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From: <nl...@us...> - 2008-02-08 01:39:12
|
Revision: 1486
http://obo.svn.sourceforge.net/obo/?rev=1486&view=rev
Author: nlw
Date: 2008-02-07 17:39:16 -0800 (Thu, 07 Feb 2008)
Log Message:
-----------
more website additions
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/developer-docs/index.shtml
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/download.shtml~
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/index.shtml~
Modified: phenote/trunk/doc/phenote-website/developer-docs/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/developer-docs/index.shtml 2008-02-08 01:25:54 UTC (rev 1485)
+++ phenote/trunk/doc/phenote-website/developer-docs/index.shtml 2008-02-08 01:39:16 UTC (rev 1486)
@@ -24,7 +24,8 @@
<li><a href="developer-docs.shtml">Adding new configuration parameters</a>
</li>
</ul>
-
+ </div>
+ </div>
<div id="sidebar_container">
<div id="sidebar_content">
@@ -48,11 +49,11 @@
<a href="" title="Java API docs">
Java API docs
</a>
- </p>
+ </p>
- </div>
+ </div>
- </div>
+ </div>
</div>
<!--#include virtual="../ssi/footer.html" -->
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2008-02-08 01:25:54 UTC (rev 1485)
+++ phenote/trunk/doc/phenote-website/download.shtml 2008-02-08 01:39:16 UTC (rev 1486)
@@ -15,10 +15,10 @@
<div class="catch_phrase">
</div>
<h2>For Users</h2>
- <h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
+ <p><b><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></b></p>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul>
- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5-beta2/phenote.jnlp">1.5 beta2</a></strong></li>-->
+ <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5-beta2/phenote.jnlp">1.5 beta2</a></strong></li>
<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
@@ -36,7 +36,7 @@
</ul>
<h2>Software requirements</h2>
<ul>
- <li> PC running Windows XP; Mac OSX; Linux </li>
+ <li> PC running Windows XP; Mac OSX; Linux; Solaris </li>
<li> Webstart: Internet browser with webstart installed </li>
<li> Command line: Java 1.5 or later; Ant </li>
</ul>
Modified: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-08 01:25:54 UTC (rev 1485)
+++ phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
@@ -25,7 +25,7 @@
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
</p>
<h2>For Developers</h2>
- Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclilpse.shtml">command line or in Eclipse</a>
+ Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclipse.shtml">command line or in Eclipse</a>
<h2>Hardware requirements</h2>
<ul>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-02-08 01:25:54 UTC (rev 1485)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-02-08 01:39:16 UTC (rev 1486)
@@ -102,16 +102,13 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, January 3, 8:30am, Online
+ <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, March 6, 8:30am, Online
</p>
</li>
</ul>
<h3>Meetings/Demos</h3>
<ul class="events">
<li class="events">
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
<!-- (none scheduled at this time)-->
</p>
</li>
@@ -130,9 +127,10 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
+ <p>02.07.2008 - With our upcoming release, Phenote will be known at <b>Phenote+</b></p>
+ <p>02.07.2008 - <b>Developer Articles</b> - A new section was added to this website to store articles for Developers. <a href="developer-docs/">Check it out...</a>. You'll find it under the "Help" menu on this site.</p>
+ <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
<p>12.20.2007 - <b>New Phenote Beta Release - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a></b></p>
- <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
- [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
<!--
<h3>Event Title</h3>
<ul class="events">
Modified: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~ 2008-02-08 01:25:54 UTC (rev 1485)
+++ phenote/trunk/doc/phenote-website/index.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
@@ -111,7 +111,8 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- (none scheduled at this time)
+ <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
+ <!-- (none scheduled at this time)-->
</p>
</li>
</ul>
@@ -129,7 +130,6 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
<p>12.20.2007 - <b>New Phenote Beta Release - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a></b></p>
<p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
[<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-02-08 01:40:04
|
Revision: 1487
http://obo.svn.sourceforge.net/obo/?rev=1487&view=rev
Author: nlw
Date: 2008-02-07 17:40:05 -0800 (Thu, 07 Feb 2008)
Log Message:
-----------
getting rid of stupied ~ files on website
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/about.shtml~
phenote/trunk/doc/phenote-website/contact.shtml~
phenote/trunk/doc/phenote-website/download.shtml~
phenote/trunk/doc/phenote-website/events.shtml~
phenote/trunk/doc/phenote-website/faq.shtml~
phenote/trunk/doc/phenote-website/features.shtml~
phenote/trunk/doc/phenote-website/funding.shtml~
phenote/trunk/doc/phenote-website/help.shtml~
phenote/trunk/doc/phenote-website/index.shtml~
Deleted: phenote/trunk/doc/phenote-website/about.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/about.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/about.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,60 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- About Phenote
- </div>
-
- <p>
- Phenote is both a complete piece of software and a software toolkit designed to facilitate the annotation of biological phenotypes using ontologies. It provides an interface to record genotype-phenotype pairs, together with the provenance for the annotation. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a user-friendly and computable way.
- </p>
- <p>
- Data annotated with Phenote is based on the <a href="http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any ontology with qualities (such as PATO).
- </p>
-
- <h3>
- <a href="contact.shtml">
- Contact us
- </a>
- </h3>
- <p>
- Who to ask for assistance (and to complain to).
- </p>
-
- <h3>
- <a href="related.shtml">
- Related Projects
- </a>
- </h3>
- <p>
- Brief descriptions and links to projects who are relevant
- to Phenote, ontologies, and annotation.
- </p>
-
- <h3>
- <a href="faq.shtml">
- Frequently Asked Questions (FAQs)
- </a>
- </h3>
- <p>
- Common questions about Phenote, ontologies, and annotation,
- along with their answers.
