Skip to content

Commit

Permalink
updated welcome and about. Fixes bug #3247 and #3248.
Browse files Browse the repository at this point in the history
  • Loading branch information
@olas
olas committed Sep 10, 2012
1 parent edff7e5 commit 7a4002e
Show file tree
Hide file tree
Showing 2 changed files with 55 additions and 60 deletions.
43 changes: 21 additions & 22 deletions plugins/net.bioclipse.ui/html/about.html
View file
Expand Up @@ -10,45 +10,44 @@
<h1>About Bioclipse</h1>

<p>
Bioclipse is a complete workbench for life science, including chemo- and bioinformatics
(e.g. small molecules, sequences, proteins, spectra) and provides
Bioclipse (<a href="http:/www.bioclipse.net">www.bioclipse.net</a>) is a complete workbench for life science, including chem- and bioinformatics
(e.g. small molecules, sequences, proteins) and provides
editing of chemical structures in 2D, interactive visualization of
chemical structures in 3D, conversion between common file formats in
life science, various analysis tools and much more - all
the life sciences, various analysis tools and much more - all
fully integrated into a user-friendly desktop application.
<p>

Bioclipse is a Java-based open source project based on the
Eclipse Rich Client Platform with its state-of-the-art plugin
architecture. This gives Bioclipse a huge advantage over other
systems, as it can easily be extended for adding
functionality in any direction.
<a href="http://wiki.eclipse.org/index.php/Rich_Client_Platform">Eclipse Rich Client Platform</a> with its advanced plugin
architecture (based on <a href="http://http://www.osgi.org/">OSGi</a>). This gives Bioclipse the possibility to be extended with
functionality in virtually any direction.
<p>

<h2>Citing Bioclipse</h2>
<p>
<b>Bioclipse: An open source workbench for chemo- and bioinformatics. </b><br>
Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. Wikberg. <br>
<i>BMC Bioinformatics 2007, 8:59 (22 February 2007)</i>
</p>

<h2>Licenses</h2>
Bioclipse contains plugins, whose code uses a number of different licenses. The Bioclipse platform, consisting of the core plugins, is licensed as EPL. The EPL allows Bioclipse plugins to have other licenses.
The EPL license is available <a href="epl-v10.html">here</a>.

<b>Bioclipse 2: A scriptable integration platform for the life sciences</b><br>
Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl M&auml;sak, Gilleain Torrance, Johannes Wagener, Egon L Willighagen, Christoph Steinbeck and Jarl ES Wikberg<br>
<i>BMC Bioinformatics 2009</i>, 10:397 <a href="http://www.biomedcentral.com/1471-2105/10/397/">doi:10.1186/1471-2105-10-397</a>
</p>

<h3>EPL-GPL Statement</h3>
<p>
The GNU Public License (GPL) is a bit special here, and is considered not to be compatible with the EPL. Indeed, a EPL licensed plugin may not use GPL code, which is why the bc_biojava plugin is licensed GPL.
Making a GPL project based on EPL code is considered not possible too, while the EPL puts some restrictions on the licensing patents, which are incompatible with the GPL.
However, the Bioclipse project considers plugins not to extend the Bioclipse platform, consisting of the bioclipse + com.tools.logging plugins, and are not considered a derivative product, and we hereby approve GPL licensed plugins for Bioclipse.
<b>Bioclipse: An open source workbench for chemo- and bioinformatics. </b><br>
Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. Wikberg. <br>
<i>BMC Bioinformatics 2007</i>, 8:59 <a href="http://www.biomedcentral.com/1471-2105/8/59">doi:10.1186/1471-2105-8-59</a>
</p>

<h2>Copyright</h2>
<p>Bioclipse is copyrighted by the Bioclipse developers, see <a href="contributors.html">Contributors</a>.


<h2>License</h2>
Bioclipse is open source and licensed under <a href="epl-v10.html">Eclipse Public License (EPL)</a>.
Bioclipse contains plugins of other open source licenses, but which are compatible with EPL.
EPL allows Bioclipse to be extended by third party plugins of other types of licenses.
</p>


<h2>Copyright</h2>
<p>Bioclipse is copyrighted by the individual Bioclipse contributors.



Expand Down
72 changes: 34 additions & 38 deletions plugins/net.bioclipse.ui/intro/overview.xml
View file
Expand Up @@ -8,8 +8,8 @@
<link label="Bioclipse concepts" url="http://org.eclipse.ui.intro/showHelpTopic?id=/net.bioclipse.ui/html/concepts.html" id="concitem" style-id="content-link">
<text>Learn the basic Bioclipse concepts, such as View, Editor, Perspective etc.</text>
</link>
<link label="Licensing" url="http://org.eclipse.ui.intro/showPage?id=licenses" id="paraitem" style-id="content-link">
<text>A description and statements of copyright and licenses in Bioclipse.</text>
<link label="License" url="http://org.eclipse.ui.intro/showPage?id=licenses" id="paraitem" style-id="content-link">
<text>A description Bioclipse license.</text>
</link>
<link label="Download additional features" url="http://org.eclipse.ui.intro/runAction?pluginId=net.bioclipse.ui&amp;class=net.bioclipse.ui.actions.LaunchUpdateIntroAction" id="updateitem" style-id="content-link">
<text>Search, download, and install additional features from one or more Bioclipse update sites.</text>
Expand Down Expand Up @@ -40,65 +40,61 @@

<text style-id="page-title" id="page-title" filteredFrom="html">What is Bioclipse</text>
<text style-id="page-description" id="page-description">
Bioclipse is a complete workbench for life science, including chemo- and bioinformatics
(e.g. small molecules, sequences, proteins, spectra) and provides
editing of chemical structures in 2D, interactive visualization of
chemical structures in 3D, conversion between common file formats in
life science, various analysis tools and much more - all
fully integrated into a user-friendly desktop application.



