Category:NCBO Virtual Machine Image - Revision history

Palexand: Removing all content from page

2010-10-26T18:14:12Z

Removing all content from page

Palexand at 01:02, 26 October 2010

2010-10-26T01:02:39Z

Palexand: /* Getting Started */

2010-10-26T01:02:07Z

Getting Started

Palexand at 02:03, 23 October 2010

2010-10-23T02:03:55Z

Palexand at 23:23, 22 October 2010

2010-10-22T23:23:16Z

Palexand: New page: The NCBO Virtual Machine Image contains a pre-installed, pre-configured version of commonly used NCBO software. The image was created using VMWare and is available for download from NCBO A...

2010-10-22T23:22:35Z

New page: The NCBO Virtual Machine Image contains a pre-installed, pre-configured version of commonly used NCBO software. The image was created using VMWare and is available for download from NCBO A...

New page

The NCBO Virtual Machine Image contains a pre-installed, pre-configured version of commonly used NCBO software. The image was created using VMWare and is available for download from NCBO ADD_DOWNLOAD_LOCATION_HERE.

The following software is included on the image:
* BioPortal Ontology Services (BioPortal Core)
* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)
* BioPortal Admin (a UI for administering BioPortal Ontology Services)
* Annotator
* Resource Index

← Older revision		Revision as of 18:14, 26 October 2010
Line 1:		Line 1:
−	The NCBO Virtual Machine Image contains a pre-installed, pre-configured version of commonly used NCBO software. The image was created using VMWare and is available for download from NCBO ADD_DOWNLOAD_LOCATION_HERE.

−	~~The following software is included on the image:~~
−	* BioPortal Ontology Services (BioPortal Core)
−	* BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)
−	* BioPortal Admin (a UI for administering BioPortal Ontology Services)
−	* Annotator
−	* Resource Index
−
−	~~Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.~~
−
−	~~== Getting Started ==~~
−	* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.
−	* '''Change default passwords'''
−	** Operating System
−	*** Username: <code>root</code>
−	*** Password: <code>changemeNOW</code>
−	** BioPortal Admin User
−	*** Username: <code>admin</code>
−	*** Password: <code>changeme</code>
−	* Add an ontology using the BioPortal Admin User here: http://example/ontologies/new
−	** BioPortal Ontology Services will automatically process new ontologies every hour at 30 minutes past the hour. This processing includes:
−	*** Parsing any new, unparsed ontologies
−	*** Calculating a set of metrics for these ontologies
−	*** Indexing these ontologies for use with search
−	* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example/bioportal_admin
−
−
−	~~== Population Workflows ==~~
−	When storing an ontology using the BioPortal Ontology Services, some amount of processing is done automatically so that the ontologies can be visualized using the Web UI. However, the Annotator and Resource Index require separate, manual data population workflows in order to function with the provided ontologies. Details on running these populations can be found in the "Howto" sections located at the bottom of this page.
−
−
−	~~== Image Format and Machine Details ==~~
−	The NCBO Virtual Machine Image is created using the [http://www.vmware.com/appliances/getting-started/learn/ovf.html Open Virtualization Format], which should allow the machine to be used in a variety of environments.
−
−	~~The operating system is CentOS 5.5 running Tomcat 6, Java 6, Rails 2.3.5, and Ruby Enterprise Edition 1.8.7, and memcached.~~
−
−	~~The following applications use these services/runtime environments:~~
−	* Tomcat, Java
−	** BioPortal Ontology Services (BioPortal Core)
−	** BioPortal Admin (a UI for administering BioPortal Ontology Services)
−	** Annotator
−	** Resource Index
−	* Rails, Ruby, memcached
−	** BioPortal Web User Interface (including ontology visualization, Flex widgets, Annotator and Resource Index UIs)
−
−
−	~~== Basic System Administration ==~~
−	* Most of our administration scripts and build environment assume that you will be running as the root user.
−	* Helper commands:
−	** <code>ncbostart</code>: the required services are started on boot automatically, but if they need to be started automatically
−	** <code>ncbostop</code>: manually stop services
−	** <code>ncborestart</code>: manually start/stop services
−	* Start individual services:
−	** <code>/sbin/service httpd start</code>
−	** <code>/sbin/service memcached start</code>
−	** <code>/sbin/service tomcat6 start</code>
−	** <code>/sbin/service mgrep start</code>
−	* Stop individual services:
−	** <code>/sbin/service httpd stop</code>
−	** <code>/sbin/service memcached stop</code>
−	** <code>/sbin/service tomcat6 stop</code>
−	** <code>/sbin/service mgrep stop</code>

@@ Line 19: / Line 19: @@
 *** Username: <code>admin</code>
 *** Password: <code>changeme</code>
-* Add an ontology using the BioPortal Admin User here: http://ncbobioportal/ontologies/new
+* Add an ontology using the BioPortal Admin User here: http://example/ontologies/new
 ** BioPortal Ontology Services will automatically process new ontologies every hour at 30 minutes past the hour. This processing includes:
 *** Parsing any new, unparsed ontologies
 *** Calculating a set of metrics for these ontologies
 *** Indexing these ontologies for use with search
-* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://ncbobioportal/bioportal_admin
+* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://example/bioportal_admin

@@ Line 11: / Line 11: @@
 == Getting Started ==
-* The default hostname for the machine is ncbobioportal
+* You can supply the hostname (machine name) for the virtual machine during the deployment process. Documentation will refer as this hostname as 'example'.
 * '''Change default passwords'''
 ** Operating System
@@ Line 25: / Line 25: @@
 *** Indexing these ontologies for use with search
 * Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://ncbobioportal/bioportal_admin

← Older revision		Revision as of 02:03, 23 October 2010
Line 9:		Line 9:

	Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.		Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.
		+
		+	== Getting Started ==
		+	* The default hostname for the machine is ncbobioportal
		+	* '''Change default passwords'''
		+	** Operating System
		+	*** Username: <code>root</code>
		+	*** Password: <code>changemeNOW</code>
		+	** BioPortal Admin User
		+	*** Username: <code>admin</code>
		+	*** Password: <code>changeme</code>
		+	* Add an ontology using the BioPortal Admin User here: http://ncbobioportal/ontologies/new
		+	** BioPortal Ontology Services will automatically process new ontologies every hour at 30 minutes past the hour. This processing includes:
		+	*** Parsing any new, unparsed ontologies
		+	*** Calculating a set of metrics for these ontologies
		+	*** Indexing these ontologies for use with search
		+	* Parsing, indexing, metrics calculation, and ontology deletion can all be manually triggered or re-triggered using the BioPortal Admin user interface, which is available here: http://ncbobioportal/bioportal_admin

← Older revision		Revision as of 23:23, 22 October 2010
Line 7:		Line 7:
	* Annotator		* Annotator
	* Resource Index		* Resource Index
		+
		+	Please see below for how-to documentation for managing the software and running data population for Annotator and Resource Index.