- </p>
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/contact.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/contact.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/contact.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,75 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
-
- <div class="catch_phrase">
- Contact Us
- </div>
- <h1>Email us</h1>
- <p>Software Development:
- <script type="text/javascript">
- obfuscate("berkeleybop.org", "mgibson", "Mark Gibson");
- </script></p>
- <p>Requirements, Analysis, Documentation:
- <script type="text/javascript">
- obfuscate("lbl.gov", "nlwashington", "Nicole Washington");
- </script></p>
- <p>Phenotype EQ model and XML data formats:
- <script type="text/javascript">
- obfuscate("berkeleybop.org", "cjm", "Chris Mungall");
- </script></p>
- <p>General Questions:
- <script type="text/javascript">
- obfuscate("lists.sourceforge.org", "obo-phenote", "Phenote Mailing List");
- </script></p>
- <h1>Mailing lists</h1>
- <p> There are several relevant mailing lists user's and/or developers
- might be interested in joining:</p>
- <p>General phenote discussion and announcements
- [ <script type="text/javascript">
- obfuscate("lists.sourceforge.org", "obo-phenote", "Email");
- </script> ]
- [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Join</a> ]</p>
- <p>Phenote software development
- [ <script type="text/javascript">
- obfuscate("lists.sourceforge.org", "obo-phenote-dev", "Email");
- </script> ]
- [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-dev">Join</a> ]</p>
- <p>Phenotype annotation discussion list
- [ <script type="text/javascript">
- obfuscate("lists.sourceforge.org", "obo-phenotype", "Email");
- </script> ]
- [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenotype">Join</a> ]</p>
- <p>General OBO ontology discussion
- [ <script type="text/javascript">
- obfuscate("lists.sourceforge.org", "obo-discuss", "Email");
- </script> ]
- [ <a href="https://lists.sourceforge.net/lists/listinfo/obo-discuss">Join</a> ]</p>
- <p>General NCBO discussion
- [ <script type="text/javascript">
- obfuscate("lists.stanford.edu", "cbio-everyone", "Email");
- </script> ]</p>
- <h1>Reporting Bugs / Requesting Features</h1>
- <p>If you come across problems during your use of Phenote software,
- or there's a new feature you are dying to have, please use our
- tracker on sourceforge to log your request:
- <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Request Tracker</a></p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/download.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/download.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,85 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container">
- <div id="main_content">
- <div class="catch_phrase">
- </div>
- <h2>For Users</h2>
- <h2><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></h2>
- <p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
- <ul>
- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5-beta2/phenote.jnlp">1.5 beta2</a></strong></li>-->
- <li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
- <li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
- </ul>
- <p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
- </p>
- <h2>For Developers</h2>
- Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclipse.shtml">command line or in Eclipse</a>
-
- <h2>Hardware requirements</h2>
- <ul>
- <li> 400 Mhz processor or faster.</li>
- <li> 500+ MB RAM </li>
- <li> 200 MB free disk space on your computer </li>
- <li> Internet connection (broadband is best). Required for automatic updates of ontologies and some functions. </li>
- </ul>
- <h2>Software requirements</h2>
- <ul>
- <li> PC running Windows XP; Mac OSX; Linux </li>
- <li> Webstart: Internet browser with webstart installed </li>
- <li> Command line: Java 1.5 or later; Ant </li>
- </ul>
-
- </div>
- </div>
-
- <div id="sidebar_container">
-
- <div id="sidebar_content">
-
- <div class="content_box_head_blue">
- Recently added features, version 1.4
- </div>
-
- <div class="content_box_blue">
- <b>feature</b>: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.<br />
- <b>feature</b>: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)<br />
- <b>feature</b>: Error for obo parse failures to info panel <br />
- <b>feature</b>: Delimited tab adapter uses column headings to map to table, rather than ordering <br />
- <b>feature</b>: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase) <br />
- <b>feature</b>: Date created automatically added into data (under the hood) <br />
- <b>feature</b>: If arrow hit with empty input then gets & displays all terms (used to inefficiently pre-load) <br />
- <b>feature</b>: Can sort completion list by ID, needed for zfin stages<br />
- <b>feature</b>: Table preserves user ordering of columns, in addition to column widths.<br />
- <b>feature</b>: Filter search field allows user to narrow down displayed data rows via matching text.<br />
- <b>feature</b>: See actual value in input field when multiple rows are selected and have the same value.<br />
- <b>feature</b>: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)<br />
- <b>feature</b>: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)<br />
- <b>change</b>: Moved test suites in with source to work with eclipse<br />
- <b>change</b>: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded<br />
- <b>change</b>: Phenote now follows standard log4j configuration conventions. Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".<br />
- <b>bugfix</b>: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red<br />
- <b>bugfix</b>: if log conf fails use backup default<br />
- <b>bugfix</b>: Input fields now commit changes with either Return or Tab<br />
- <b>bugfix</b>: Native lib is loaded properly for Mac interface on webstart, allowing traversal of aliases in file dialog, as well as user sidebar items in file dialog<br />
- <b>bugfix</b>: Noncontiguous row selection works now on Mac<br />
-</ul>
- </div>
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/events.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/events.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,106 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- News and Events
- </div>
-
- <h1>Upcoming Events, 2007</h1>
-
- <h2>November</h2>
- <ul>
- <li>Nov 1, Phenote Users Group, Online via WebEx
- </li>
- <li>Nov 4, Talk, <a href="http://meetings.cshl.edu/meetings/info07.shtml">Genome Informatics</a>
- </li>
- <li>Nov 27, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
- </ul>
-
- <h2>December</h2>
- <ul>
- <li>Dec 4, Phenote Users Group, Online
- </li>
- </ul>
-
- <h1>Past News and Events, 2007</h1>
- <h2>October</h2>
- <ul>
- <li>Oct 23-25, <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">Biocurator Meeting</a>, Hayes Mansion, San Jose, CA [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]
- </li>
- <li>Oct 10, New Phenote Release - <a href="http://www.phenote.org/download.shtml">version 1.4</a>
- </li>
- <li>Oct 2, Phenote Users Group, Online via WebEx
- </li>
- </ul>
-
-
- <h2>September</h2>
- <ul>
- <li>Sept 17, - New website rolled out! The website has the same content as the old one, just with a new look-and-feel.</li>
- <li>Sept 4, Phenote Users Group, Online
- </li>
- </ul>
- <h2>August</h2>
- <ul>
- <li>Aug 29, Phenote Demo, <a href="http://darwin.nerc-oxford.ac.uk/gc_wiki/index.php/EnvO_Workshop">Environment Ontology Workshop</a>, Oxford, UK</li>
- <li>Aug 28, new 1.4 beta 3 released [<a href="http://www.phenote.org/downloads.shtml">Release notes</a>...]</li>
- <li>Aug 22-24, Phenote Demo, <a href="http://wiki.modencode.org/index.php/White">K. White group, ModENCODE</a>, Chicago, IL
- </li>
- <li>Apr 16, site visit, <a href="http://www.wormbase.org">Wormbase</a>, Pasadena, CA
- </li>
- <li>Aug 13-15, site visit, <a href="http://www.nbirn.net/research/mouse/index.shtm">BIRN</a>, San Diego, CA
- </li>
- <li>Aug 7, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
- </li>
- </ul>
- <h2>July</h2>
- <ul>
- <li>July 3, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
- </li>
- </ul>
- <h2>June</h2>
- <ul>
- <li>June 6, "Representing Phenotypes in OWL", <a href="http://owled2007.iut-velizy.uvsq.fr">OWL: Experiences and Directions Conference</a> Presentation, Innsbruck, Austria. [<a href="http://owled2007.iut-velizy.uvsq.fr/PapersPDF/paper_40.pdf">PDF</a>]
- </li>
- <li>June 5, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
- </li>
- </ul>
- <h2>May</h2>
- <ul>
- <li>May 1, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
- </li>
- </ul>
- <h2>April</h2>
- <ul>
- <li>Apr 12-13, site visit, <a href="http://www.nbirn.net/research/mouse/index.shtm">BIRN</a>, San Diego, CA
- </li>
- <li>Apr 11-12, site visit, <a href="http://www.wormbase.org">Wormbase</a>, Pasadena, CA
- </li>
- <li>Apr 10, <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote:Agendas_.26_Transcripts">Phenote Users Group</a>, Online
- </li>
- <li>Apr 5, <a href="http://www.bioontology.org/">NCBO</a> Scientific Advisory Board meeting</li>
- </ul>
- <h2>March</h2>
- <ul>
- <li>Mar 28-29, site visit, <a href="http://zfin.org">ZFin</a>, Eugene, OR
- </li>
- </ul>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
-</body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/faq.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/faq.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/faq.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,93 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote: A Phenotype Annotation Tool</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Frequently Asked Questions (FAQ)
- </div>
-
- <h1>General</h1>
- <h3>How do I get started?</h3>
-
- You can lauch Phenote directly from your browser. Simply click on the Launch Phenote 'quick link' from the <a href="http://www.phenote.org/">main page</a> or the <a href="http://www.phenote.org/download.shtml">Downloads</a> page, and it will launch directly from your browser. It will take a couple of minutes to download all the components, but that's it.
