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| - %META:TOPICPARENT{name="VirtInstallationEC2"}%
---+ Prepopulated Virtuoso hosting of NeuroCommons on EC2 AMI
---++What is NeuroCommons Project?
As articulated in the [[http://sciencecommons.org/about/science-commons-dylan-video/][Science Commons mission statement video]], [[http://www.neurocommons.org/][NeuroCommons]] project within [[http://sciencecommons.org/about/][Science Commons]] aimed at creating openly accessible neuroscience and computational biology knowledgebases on the Web.
---++NeuroCommons Installation on Virtuoso EC2 AMI instance
OpenLink Software provides a backup up of the current NeuroCommons Database as hosted on the live service at
http://sparql.neurocommons.org/, that users can restore into a Virtuoso EC2 AMI instance in the
cloud, providing them with an instance of NeuroCommons for their own use.
---+++Installation
1 Start a [[VirtInstallationEC2][Virtuoso EC2 AMI instance]]. Note a Virtuoso Release 5 AMI instance ( ami-ids ami-59628630 or ami-c46084ad ) *must* be used with this backup. We recommended a 64-bit large image AMI instance with 8GB of memory be used, which is a m1.large EC2 instance type.
%BR%%BR% %BR%%BR%
1 Note for best performance particularly under extensive usage it is recommended the 16GB m1.xlarge EC2 instance type be used.
1 Load the Virtuoso Conductor Administration interface of the running EC2 AMI instance with a URL of the form
http://your-ec2-instance-cname/conductor.
%BR%%BR% %BR%%BR%
1 From the Virtuoso Conductor, navigate to the "System Admin" -> "Packages" tab to obtain a list of available
Virtuoso packages (VADs) to install.
%BR%%BR% %BR%%BR%
1 Click the "Install" button to initiate installation of the "EC2 Extensions" VAD package for use in performing backup
and restore tasks.
%BR%%BR% %BR%%BR%
1 Click the "Proceed" button to install the "EC2 Extensions" VAD package.
1 Go to the URL http://your-ec2-instance-cname/ec2exts to load the Virtuoso
Extensions for Amazon EC2 Images login page and log in as the "dba" user.
%BR%%BR% %BR%%BR%
1 From the Virtuoso Extensions for Amazon EC2 Images main page, click the "Restore a Remote Backup" link.
%BR%%BR% %BR%%BR%
1 On the "Restore a Remote Backup" page, set the follow options.
Protocol: WebDAV/HTTP
Host: s3.amazonaws.com
Path or Bucket: neurocommons-virtuoso-bundle
Backup File Prefix: neurocommons-bundle
%BR%%BR%
1 Click the "Restore" button to begin the restoration of the NeuroCommons database from backup.
%BR%%BR% %BR%
.
%BR%
.
%BR%
.
%BR% %BR%%BR%
1 Click on the "Continue" button to begin the re-assembly of the database from the restored backup files. Output
similar to the following will be displayed when the re-assembly of the database is complete.
%BR% %BR%
Once complete the server will have been restarted automatically with the restored NeuroCommons database ready for use.
---+++Usage Examples
%BR%
You can then access pages such as these on your NeuroCommons server:
* NeuroCommons SPARQL endpoint — http://your-ec2-instance-cname/nsparql.html
%BR%%BR% %BR%%BR%
* NeuroCommons XHTML Description page — http://your-ec2-instance-cname/commons/record/pmid/12477932
%BR%%BR% %BR%%BR%
---+++ NeuroCommons VAD Application Package
For those running a NeuroCommons Virtuoso EC2 AMI instance created before December 8, 2008, you will need to update your NeuroCommons
VAD Application package to obtain the latest enhancements, by taking the following steps
1 Download the NeuroCommons VAD Application
(neurocommons_dav.vad) package.
1 Navigate to the "System Admin" -> "Packages" tab of the Virtuoso Conductor.
%BR%%BR% %BR%%BR%
1 Scroll down to the "Install Package" section of the tab, use the "Upload Package" option "browse" button.
%BR%%BR% %BR%%BR%
1 Navigate to the location of the downloaded neurocommons_dav.vad file and click the "open" button to select it.
%BR%%BR% %BR%%BR%
1 Click the "Proceed" button to begin the installation process.
%BR%%BR% %BR%%BR%
---+++ Results
* The NeuroCommons SPARQL endpoint can be accessed on http://your-ec2-instance-cname/sparql
* The OpenLink [[http://wikis.openlinksw.com/dataspace/owiki/wiki/OATWikiWeb/InteractiveSparqlQueryBuilder][Interactive SPARQL Query Builder]] can be accessed on http://your-ec2-instance-cname/isparql, enabling the visual construction of queries (Graph Patterns).
