsSRB_Tab.jpg]] | ||
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==== Setting the SRB connection parameters ==== | ==== Setting the SRB connection parameters ==== |
Revision as of 18:47, 10 February 2012
Connecting to SRB BIRN
In this chapter . . .
- "Requesting the SRB account"
- "Setting MIPAV SRB options and opening files"
- "Setting the SRB connection parameters"
- "Uploading files to SRB BIRN"
- "Transferring files from MIPAV to SRB BIRN and vise versa"
- "Set up the NDAR pipeline"
- "Saving files to SRB"
Biomedical Informatics Research Network(BIRN, http://www.nbirn.net/) is a shared biomedical IT infrastructure supported by NIH, which hastens the process of new understanding and treatment of disease through use of distributed knowledge. BIRN supports collaboration between groups with different expertise and resources (e.g., technical, scientific, social and political). The Storage Resource Broker (SRB), developed at SDSC, is a client-server middleware designed for managing file collections in a heterogeneous, distributed environment. All files within the environment are part of a single data grid BIRN file system where a file's logical location within the file system is represented independently of its physical location. The SRB middleware is capable of managing large data sets and is currently managing the BIRN data grid.
Get Connected to SRB BIRN
To be able to connect to SRB BIRN from inside MIPAV and open the image files using SRB you need to:
Requesting the SRB account
Setting MIPAV SRB options and opening files
To set up the MIPAV SRB options:
Setting the SRB connection parameters
The connection parameters that must be used to connect to SRB BIRN from inside MIPAV are slightly different from the parameters which you used to connect to the NDAR portal. To obtain these parameters,
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As shown in [MIPAV_ConnectingToSRBBIRN.html#1260927 Figure 95] the following parameters are used to connect to SRB:
General SRB User Parameter
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MIPAV
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Host
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Host
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Port
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Port
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User Name
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Name
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Home Directory
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Â
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user Domain
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Domain
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Default Resource
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Storage Resource
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Uploading files to SRB BIRN
To test your access to SRB BIRN from inside MIPAV, you might choose to upload a couple of files to your home catalog, first. In order to do that,
Later, you can upload your image files to SRB BIRN from MIPAV using the SRB Transfer and Save to SRB menus.
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Transferring files from MIPAV to SRB BIRN and vise versa
To transfer files from MIPAV to SRB BIRN and back to MIPAV:
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Set up the NDAR pipeline
You can run MIPAV scripts on the DICOM images stored on the DICOM server and automatically save results to the chosen SRB BIRN catalogue.
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