- </p>
- <h3>What's the best forum to ask my burning questions?</h3>
- <p>
- There's several discussion groups that are relevant to Phenote users. You'll find a list on our <a href="http://www.phenote.org/contact.shmtl">Contact</a> page.
- </p>
- <h3>I found a bug in Phenote. How do I report errors?</h3>
- <p>
- We want to know if there's any errors. Please use our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Bug Report tracker</a>.
- </p>
- <h3>There's a function/feature I wish Phenote had. Can you add it?</h3>
- <p>
- You can request new features through our <a href="http://www.sourceforge.net/tracker/?group_id=76834&atid=887913">Feature Request tracker</a>. Please be sure to label the "Group" as a "new feature".
- </p>
- <h1>Ontologies</h1>
- <h3>What kinds of ontologies can I use?</h3>
- <p>
- You can use any kind of domain specific ontologies. While Phenote is a tool being developed for annotation of biological phenotypes, it can certainly be adapted to any domain whose knowledge is captured with ontologies.
- </p>
- <h3>Can I use OBO and/or OWL format ontologies?</h3>
- <p>
- Yes! However, there's a little catch. You will need to convert your OWL ontology to OBO format first. In the future, we plan to include a feature to convert on-the-fly.
- </p>
- <h3>How can I convert my OWL ontology to OBO format?</h3>
- <p>
- There's an online tool to help with this conversion: <a href="http://www.berkeleybop.org/obo-conv.cgi">OWL-OBO converter</a>
- </p>
- <h3>Can I use my own ontologies?</h3>
- <p>
- Yes you can! You don't have to use ontologies that are in public repositories if you don't want to. Please consult the <a href="http://www.phenote.org/help/">User Guide</a> for more detailed instructions...
- </p>
- <h3>Can I use my own pre-coordinated phenotype ontology?</h3>
- <p>
- Yes! Phenote is a generic tool that allows you to use any kind of ontology. Its simplicity allows the user to mix and match different kinds of annotations from different kinds of ontologies. So, you might use your pre-coordinated phenotype ontology for one kind of statement, and then combine a different entity+quality ontology for another statement.
- </p>
- <h3>What's the difference between using a pre-coordinated phenotype ontology, and E+Q statements?</h3>
- <p>
- </p>
- <h3>Is there one place I can go to browse through all the available ontologies?</h3>
- <p>
- Yep! There are several online resources that can help you learn more. Some of these include:</p>
- <ul>
- <li><a href="http://www.bioontology.org/">National Center for Biomedical Ontology</a></li>
- <li><a href="http://www.obofoundry.org/">OBO Foundry</a></li>
- </ul>
- <h1>Using Phenote</h1>
- <h3>Is there some online documentation?</h3>
- <p>
- You bet! Check out our <a href="http://www.phenote.org/help/">User's Guide</a></p>
- <h3>When I'm annotating, I can't seem to find the right terms?</h3>
- <p>
- Sometimes a term you are looking for is really just a synonym of another term. Make sure you have "synonyms" selected under the "Settings" menu. </p>
- <p>If you still can't find it, it might be that the ontology is really missing a term. Ontologies, while extensive, are never complete, and are under active development. There are usually online term request resources for each ontology. You will need to contact each ontology resource separately. </p>
- <h3>Can I output my data in RDF-OWL?</h3>
- <p>
- Not yet, but that feature is coming soon.
- </p>
- <h3>Are there any tools that allow me to analyze my annotations?</h3>
- <p> Presently Phenote does not include any analysis tools. However,
- <a href="http://www.bioontology.org/wiki/index.php/OBD:Main_Page">tools</a>
- are being developed within the NCBO that will allow
- for data warehousing, querying, and analysis. Our hope is to have
- them integrated in Phenote whenever possible. Please stay tuned
- for future updates and take a look at our <a href="roadmap.shtml">
- roadmap</a> to find out more.</p>
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/features.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/features.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/features.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,75 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container">
- <div id="main_content">
- <div class="catch_phrase">
- Phenote Features
- </div>
- <ul>
- <li>Friendly spreadsheet-like interface
- </li>
- <li>Type-ahead-suggest (autocompletion) for terms within ontologies
- </li>
- <li>Use of any OBO-format ontology
- </li>
- <li>Ontology navigation and term information display
- </li>
- <li>Bulk copy/edit/delete/sort of phenotype-genotype character entries
- </li>
- <li>Excel-compatible output format (tab-delimited)
- </li>
- <li>Additional export formats: phenosyntax, xml
- </li>
- <li>configurable input fields to allow custom data entry and user-specified ontologies
- </li>
- <li>Preconfigurations available for different communities
- </li>
- <li>Customized configurations easily added
- </li>
- </ul>
- </div>
- </div>
-
- <div id="sidebar_container">
-
- <div id="sidebar_content">
-
- <div class="content_box_head_blue">
- Quick Links
- </div>
-
- <div class="content_box_blue">
-
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/phenote.jnlp"
- title="Lauch Phenote via Webstart">
- Launch Phenote v1.4-beta3 via Webstart
- </a>
- </p>
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://obo.svn.sourceforge.net/viewvc/obo/phenote/" title="Browse Repository"> Browse Repository
- </a>
- </p>
-
- </div>
-
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/funding.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/funding.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/funding.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,53 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Phenote Funding and Support
- </div>
- <p>Phenote is being developed by the <a href="http://www.berkeleybop.org/">
- Bioinformatics Core</a> of the <a href="http://www.bioontology.org/">
- National Center for Biomedical Ontology</a>, which is part of the
- <a href="http://www.bisti.nih.gov/ncbc/index.cfm">
- National Center for Biomedical Computing</a> network.
- Funding is given by the <a href="http://nihroadmap.nih.gov/">NIH Roadmap</a> initiative. </p>
-
- <p> There are three funded groups driving the development of this
- software project through the NCBO:</p>
-
- <table border="0">
- <tr>
- <td><a href="http://flybase.bio.indiana.edu/">
- <img class="portrait" height="50" border="0" src="/images/fly_logo.png"alt="Flybase" /></a>
- </td>
- <td><p><strong>Flybase: The Drosophila Genome Database</strong>[<a href="http://www.bioontology.org/dbp_drosophila.html">...</a>]</p></td>
- </tr>
- <tr>
- <td><a href="http://www.zfin.org/"><img class="portrait" border="0" src="/images/zfin_logo.gif" height="50" alt="Zfin" /></a>
- </td>
- <td><p><strong>Zfin: Zebrafish Information Network</strong> [<a href="http://www.bioontology.org/dbp_zfin.html">...</a>]</p></td>
- </tr>
- <td><a href="http://www.nbirn.net/research/mouse/index.shtm">
- <img class="portrait" height="50" border="0" src="/images/BIRN_logo.gif"alt="BIRN" /></a>
- </td>
- <td><p><strong>mouseBIRN: mouse Biomedical Informatics Research Network</strong></p></td>
- </tr>
- </table>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/help.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/help.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/help.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,33 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
-
- <div class="catch_phrase">
- Getting Help with Phenote
- </div>
- <h2><a href="http://www.phenote.org/faq.shtml/">Frequently Asked Questions (FAQs)</a></h2>
- <p>A resource for some basic questions and those we are most frequently asked</p>
- <h2><a href="http://www.phenote.org/help/">Online Help</a></h2>
- <p>We provide a searchable online help tool to help answer your questions. This is the same help content provided in the software.</p>
- <h2><a href="http://www.phenote.org/contact.shtml">Contact Us</a></h2>
- <p>We are here to help you whenever you might need it. You can contact
- us directly or pose your questions to our user community with the links provided here.