---+++Related
* [[VirtSPARQLEndpointProtection][Safeguarding your Virtuoso-hosted SPARQL Endpoint]]
* [[VirtEBSBackedBYOLAMI][EBS-backed BYOL ("Bring Your Own License") Virtuoso EC2 AMI]]
* [[VirtTipsAndTricksGuideSPARQLEndpointProtection][SPARQL Endpoint Protection Methods Collection]]
* [[http://docs.openlinksw.com/virtuoso/][Virtuoso documentation]]
* [[http://docs.openlinksw.com/virtuoso/rdfsparql.html#rdfsupportedprotocolendpoint][SPARQL Service Endpoint]]
* [[http://docs.openlinksw.com/virtuoso/rdfsparql.html#rdfsupportedprotocolendpointuri][Service Endpoint Security]]
* [[http://docs.openlinksw.com/virtuoso/rdfsparql.html#sparqwebservicetbl][Managing a SPARQL Web Service Endpoint]]
* [[http://docs.openlinksw.com/virtuoso/rdfsparql.html][SPARQL]]
* [[VirtTipsAndTricksGuide][Virtuoso Tips and Tricks Collection]]
* [[VirtSPARQLDET][SPARQL Endpoint DET Configuration Guide]]
* [[VirtSPARQLSecurityWebID][WebID Protocol & SPARQL Endpoint ACLs Tutorial]]
* [[VirtOAuthSPARQL][SPARQL OAuth Tutorial]]
* [[VirtTipsAndTricksGuideSPARQLEndpoints][Securing SPARQL endpoints]]
* [[http://ods.openlinksw.com/wiki/ODS/OdsSPARQLAuth][SPARUL over SPARQL using the http://cname:port/sparql-auth endpoint]]
* [[VirtAuthServerUI][Virtuoso Authentication Server UI]]
* [[VirtSPARQLSSL][Manage a SPARQL-WebID based Endpoint]]
* [[VirtSetupSSL][Configure Virtuoso instance as an X.509 Certificate Authority and HTTPS listener]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSSetupSSL][Configure Virtuoso+ODS instance as an X.509 Certificate Authority and HTTPS listener]]
* [[http://ods.openlinksw.com/wiki/ODS/VirtODSSecurityWebID][WebID Protocol Support in OpenLink Data Spaces]].
* Manage ODS Datadspaces Objects WebID Access Control Lists (ACLs):
* [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebID][ODS Briefcase WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDPerson][Person Entity WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDGroup][Group Entity WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDPublic][Public WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACL][ODS Feed Manager WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACLPerson][Person Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACLGroup][Group Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSFeedManagerWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACL][ODS Calendar WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACLPerson][Person Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACLGroup][Group Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSCalendarWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACL][ODS Bookmark Manager WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACLPerson][Person Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACLGroup][Group Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBookmarksWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACL][ODS Addressbook WebID based ACL Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACLPerson][Person Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACLGroup][Group Entity Specific ACL]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSAddressBookWebIDACLPublic][Public Specific ACL for anyone with a WebID]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSPkiSetup][Guide for Set up a X.509 certificate issuer and HTTPS listener and generate ODS user certificates.]]
* [[http://ods.openlinksw.com/wiki/ODS/VirtODSPubSubHub][Setting up PubSubHub in ODS]]
* [[http://ods.openlinksw.com/wiki/ODS/VirtPubSubHub][PubSubHubBub Demo Client Example]]
* [[http://ods.openlinksw.com/wiki/ODS/VirtFeedPubSubHub][Feed subscription via PubSubHub protocol Example ]]
* [[http://ods.openlinksw.com/wiki/ODS/VirtPubSubHubACL][Setting Up PubSubHub to use WebID Protocol or IP based control lists]]
* [[http://ods.openlinksw.com/wiki/ODS/OdsKeyImport][CA Keys Import using Conductor]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSGenerateX509Certificate][Generate an X.509 Certificate hosted WebID Guide]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSGenerateWebIDX509CertOSKeystore][Generate an X.509 Certificate (with a WebID watermark) to be managed by host operating system keystore]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSGenerateWebIDX509CertBrsKeystore][Generate an X.509 Certificate (with a WebID watermark) to be managed by a browser-based keystore]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSWebIDIdP][Using Virtuoso's WebID Verification Proxy Service with a WebID-bearing X.509 certificate]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSWebIDIdpProxy][Using Virtuoso's WebID Identity Provider (IdP) Proxy Service with an X.509 certificate]]
* [[http://ods.openlinksw.com/wiki/ODS/ODSBriefcaseWebIDShareFile][ODS Briefcase WebID Protocol Share File Guide]]
* [[http://esw.w3.org/topic/foaf+ssl][WebID Protocol Specification]]
* [[https://foaf.me/simpleLogin.php][Test WebID Protocol Certificate page]]
* [[http://test.foafssl.org/cert/][WebID Protocol Certificate Generation page]] |
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