Bioclipse is a complete workbench for life science, including chem- and bioinformatics
(e.g. small molecules, sequences, proteins) and provides
editing of chemical structures in 2D, interactive visualization of
chemical structures in 3D, conversion between common file formats in
the life sciences, various analysis tools and much more - all
fully integrated into a user-friendly desktop application.
</text>

<text style-id="page-description" id="page-description">
Bioclipse is a Java-based open source project based on the
Eclipse Rich Client Platform with its state-of-the-art plugin
architecture. This gives Bioclipse a huge advantage over other
systems, as it can easily be extended for adding
functionality in any direction.
Bioclipse is a Java-based open source project based on the Eclipse Rich Client Platform with its advanced plugin
architecture. This gives Bioclipse the possibility to be extended with
functionality in virtually any direction.
</text>

<text style-id="page-content" id="page-content">
Bioclipse original publication
<text style-id="page-description" id="page-description">
Ola Spjuth, Jonathan Alvarsson, Arvid Berg, Martin Eklund, Stefan Kuhn, Carl Mäsak, Gilleain Torrance, Johannes Wagener, Egon L Willighagen, Christoph Steinbeck and Jarl ES Wikberg.
BMC Bioinformatics 2009, 10:397
</text>

<!--link label="Bioclipse2 article (Open Access)" url="http://www.biomedcentral.com/1471-2105/10/397" id="weblink" style-id="weblink" /-->

<text style-id="page-description" id="page-description">

Ola Spjuth, Tobias Helmus, Egon L Willighagen, Stefan Kuhn, Martin Eklund, Johannes Wagener, Peter Murray-Rust, Christoph Steinbeck, Jarl E.S. Wikberg.
Bioclipse: An open source workbench for chemo- and bioinformatics.
BMC Bioinformatics 2007, 8:59 (22 February 2007)
BMC Bioinformatics 2007, 8:59
</text>
<link label="Link to Bioclipse original article (Open Acces)" url="http://www.biomedcentral.com/1471-2105/8/59/abstract" id="weblink" style-id="weblink" />
<!--link label="Bioclipse article (Open Access)" url="http://www.biomedcentral.com/1471-2105/8/59/abstract" id="weblink" style-id="weblink" /-->


</group>
</page>

<page id="licenses" style="/intro/overview.css" style-id="page">
<title style-id="intro-header">Licensing</title>
<title style-id="intro-header">License</title>
<include path="overview/navigation-links"/>
<group id="page-content">
<group id="content-header" label="Bioclipse licenses" filteredFrom="swt">
<group id="content-header" label="License" filteredFrom="swt">
</group>
<text style-id="page-title" id="page-title" filteredFrom="html">Bioclipse licenses</text>
<text style-id="page-title" id="page-title" filteredFrom="html">License</text>
<!-- Add content here -->
<text style-id="page-content" id="page-content">The Bioclipse Platform</text>
<text style-id="page-description" id="page-description">
Bioclipse contains plugins, whose code uses a number of different licenses. The
Bioclipse platform, consisting of the core plugins, is licensed as EPL. The EPL
allows Bioclipse plugins to have other licenses, including commercial.
</text>
<link label="Link to EPL license" url="http://org.eclipse.ui.intro/openURL?url=html/epl-v10.html&amp;?pluginId=net.bioclipse.ui" class="link" id="weblink" style-id="content-link" />

<text style-id="page-content" id="page-content">EPL-GPL Statement</text>
<text style-id="page-description" id="page-description">
The GNU Public License (GPL) is a bit special here, and is considered
not to be compatible with the EPL. Indeed, a EPL licensed plugin may not
use GPL code, which is why the bc_biojava plugin is licensed GPL. Making a
GPL project based on EPL code is considered not possible too, while the
EPL puts some restrictions on the licensing patents, which are incompatible
with the GPL. However, the Bioclipse project considers plugins not to extend
the Bioclipse platform, consisting of the bioclipse + com.tools.logging plugins,
and are not considered a derivative product, and we hereby approve GPL
licensed plugins for Bioclipse.
Bioclipse is open source and licensed under Eclipse Public License (EPL).
Bioclipse contains plugins of other open source licenses, but which are compatible with EPL.
EPL allows Bioclipse to be extended by third party plugins of other types of licenses.

</text>
<link label="Link to EPL license" url="http://www.eclipse.org/legal/epl-v10.html" class="link" id="weblink" style-id="content-link" />



</group>
</page>
Expand Down

0 comments on commit 7a4002e

Please sign in to comment.