- </p>
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/index.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml~ 2008-02-08 01:39:16 UTC (rev 1486)
+++ phenote/trunk/doc/phenote-website/index.shtml~ 2008-02-08 01:40:05 UTC (rev 1487)
@@ -1,154 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container">
- <div id="main_content">
- <div class="catch_phrase">
- Welcome to Phenote
- </div>
- <p>
- Phenote is both a complete piece of software and a software toolkit designed to facilitate the <b>annotation of biological phenotypes using ontologies</b>. It provides an interface and infrastructure to record genotype-phenotype pairs, together with the provenance for the annotation. Typical users of Phenote include literature curators, laboratory researchers, and clinicians looking for a method to record data in a <b>user-friendly</b> and <b>computable</b> way.
- </p>
- <p>
- Data annotated with Phenote is based on the <a href="http://www.fruitfly.org/~cjm/obd/formats.html">EQ model</a> for representing phenotypes, combining entities from any ontology with qualities (such as PATO).
- </p>
- <h2>Features include:</h2>
- <ul>
- <li>Friendly spreadsheet-like interface
- </li>
- <li>Type-ahead-suggest (autocompletion) for terms within ontologies
- </li>
- <li>Use of any OBO-format ontology (or OWL->OBO converted)
- </li>
- <li>Ontology navigation and all-in-one term information display
- </li>
- <li>Bulk copy/edit/delete/sort of phenotype-genotype character entries
- </li>
- <li>Excel-compatible output format (tab-delimited)
- </li>
- <li>Additional export formats: phenosyntax, xml
- </li>
- <li>configurable input fields to allow custom data entry and user-specified ontologies
- </li>
- <li>Preconfigurations available for different communities
- </li>
- <li>Customized configurations easily added
- </li>
- </ul>
-
- </div>
- </div>
-
- <div id="sidebar_container">
-
- <div id="sidebar_content">
-
- <div class="content_box_head_blue">
- Frequently Used Links
- </div>
-
- <div class="content_box_blue">
-
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp"
- title="Lauch Phenote via Webstart">
- Launch Phenote via Webstart
- </a>
- </p>
-
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <a href="faq.shtml" title="Frequently asked questions">
- Frequently asked questions (FAQ)
- </a>
- </p>
-
- </div>
-
- <div class="content_box_head_green">
- <img src="images/calendar.gif"
- alt="Upcoming Events"
- class="icon_blue"/>
- <a href="events.shtml">Upcoming Events</a>
- </div>
-
- <div class="content_box_green">
-
- <!-- Comment this out instead of erasing it. -->
- <!--There are no upcoming events at this time.-->
-
- <!-- Do not destry the following event template -->
-<!-- <ul class="events">
- <li class="events">
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <a href="link">Event</a>, Date, Location
- </p>
- </li>
- </ul>
- -->
- <h3>Phenote User's Group</h3>
- <ul class="events">
- <li class="events">
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, January 3, 8:30am, Online
- </p>
- </li>
- </ul>
- <h3>Meetings/Demos</h3>
- <ul class="events">
- <li class="events">
- <p class="quick_link">
- <img src="images/star.gif" alt="" class="icon_green"/>
- <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
- <!-- (none scheduled at this time)-->
- </p>
- </li>
- </ul>
- <!--h3><a href="http://www.phenote.org/events.shtml">Past Events...</a></h3-->
- </div>
-
- <div class="content_box_head_green">
- <img src="images/document.gif" alt="News" class="icon_blue" />
- <a href="events.shtml">News</a>
- </div>
-
- <div class="content_box_green">
-
- <!-- Comment this out instead of erasing it. -->
- <!--No news is good news!-->
-
- <!-- Do not destry the following event template -->
- <p>12.20.2007 - <b>New Phenote Beta Release - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a></b></p>
- <p>10.23-25.2007 - <a href="http://www.cs.uoregon.edu/~dhowe/biocurator/">BioCurator meeting</a>, San Jose, CA
- [<a href="http://www.phenote.org/resources/Biocurator_2007.ppt">Download presentation</a>]</p>
- <!--
- <h3>Event Title</h3>
- <ul class="events">
- <li class="events">
-
- Event Information
-
- </li>
- </ul>
- -->
-
- </div>
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-02-08 01:49:27
|
Revision: 1488
http://obo.svn.sourceforge.net/obo/?rev=1488&view=rev
Author: nlw
Date: 2008-02-07 17:49:31 -0800 (Thu, 07 Feb 2008)
Log Message:
-----------
more website
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/events.shtml
phenote/trunk/doc/phenote-website/index.shtml
Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml 2008-02-08 01:40:05 UTC (rev 1487)
+++ phenote/trunk/doc/phenote-website/events.shtml 2008-02-08 01:49:31 UTC (rev 1488)
@@ -16,21 +16,23 @@
News and Events
</div>
- <h1>Upcoming Events, 2007</h1>
-
- <h2>December</h2>
+ <h1>Upcoming Events, 2008</h1>
+ <h2>February</h2>
<ul>
- <li>Dec 6, Phenote Users Group, Online
- </li>
+ <li>Major release scheduled with new dockable components</li>
</ul>
-
- <h1>2008</h1>
- <h2>January</h2>
+ <h1>Past News and Events</h1>
+ <h2>January, 2008</h2>
<ul>
- <li>Major release scheduled</li>
+ <li>January 10, Seminar, <a href="http://www.nescent.org/">NESCent</a>, Duke University, NC</li>
+ <li>January 3, Phenote Users Group, Online
+ </li>
</ul>
-
- <h1>Past News and Events, 2007</h1>
+ <h2>December, 2007</h2>
+ <li>Dec 20, New Phenote Beta - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a>
+ </li>
+ <li>Dec 6, Phenote Users Group, Online
+ </li>
<h2>November</h2>
<ul>
<li>Nov 1, Phenote Users Group, Online via WebEx
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-02-08 01:40:05 UTC (rev 1487)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-02-08 01:49:31 UTC (rev 1488)
@@ -109,8 +109,7 @@
<h3>Meetings/Demos</h3>
<ul class="events">
<li class="events">
- <!-- (none scheduled at this time)-->
- </p>
+ <p>(none scheduled at this time)</p>
</li>
</ul>
<!--h3><a href="http://www.phenote.org/events.shtml">Past Events...</a></h3-->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2008-02-13 22:14:24
|
Revision: 1501
http://obo.svn.sourceforge.net/obo/?rev=1501&view=rev
Author: mgibson
Date: 2008-02-13 14:14:14 -0800 (Wed, 13 Feb 2008)
Log Message:
-----------
phenote plus webstart
release 1.5 webstart to try out
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote.html
Added Paths:
-----------
phenote/trunk/doc/phenote-website/phenote-plus.jnlp
