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

69
doc/upgrade-1.2.html
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<meta charset="utf-8" />
<title>VIVO Release 1 V1.2 Upgrade Guide</title>
<link rel="stylesheet" href="./css/doc.css" media="screen" />
<link rel="stylesheet" href="./css/print.css" media="print" />
</head>
<body>
<div id="branding" role="banner">
@ -14,7 +13,7 @@
<div id="wrapper-content" role="main">
<h1>VIVO Release 1 v1.2 Upgrade Guide</h1>
<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
</small>
<toc>
@ -42,51 +41,40 @@
</p>
<!-- Release Announcement --><h2 id="announcement">Release anouncement for V1.2</h2>
<p>
The VIVO 1.2 release incorporates major changes throughout the
application - notably a new templating system to support more flexible
display and navigation, plus improvements to address scalability. The
release also features two new visualization options: temporal graphing
for organizations, and personal visualizations extended to cover grants
as well as publications. The VIVO Harvester library has also been
significantly improved and expanded in scope for its 1.0 release
through the VIVO SourceForge project at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
The VIVO 1.2 release incorporates major changes throughout the application -
notably a new templating system to support more versatile page rendering, plus
improvements to address scalability. The release also features a new personal
visualization option covering grants as well as publications. The VIVO Harvester
library has also been significantly improved and expanded in scope for its 1.0
release through the VIVO SourceForge project at
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p>
<h4>Templating system for page generation, navigation, and theming</h4>
<p>
A new installation of VIVO 1.2 looks strikingly different, with a
new navigation and browse interface as well as a more modular page
design that is easier to customize and brand for your local
institution. Page displays now support inline navigation to streamline
viewing of expanded personal and organizational profiles, as well as
improved graphic layout and organization. New browsing controls on the
home page and each menu page include interactive visual controls to
provide an immediate overview of the size and range of content and
quick access down to the individual person, organization, research
feature, or event. VIVO's navigation has also been completely
overhauled.
A fresh installation of VIVO 1.2 looks strikingly different, with the introduction
of a new default theme which takes advantage of the navigation and browse features
delivered by the templating system. Individual pages now offer inline navigation to
streamline viewing of expanded personal and organizational profiles, as well as
improved content layout and organization. New browse controls on the home page and
menu pages help to provide an immediate overview of the size and range of content
and quick access down to the individual person, organization, research feature, or
event.
</p>
<h4>Storage model</h4>
<p>
While server memory capacity has increased significantly in recent
years, VIVO's reliance on in-memory caching of RDF data had put limits
on the ultimate scalability of VIVO instances and potentially increased
the cost of servers required to support VIVO.&nbsp;
<br>
While server memory capacity has increased significantly in recent years, VIVO's reliance
on in-memory caching of RDF data had put limits on the ultimate scalability of VIVO instances
and potentially increased the cost of servers required to support VIVO.
</p>
<p>
With version 1.2, VIVO has been converted to optionally use Jena's
SPARQL database (SDB) subsystem. SDB significantly reduces the baseline
memory footprint, allowing VIVO installations to scale well beyond what
has previously been possible.
With version 1.2, VIVO has been converted to optionally use Jena's SPARQL database (SDB)
subsystem. SDB significantly reduces the baseline memory footprint, allowing VIVO installations
to scale well beyond what has previously been possible.
</p>
<h4>New visualizations</h4>
<p>
VIVO continues to expand visualization options including all-new
user-configurable temporal comparisons of publications and grants,
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.
Visualizations of networks of co-authors are now complemented by visualizations of co-investigators
on grants, with similar interactivity and options for export as images or data.
</p>
<h4>Ontology</h4>
<p>
@ -99,10 +87,11 @@
<h3>Associated VIVO releases</h3>
<h4>VIVO Harvester</h4>
<p>
The Harvester development team is releasing version 1.0 of the VIVO
Harvester library, an extensible data ingest and updating framework
with sample configurations for loading PubMed publication, grants, and
human resources data. The Harvester is available at <a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
The Harvester development team is releasing version 1.0 of the VIVO Harvester library shortly
following the release of VIVO 1.2. The Harvester is an extensible data ingest and updating
framework with sample configurations for loading PubMed publication, grants, and human resources
data. Pre-release versions of the Harvester are available at
<a href="http://sourceforge.net/projects/vivo">http://sourceforge.net/projects/vivo</a>.
</p>
<hr><!-- Page break --><!-- Upgrade process for V1.2 --><h2 id="upgrade">Upgrade process for V1.2</h2>
<toc>