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doc/install.html
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@ -4,7 +4,6 @@
<meta charset="utf-8" /> <meta charset="utf-8" />
<title>VIVO Release 1 V1.2 Installation Guide</title> <title>VIVO Release 1 V1.2 Installation Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen" /> <link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" />
</head> </head>
<body> <body>
<div id="branding" role="banner"> <div id="branding" role="banner">
@ -14,7 +13,7 @@
<div id="wrapper-content" role="main"> <div id="wrapper-content" role="main">
<h1>VIVO Release 1 V1.2 Installation Guide</h1> <h1>VIVO Release 1 V1.2 Installation Guide</h1>
<small> <small>
January 28, 2011 February 16, 2011
</small> </small>
<toc> <toc>
<ul> <ul>
@ -28,51 +27,40 @@
</toc> </toc>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2> <!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
<p> <p>
The VIVO 1.2 release incorporates major changes throughout the The VIVO 1.2 release incorporates major changes throughout the application -
application - notably a new templating system to support more flexible notably a new templating system to support more versatile page rendering, plus
display and navigation, plus improvements to address scalability. The improvements to address scalability. The release also features a new personal
release also features two new visualization options: temporal graphing visualization option covering grants as well as publications. The VIVO Harvester
for organizations, and personal visualizations extended to cover grants library has also been significantly improved and expanded in scope for its 1.0
as well as publications. The VIVO Harvester library has also been release through the VIVO SourceForge project at
significantly improved and expanded in scope for its 1.0 release <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
through the VIVO SourceForge project at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<h4>Templating system for page generation, navigation, and theming</h4> <h4>Templating system for page generation, navigation, and theming</h4>
<p> <p>
A new installation of VIVO 1.2 looks strikingly different, with a A fresh installation of VIVO 1.2 looks strikingly different, with the introduction
new navigation and browse interface as well as a more modular page of a new default theme which takes advantage of the navigation and browse features
design that is easier to customize and brand for your local delivered by the templating system. Individual pages now offer inline navigation to
institution. Page displays now support inline navigation to streamline streamline viewing of expanded personal and organizational profiles, as well as
viewing of expanded personal and organizational profiles, as well as improved content layout and organization. New browse controls on the home page and
improved graphic layout and organization. New browsing controls on the menu pages help to provide an immediate overview of the size and range of content
home page and each menu page include interactive visual controls to and quick access down to the individual person, organization, research feature, or
provide an immediate overview of the size and range of content and event.
quick access down to the individual person, organization, research
feature, or event. VIVO's navigation has also been completely
overhauled.
</p> </p>
<h4>Storage model</h4> <h4>Storage model</h4>
<p> <p>
While server memory capacity has increased significantly in recent While server memory capacity has increased significantly in recent years, VIVO's reliance
years, VIVO's reliance on in-memory caching of RDF data had put limits on in-memory caching of RDF data had put limits on the ultimate scalability of VIVO instances
on the ultimate scalability of VIVO instances and potentially increased and potentially increased the cost of servers required to support VIVO.
the cost of servers required to support VIVO.&nbsp;
<br>
</p> </p>
<p> <p>
With version 1.2, VIVO has been converted to optionally use Jena's With version 1.2, VIVO has been converted to optionally use Jena's SPARQL database (SDB)
SPARQL database (SDB) subsystem. SDB significantly reduces the baseline subsystem. SDB significantly reduces the baseline memory footprint, allowing VIVO installations
memory footprint, allowing VIVO installations to scale well beyond what to scale well beyond what has previously been possible.
has previously been possible.
</p> </p>
<h4>New visualizations</h4> <h4>New visualizations</h4>
<p> <p>
VIVO continues to expand visualization options including all-new Visualizations of networks of co-authors are now complemented by visualizations of co-investigators
user-configurable temporal comparisons of publications and grants, on grants, with similar interactivity and options for export as images or data.
grouped by organization or by affiliated person. Visualizations of
networks of co-authors are now complemented by visualizations of
co-investigators on grants, with a similar interactivity and options
for export as images or data.
</p> </p>
<h4>Ontology</h4> <h4>Ontology</h4>
<p> <p>
@ -85,10 +73,11 @@
<h3>Associated VIVO releases</h3> <h3>Associated VIVO releases</h3>
<h4>VIVO Harvester</h4> <h4>VIVO Harvester</h4>
<p> <p>
The Harvester development team is releasing version 1.0 of the VIVO The Harvester development team is releasing version 1.0 of the VIVO Harvester library shortly
Harvester library, an extensible data ingest and updating framework following the release of VIVO 1.2. The Harvester is an extensible data ingest and updating
with sample configurations for loading PubMed publication, grants, and framework with sample configurations for loading PubMed publication, grants, and human resources
human resources data. The Harvester is available at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>. data. Pre-release versions of the Harvester are available at
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2> <hr><!-- Page break --><!-- Installation process for V1.2 --><h2 id="installation">Installation process for V1.2</h2>
<p> <p>
@ -577,10 +566,10 @@
The number of grants and publications is large. The number of grants and publications is large.
</li> </li>
</ul> </ul>
The VIVO developers are working to make this visualization more efficient. The VIVO developers are working to make this visualization more efficient.