Added: phenote/trunk/doc/phenote-website/phenote-plus.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-plus.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-13 22:14:14 UTC (rev 1501)
@@ -0,0 +1,69 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://phenote.org/phenote/@@phenote.version@@"
+href="phenote.jnlp">
+<information>
+ <title>Phenote @@phenote.version@@</title>
+ <vendor>National Center for Biomedical Ontology</vendor>
+ <icon href="/images/elephant_icon.jpg" />
+ <description>Phenote standalone app via webstart</description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="600m" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/obo.jar" />
+ <jar href="jars/bbop.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
+ <jar href="jars/jh.jar" />
+ <jar href="jars/jetty-6.1.4.jar" />
+ <jar href="jars/jetty-util-6.1.4.jar" />
+ <jar href="jars/swixml.jar" />
+ <jar href="jars/jdom.jar" />
+ <jar href="jars/quaqua.jar" />
+ <jar href="jars/jebl-0.4.jar" />
+ <jar href="jars/glazedlists-1.7.0_java15.jar" />
+ <jar href="jars/swing-layout.jar"/>
+ <jar href="jars/swingx-2007_10_14.jar"/>
+ <nativelib href="jars/phenote-nativelibs.jar"/>
+
+ <!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
+ commons-lang, eutils,jaxrpc, jdom, jebl, jhindexer, jlfgr, jnlp, jsp, jsr
+ jst, junit, jwf, layouts, libquaqua, macify? -->
+ <!-- jars needed for phenote2 but not phenote1? idw-gpl, commons*? -->
+
+
+
+ <property name="phenote.version" value="@@phenote.version@@"/>
+ <property name="phenote.build" value="@@phenote.build@@"/>
+</resources>
+<!-- no cmd line param will ask user for config at initialization -->
+<application-desc main-class="phenote.main.Phenote2">
+</application-desc>
+</jnlp>
+
+
+
Modified: phenote/trunk/doc/phenote-website/phenote.html
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.html 2008-02-13 16:20:05 UTC (rev 1500)
+++ phenote/trunk/doc/phenote-website/phenote.html 2008-02-13 22:14:14 UTC (rev 1501)
@@ -19,7 +19,7 @@
ontologies. It uses term completion to allow curators quick access to
the ontology terms they want to use. <br>
-<br><a href="1.5-beta4/phenote.jnlp">Phenote 1.5-beta4</a><br><a href="1.5-beta3/phenote.jnlp">Phenote 1.5-beta3</a><br><a href="1.5-beta2/phenote.jnlp">Phenote 1.5-beta2</a><br>
+<br><a href="1.5/phenote.jnlp">Phenote 1.5</a><br><a href="1.5/phenote-plus.jnlp">Phenote+ 1.5</a><br><br><br><a href="1.5-beta4/phenote.jnlp">Phenote 1.5-beta4</a><br><a href="1.5-beta3/phenote.jnlp">Phenote 1.5-beta3</a><br><a href="1.5-beta2/phenote.jnlp">Phenote 1.5-beta2</a><br>
<br>
<br>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2008-02-14 20:45:04
|
Revision: 1512
http://obo.svn.sourceforge.net/obo/?rev=1512&view=rev
Author: mgibson
Date: 2008-02-14 12:45:02 -0800 (Thu, 14 Feb 2008)
Log Message:
-----------
eutils needed for both
its the soap for ncbi
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-plus.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-plus.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-14 20:03:59 UTC (rev 1511)
+++ phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-14 20:45:02 UTC (rev 1512)
@@ -48,12 +48,12 @@
<jar href="jars/glazedlists-1.7.0_java15.jar" />
<jar href="jars/swing-layout.jar"/>
<jar href="jars/swingx-2007_10_14.jar"/>
+ <jar href="jars/eutils.jar"/>
- <!-- for phenote+ 2 only -->
+ <!-- for phenote+ (formerly phenote2) only -->
<jar href="jars/macify-1.1.jar"/>
<jar href="jars/tablelayout.jar"/>
<jar href="jars/idw-gpl.jar"/>
- <jar href="jars/eutils.jar"/>
<jar href="jars/jaxrpc.jar"/>
<jar href="jars/axis.jar"/>
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-14 20:03:59 UTC (rev 1511)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-14 20:45:02 UTC (rev 1512)
@@ -48,6 +48,7 @@
<jar href="jars/glazedlists-1.7.0_java15.jar" />
<jar href="jars/swing-layout.jar"/>
<jar href="jars/swingx-2007_10_14.jar"/>
+ <jar href="jars/eutils.jar"/>
<nativelib href="jars/phenote-nativelibs.jar"/>
<!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
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|
|
From: <nl...@us...> - 2008-02-19 18:40:58
|
Revision: 1529
http://obo.svn.sourceforge.net/obo/?rev=1529&view=rev
Author: nlw
Date: 2008-02-19 10:40:39 -0800 (Tue, 19 Feb 2008)
Log Message:
-----------
added links to the javadocs
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/developer-docs/index.shtml
phenote/trunk/doc/phenote-website/index.shtml
Modified: phenote/trunk/doc/phenote-website/developer-docs/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/developer-docs/index.shtml 2008-02-19 18:28:43 UTC (rev 1528)
+++ phenote/trunk/doc/phenote-website/developer-docs/index.shtml 2008-02-19 18:40:39 UTC (rev 1529)
@@ -13,12 +13,13 @@
<div id="main_container">
<div id="main_content">
<div class="catch_phrase">
- Welcome to the Phenote Developer Documentation Resource Page
+ Phenote Developer Documentation Resource Page
</div>
<p>This page is your starting point if you are a developer on the Phenote project. Some interesting articles can be found below:</p>
<ul>
<li><a href="getting-source-code-in-eclipse.shtml">Getting the Source code</a> (command line or in Eclipse)
</li>
+ <li><a href-"http://www.phenote.org/doc/api/">Browse the API Javadocs</a></li>
<li><a href="dataadapter.shtml">Working with Data Adapters</a>
</li>
<li><a href="developer-docs.shtml">Adding new configuration parameters</a>
@@ -46,7 +47,7 @@
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="" title="Java API docs">
+ <a href="http://www.phenote.org/doc/api/" title="Java API docs">
Java API docs
</a>
</p>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-02-19 18:28:43 UTC (rev 1528)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-02-19 18:40:39 UTC (rev 1529)
@@ -126,6 +126,7 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
+ <p>02.19.2008 - <a href="/doc/api">API documentation</a> added to website</p>
<p>02.07.2008 - With our upcoming release, Phenote will be known at <b>Phenote+</b></p>
<p>02.07.2008 - <b>Developer Articles</b> - A new section was added to this website to store articles for Developers. <a href="developer-docs/">Check it out...</a>. You'll find it under the "Help" menu on this site.</p>
<p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
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|
|
From: <nl...@us...> - 2008-02-20 18:25:08
|
Revision: 1539
http://obo.svn.sourceforge.net/obo/?rev=1539&view=rev
Author: nlw
Date: 2008-02-20 10:25:10 -0800 (Wed, 20 Feb 2008)
Log Message:
-----------
adding more jars to jnlps
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-plus.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-plus.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-20 18:03:17 UTC (rev 1538)
+++ phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-20 18:25:10 UTC (rev 1539)
@@ -49,6 +49,9 @@
<jar href="jars/swing-layout.jar"/>
<jar href="jars/swingx-2007_10_14.jar"/>
<jar href="jars/eutils.jar"/>
+ <jar href="jars/commons-discovery-0.2.jar"/>
+ <jar href="jars/commons-lang-2.1.jar"/>
+ <jar href="jars/commons-beanutils-1.6.jar"/>
<jar href="jars/commons-logging-1.0.4.jar"/>
<!-- for phenote+ (formerly phenote2) only -->
<jar href="jars/macify-1.1.jar"/>
@@ -56,7 +59,11 @@
<jar href="jars/idw-gpl.jar"/>
<jar href="jars/jaxrpc.jar"/>
<jar href="jars/axis.jar"/>
+ <jar href="jars/ProtocolEditor.jar"/>
+ <jar href="jars/ols-client.jar"/>
+
+
<nativelib href="jars/phenote-nativelibs.jar"/>
<!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-20 18:03:17 UTC (rev 1538)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-20 18:25:10 UTC (rev 1539)
@@ -49,6 +49,9 @@
<jar href="jars/swing-layout.jar"/>
<jar href="jars/swingx-2007_10_14.jar"/>
<jar href="jars/eutils.jar"/>
+ <jar href="jars/commons-discovery-0.2.jar"/>
+ <jar href="jars/commons-lang-2.1.jar"/>
+ <jar href="jars/commons-beanutils-1.6.jar"/>
<jar href="jars/commons-logging-1.0.4.jar"/>
<nativelib href="jars/phenote-nativelibs.jar"/>
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|
|
From: <nl...@us...> - 2008-02-20 18:32:48
|
Revision: 1540
http://obo.svn.sourceforge.net/obo/?rev=1540&view=rev
Author: nlw
Date: 2008-02-20 10:32:52 -0800 (Wed, 20 Feb 2008)
Log Message:
-----------
adding more jars to jnlps
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-plus.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-plus.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-20 18:25:10 UTC (rev 1539)
+++ phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-20 18:32:52 UTC (rev 1540)
@@ -53,6 +53,8 @@
<jar href="jars/commons-lang-2.1.jar"/>
<jar href="jars/commons-beanutils-1.6.jar"/>
<jar href="jars/commons-logging-1.0.4.jar"/>
+ <jar href="jars/saaj.jar"/>
+ <jar href="jars/jaxrpc.jar"/>
<!-- for phenote+ (formerly phenote2) only -->
<jar href="jars/macify-1.1.jar"/>
<jar href="jars/tablelayout.jar"/>
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-20 18:25:10 UTC (rev 1539)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-20 18:32:52 UTC (rev 1540)
@@ -54,6 +54,8 @@
<jar href="jars/commons-beanutils-1.6.jar"/>
<jar href="jars/commons-logging-1.0.4.jar"/>
<nativelib href="jars/phenote-nativelibs.jar"/>
+ <jar href="jars/saaj.jar"/>
+ <jar href="jars/jaxrpc.jar"/>
<!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
commons-lang, eutils,jaxrpc, jdom, jebl, jhindexer, jlfgr, jnlp, jsp, jsr
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-02-20 19:05:17
|
Revision: 1541
http://obo.svn.sourceforge.net/obo/?rev=1541&view=rev
Author: nlw
Date: 2008-02-20 11:05:20 -0800 (Wed, 20 Feb 2008)
Log Message:
-----------
fixing phenote.jnlp - addin another jar
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-plus.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-plus.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-20 18:32:52 UTC (rev 1540)
+++ phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-02-20 19:05:20 UTC (rev 1541)
@@ -63,6 +63,7 @@
<jar href="jars/axis.jar"/>
<jar href="jars/ProtocolEditor.jar"/>
<jar href="jars/ols-client.jar"/>
+ <jar href="jars/wsdl4j-1.5.1.jar"/>
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-20 18:32:52 UTC (rev 1540)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2008-02-20 19:05:20 UTC (rev 1541)
@@ -56,6 +56,7 @@
<nativelib href="jars/phenote-nativelibs.jar"/>
<jar href="jars/saaj.jar"/>
<jar href="jars/jaxrpc.jar"/>
+ <jar href="jars/wsdl4j-1.5.1.jar"/>
<!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
commons-lang, eutils,jaxrpc, jdom, jebl, jhindexer, jlfgr, jnlp, jsp, jsr
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|
|
From: <no...@us...> - 2008-02-20 21:13:33
|
Revision: 1544
http://obo.svn.sourceforge.net/obo/?rev=1544&view=rev
Author: nomi
Date: 2008-02-20 13:12:40 -0800 (Wed, 20 Feb 2008)
Log Message:
-----------
I'm sure these were committed by accident--I just happened to notice them.
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/related.shtml~
phenote/trunk/doc/phenote-website/release-notes.shtml~
phenote/trunk/doc/phenote-website/resources.shtml~
phenote/trunk/doc/phenote-website/screenshots.shtml~
phenote/trunk/doc/phenote-website/team.shtml~
phenote/trunk/doc/phenote-website/users.shtml~
Deleted: phenote/trunk/doc/phenote-website/related.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/related.shtml~ 2008-02-20 20:24:24 UTC (rev 1543)
+++ phenote/trunk/doc/phenote-website/related.shtml~ 2008-02-20 21:12:40 UTC (rev 1544)
@@ -1,173 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Related Projects
- </div>
- <h1>Ontologies</h1>
- <h2>
- <a href="http://www.bioontology.org/wiki/index.php/PATO:Main_Page">
- Phenotype and Trait Ontology (PATO)</a>
- </h2>
- <p>
- An ontology of phenotypic qualities (properties). This ontology
- can be used in conjunction with other ontologies such as GO or
- anatomical ontologies to refer to phenotypes. Examples of
- qualities are red, ectopic, high temperature, fused, small,
- edematous and arrested.
- </p>
- <h2>
- <a href="http://www.geneontology.org/">
- Gene Ontology (GO)</a>
- </h2>
- <p>
- The Gene Ontology (GO) project is a collaborative effort to address
- the need for consistent descriptions of gene products in different
- databases.
- The Gene Ontology project provides a controlled vocabulary to
- describe gene and gene product attributes in any organism. There
- are three distinct ontologies developed by GO: molecular function,
- biological process, and cellular component.
- <h2>
- <a href="http://obi.sourceforge.net/">
- Ontologies for Biomedical Investigations
- </a>
- </h2>
- <p>
- The Ontology for Biomedical Investigations (OBI) project is
- developing an integrated ontology for the description of
- biological and medical experiments and investigations. This
- ontology will support the consistent annotation of
- biomedical investigations, regardless of the particular
- field of study.