In the meantime, VIVO release 1.2 guards against this impact by disabling In the meantime, VIVO release 1.2 guards against this impact by disabling
the temporal graph visualization unless the "visualization.temporal" flag the temporal graph visualization unless the "visualization.temporal" flag
is set to "enabled". To enable it, uncomment the line for this setting. is set to "enabled". To enable it, uncomment the line for this setting.
</td> </td>
</tr> </tr>
<tr class="odd_row"> <tr class="odd_row">

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doc/upgrade-1.2.html
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<meta charset="utf-8" /> <meta charset="utf-8" />
<title>VIVO Release 1 V1.2 Upgrade Guide</title> <title>VIVO Release 1 V1.2 Upgrade Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen" /> <link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" />
</head> </head>
<body> <body>
<div id="branding" role="banner"> <div id="branding" role="banner">
@ -14,7 +13,7 @@
<div id="wrapper-content" role="main"> <div id="wrapper-content" role="main">
<h1>VIVO Release 1 v1.2 Upgrade Guide</h1> <h1>VIVO Release 1 v1.2 Upgrade Guide</h1>
<small> <small>
January 28, 2011 - Upgrading from Release 1 v1.1 to Release 1 February 16, 2011 - Upgrading from Release 1 v1.1 to Release 1
v1.2 v1.2
</small> </small>
<toc> <toc>
@ -42,51 +41,40 @@
</p> </p>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2> <!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
<p> <p>
The VIVO 1.2 release incorporates major changes throughout the The VIVO 1.2 release incorporates major changes throughout the application -
application - notably a new templating system to support more flexible notably a new templating system to support more versatile page rendering, plus
display and navigation, plus improvements to address scalability. The improvements to address scalability. The release also features a new personal
release also features two new visualization options: temporal graphing visualization option covering grants as well as publications. The VIVO Harvester
for organizations, and personal visualizations extended to cover grants library has also been significantly improved and expanded in scope for its 1.0
as well as publications. The VIVO Harvester library has also been release through the VIVO SourceForge project at
significantly improved and expanded in scope for its 1.0 release <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
through the VIVO SourceForge project at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<h4>Templating system for page generation, navigation, and theming</h4> <h4>Templating system for page generation, navigation, and theming</h4>
<p> <p>
A new installation of VIVO 1.2 looks strikingly different, with a A fresh installation of VIVO 1.2 looks strikingly different, with the introduction
new navigation and browse interface as well as a more modular page of a new default theme which takes advantage of the navigation and browse features
design that is easier to customize and brand for your local delivered by the templating system. Individual pages now offer inline navigation to
institution. Page displays now support inline navigation to streamline streamline viewing of expanded personal and organizational profiles, as well as
viewing of expanded personal and organizational profiles, as well as improved content layout and organization. New browse controls on the home page and
improved graphic layout and organization. New browsing controls on the menu pages help to provide an immediate overview of the size and range of content
home page and each menu page include interactive visual controls to and quick access down to the individual person, organization, research feature, or
provide an immediate overview of the size and range of content and event.
quick access down to the individual person, organization, research
feature, or event. VIVO's navigation has also been completely
overhauled.
</p> </p>
<h4>Storage model</h4> <h4>Storage model</h4>
<p> <p>
While server memory capacity has increased significantly in recent While server memory capacity has increased significantly in recent years, VIVO's reliance
years, VIVO's reliance on in-memory caching of RDF data had put limits on in-memory caching of RDF data had put limits on the ultimate scalability of VIVO instances
on the ultimate scalability of VIVO instances and potentially increased and potentially increased the cost of servers required to support VIVO.
the cost of servers required to support VIVO.&nbsp;
<br>
</p> </p>
<p> <p>
With version 1.2, VIVO has been converted to optionally use Jena's With version 1.2, VIVO has been converted to optionally use Jena's SPARQL database (SDB)
SPARQL database (SDB) subsystem. SDB significantly reduces the baseline subsystem. SDB significantly reduces the baseline memory footprint, allowing VIVO installations
memory footprint, allowing VIVO installations to scale well beyond what to scale well beyond what has previously been possible.
has previously been possible.
</p> </p>
<h4>New visualizations</h4> <h4>New visualizations</h4>
<p> <p>
VIVO continues to expand visualization options including all-new Visualizations of networks of co-authors are now complemented by visualizations of co-investigators
user-configurable temporal comparisons of publications and grants, on grants, with similar interactivity and options for export as images or data.
grouped by organization or by affiliated person. Visualizations of
networks of co-authors are now complemented by visualizations of
co-investigators on grants, with a similar interactivity and options
for export as images or data.
</p> </p>
<h4>Ontology</h4> <h4>Ontology</h4>
<p> <p>
@ -99,10 +87,11 @@
<h3>Associated VIVO releases</h3> <h3>Associated VIVO releases</h3>
<h4>VIVO Harvester</h4> <h4>VIVO Harvester</h4>
<p> <p>
The Harvester development team is releasing version 1.0 of the VIVO The Harvester development team is releasing version 1.0 of the VIVO Harvester library shortly
Harvester library, an extensible data ingest and updating framework following the release of VIVO 1.2. The Harvester is an extensible data ingest and updating
with sample configurations for loading PubMed publication, grants, and framework with sample configurations for loading PubMed publication, grants, and human resources
human resources data. The Harvester is available at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>. data. Pre-release versions of the Harvester are available at
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p> </p>
<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2> <hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
<toc> <toc>