- </p>
-
-
- <h1>Resources</h1>
- <h2>
- <a href="http://www.bioontology.org/">
- National Center for Biomedical Ontology</a>
- </h2>
- <p>
- The NCBO is a consortium of leading biologists, clinicians,
- informaticians, and ontologists who develop innovative technology
- and methods that allow scientists to create, disseminate, and
- manage biomedical information and knowledge in machine-processable
- form.
- </p>
- <h2>
- <a href="http://www.obofoundry.org/">
- OBO Foundry</a>
- </h2>
- <p>
- The OBO Foundry is an open, inclusive, and collaborative core of
- interoperable ontologies developed by the research community. The
- goal is to facilitate the creation of consistent, compatible, and
- unambiguous ontologies thereby supporting the biomedical research
- community. The contributors are those biological researchers and
- ontology developers who have agreed to work together on an evolving
- set of design principles that can foster interoperability of
- ontologies, and ensure a gradual improvement of quality and formal
- rigor in ontologies, in ways designed to meet the increasing needs
- of data and information integration in the biomedical domain.
-
- </p>
- <h2>
- <a href="http://www.gmod.org/">
- Generic Model Organism Databases</a>
- </h2>
- <p>
- The Generic Model Organism Project (GMOD) is a joint effort
- by the model organism system databases WormBase, FlyBase,
- MGI, SGD, Gramene, Rat Genome Database, EcoCyc, and TAIR to
- develop reusable components suitable for creating new
- community databases of biology.
- </p>
-
- <h2>
- <a href="http://ifomis.org">
- Institute for Formal Ontology and Medical Information
- Science (IFOMIS)
- </a>
- </h2>
- <p>
- The Institute for Formal Ontology and Medical Information
- Science (IFOMIS) comprehends an interdisciplinary research
- group with members from Philosophy, Computer and Information
- Science, Logic, Medicine, and Medical Informatics, focusing
- on theoretically grounded research in both formal and
- applied ontology.
- </p>
-
- <h2>
- <a href="http://mged.sf.net/">
- MGED
- </a>
- </h2>
- <p>
- The Microarray Gene Expression Data (MGED) Society is an
- international organisation of biologists, computer
- scientists, and data analysts that aims to facilitate the
- sharing of microarray data generated by functional genomics
- and proteomics experiments.
- </p>
-
- <h2>
- <a href="http://www.ebi.ac.uk/ontology-lookup/">
- Ontology Lookup Service
- </a>
- </h2>
- <p>
- The Ontology Lookup Service is a spin-off of the PRIDE
- project, which required a centralized query interface for
- ontology and controlled vocabulary lookup. While many of the
- ontologies queriable by the OLS are available online, each
- has its own query interface and output format. The OLS
- provides a web service interface to query multiple
- ontologies from a single location with a unified output
- format.
- </p>
-
- <h2>
- <a href="http://www.plantontology.org/">
- Plant Ontology Consortium
- </a>
- </h2>
- <p>
- The Plant Ontology Consortium (POC) aims to develop, curate
- and share structured controlled vocabularies (ontologies)
- that describe plant structures and growth/developmental
- stages. Through this effort, the project aims to facilitate
- cross database querying by fostering consistent use of these
- vocabularies in the annotation of tissue and/or growth stage
- specific expression of genes, proteins and phenotypes.
- </p>
-
- <h2>
- <a href="http://www.psidev.info/index.php?q=node/258">
- Proteomics Standards Initiative
- </a>
- </h2>
- <p>
- Is also interested in guidelines for the development of
- Controlled Vocabularies.
- </p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/release-notes.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/release-notes.shtml~ 2008-02-20 20:24:24 UTC (rev 1543)
+++ phenote/trunk/doc/phenote-website/release-notes.shtml~ 2008-02-20 21:12:40 UTC (rev 1544)
@@ -1,579 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote: A Phenotype Annotation Tool using Ontologies</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container">
- <div id="main_content">
- <div class="catch_phrase">
- Phenote Release Notes
- </div>
-
- <h1>1.4 </h1>
- <h2>08.28.2007, version <a href="phenote/1.4-beta3/phenote.jnlp">1.4-beta3</a></h2>
- <ul>
- <li>feature: Native look-and-feel enabled for interface. Users should now see Mac or Windows style depending on their system.</li>
- <li>feature: read-only field (needs work)</li>
- <li>feature: config disabling of copy of field (for db ids)</li>
- <li>feature: display property values of terms in term info</li>
- <li>feature: Phylogeny Chooser for NESCent/PhenoMap project. A user can import a phylogenetic tree in Newick format. The user can use the tree
- viewer to select rows within the character template - typically taxonomic groups.</li>
- <li>feature: term fields can be nullified</li>
- <li>feature: separate queries to backend for different groups, implemented in worm</li>
- <li>feature: ID field type, requires ":"</li>
- <li>feature: can get unique list of deleted annots</li>
- <li>feature: added group adapter framework</li>
- <li>feature: fly genotype group adapter makes fly genotype strings from tab/group</li>
- <li>feature: worm group adapter makes reference terms from ref query</li>
- <li>change: on term completion if adding a letter use previous completion list</li>
- <li>change: worm adapter query tab working properly</li>
- <li>change: build file takes param for webstart version deployment, and puts in jnlp</li>
- <li>change: group adapters can listen for CharList changes</li>
- <li>change: added/corrected birn ontologies</li>
- <li>bugfix: load of file doesnt crash on post comp parsing bug</li>
- <li>bugfix: doesnt load obo files specified twice twice</li>
- <li>bugfix: view menu show up at initialization</li>
- <li>bugfix: layout of term history with split pane proper</li>
-</ul>
-
-<h2>07.20.2007, version <a href="phenote/1.4-beta2/phenote.jnlp">1.4-beta2</a></h2>
-
-<ul>
-
- <li>feature: RESTful data input for BIRN's smart atlas</li>
-
- <li>feature: Character Template for NESCent/CToL (Jim Balhoff). This
-is an additional window which edits a separate list of characters using
-a subset of the fields in the main window. The fields to include are
-denoted by a group in the config file. This functionality will be used
-by the PhenoMap project to create a specimen list. The same EQ
-statement can be applied to many specimens at once by selecting the
-relevant specimens and generating characters in the main window with
-the template fields pre-filled. All the new characters are selected and
-can then be bulk edited.</li>
-
- <li>feature: Progress on gui for config (in progress)</li>
-
- <li>feature: Progress on field groups (genotype maker, pub querying...)</li>
-
- <li>feature: right-click editing functions for free-text fields in data input frame. right-click copy in table.</li>
-
- <li>feature: incorporation of help documentation into Phenote under menu item Help->PhenoteHelp </li>
-
- <li>feature: added plant_grammene.cfg configuration, plus appropriate obo files.</li>
-
- <li>feature: navigation bar added to top of term info; buttons to traverse worn paths; term name moved up to top of box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1685540&group_id=76834&atid=887913">1685540</a>]</li>
-
- <li>feature: dbxrefs are listed in term info (no external links yet) [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1739399&group_id=76834&atid=887913">1739399</a>]</li>
-
- <li>change: ontology files can be read with dangling references</li>
-
- <li>change: Command line read & write of .tab</li>
-
- <li>change: 'use term' button moved and replaced with checkmark button in navigation bar</li>
-
- <li>change: ncbo.cfg changed to always update from master file at url</li>
-
- <li>change: birn2.cfg gene_ontology replaced with gene_ontology_edit.obo reference</li>
-
- <li>change: Windows splash screen text edited from 'biomedial' to 'biomedical'</li>
-
- <li>bugfix: obsolete terms were not being read in from annotation files as Ontology.getTerm was only looking at non obsoleted terms</li>
-
- <li>known bug: ontology files using import statements not properly read</li>
-
-</ul>
-
-
-<h2>version 1.4-beta1 - oops - skipped!</h2>
-
-
-
-<h1>1.3</h1>
-
-
-<h2>05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a></h2>
-
-<ul>
-
- <li>feature: <a href="http://www.phenote.org/help/">Web-based documentation and Help features.</a></li>
-
- <li>feature: Metadata fields added to configuration. User can name their configuration, add a description, and author [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1676756&group_id=76834&atid=887913">1676756</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1672080&group_id=76834&atid=887913">1672080</a>]</li>
-
- <li>feature: Descriptions can be added for fields </li>
-
- <li>feature: Master-to-local overwrite stuff</li>
-
- <li>feature: Dialog allows user to back out of exiting from File->Exit</li>
-
- <li>feature: Autocompletion search default settings configurable <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1677411&group_id=76834&atid=887913">1677411</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1669579&group_id=76834&atid=887913">1669579</a>]
- </li>
-
- <li>feature: User can save search setting defaults if changed during Phenote session</li>
-
- <li>change: File->New is disabled until next version</li>
-
- <li>change: ncbo, zfin-standalone, flybase, demo configurations
-modified to include master-overwrite feature; keeping track of revision
-history in file comments </li>
-
- <li>change: can read http, https, ftp, ftps for ontology update URLs, not just http [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1718945&group_id=76834&atid=887913">1718945</a>]</li>
-
- <li>bugfix: Bulk-editing functions are working again</li>
-
- <li>bugfix: Undo wasn't working for several functions due to a bug in the Copy function [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721044&group_id=76834&atid=887913"> 1721044</a>]</li>
-
- <li>bugfix: multi-select deletes free-text content replaces with * [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721032&group_id=76834&atid=887913">1721032</a>]</li>
-
- <li>bugfix: pre 1.2 post comp data wasnt able to load<big> </big>[<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1721470&group_id=76834&atid=887913">1721470</a>]</li>
-
-</ul>
-
-
-
-
-<h2>05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a></h2>
-
-
-
-<ul>
-
- <li>feature: Added sample config for BIRN</li>
-
- <li>feature: Added SAO.obo ontology for BIRN</li>
-
- <li>feature: Namespace config writes back</li>
-
- <li>feature: Can specify more than one website for ontology update</li>
-
- <li>feature: Empty field shows all terms in ontology rather than none</li>
-
- <li>feature: Can add more differentia to post comp</li>
-
- <li>bugfix: Config update/merge bug where fields in wrong order fixed.</li>
-
- <li>known bug: can't read post-compositions from phenote versions 1.1 and prior</li>
-
-</ul>
-
-
-
-
-<h1>1.2</h1>
-
-<h2>05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a></h2>
-<ul>
-
- <li>feature: Can post-compose with >2 terms </li>
-
- <li>feature: Term history display can be toggled on/off (Settings->Term History menu)</li>
-
- <li>feature: Synonyms delineated by scope in Term Info: Exact,
-Narrow, Broad, General, Related. If the synonym category is given, it
-is displayed. For example, the term 'water' has the <i>related</i> synonym H2O, which has the category of a chemical <i>formula</i>.</li>
-
- <li>feature: Obsolete replacements or consideration terms are displayed in term info with links</li>
-
- <li>feature: Display term comments in Term Info beneath relationships</li>
-
- <li>feature: Loading splash screen </li>
-
- <li>feature: Can configure by namespace for ontologies</li>
-
- <li>feature: Can automatically update ontologies during startup (configurable)</li>
-
- <li>feature: Timer added to configuration during ontology update check (configurable)</li>
-
- <li>feature: Can check which version of phenote is running by selecting Help->About.</li>
-
- <li>feature: Added common configuration for OMIM curation for use by NCBO (ncbo.cfg).</li>
-
- <li>feature: can forward and reverse sort columns by repeatedly clicking on column header [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574916&group_id=76834&atid=887913">1574916</a>]</li>
-
- <li>feature: display ontology namespace in term info box [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1598048&group_id=76834&atid=887913">1598048</a>]</li>
-
- <li>change: Search filters moved into menu </li>
-
- <li>change: Updates to the zfin-standalone.cfg for the zebrafish community annotation; only includes GO and ZFanatomy ontologies. </li>
-
- <li>bugfix: Free-text field text not sticking in "new" or blank rows </li>
-
-</ul>
-
-
-
-
-<h1>1.1</h1>
-
-
-
-<h2>04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a></h2>
-
-
-<ul>
-
- <li>feature: User can change the configuration they want to use at
-initialization from file menu; change takes effect after restart.
-(previously user had to edit the .phenote/conf/my-phenote file).</li>
-
-</ul>
-
-
-
-<h2>03.28.2007, version 1.1.1</h2>
-
-<ul>
-
- <li>feature: Phenote is now a single webstart app; user chooses
-their configuration at startup (used to be hard wired to a
-configuration)</li>
-
- <li>feature: Phenote will merge its default configuration with users' configuration,
-preserving user changes as well as adding anything new from phenote
-upgrade.</li>
-
- <li>feature: Beginnings of term history to display recently used ontology terms. Will be clickable in future.</li>
-
- <li>feature: Data entry panel will spill over into multiple tabs if >12 fields included</li>
-
- <li>feature: Tab delimited data adapter; data in/output format compatible with excel and other spreadsheet software [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661778&group_id=76834&atid=887913">1661778</a>]</li>
-
- <li>feature: QueryableDataAdapter interface for developers; enables
-connection between input fields and a database backend for quering.
-Queryable fields get a retrieve button.</li>
-
- <li>feature: Autocompletion search with ALL ontologies in a field instead of just one [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1575241&group_id=76834&atid=887913">1575241</a>]</li>
-
- <li>feature: Retrieve ontology files from URL if more up to date or no local found; only from a single repository for all [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1648337&group_id=76834&atid=887913">1648337</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574906&group_id=76834&atid=887913">1574906</a>]</li>
-
- <li>feature: fixed releases available for checkout via sourceforge [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1670345&group_id=76834&atid=887913">1670345</a>]</li>
-
- <li>feature: display xtns in load/save menu choices [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1594508&group_id=76834&atid=887913">1594508</a>]</li>
-
- <li>change: Refactored code for field guis</li>
-
- <li>change: Layout improved</li>
-
- <li>change: OBSOLETE is displayed in red next to obsolete term in term info [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1581589&group_id=76834&atid=887913">1581589</a>]</li>
-
- <li>change: human.cfg configuration to include obo foundary ontologies GO, SO, CL, ChEBI, PATO, OBI, Relations, unit, and spatial [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1633287&group_id=76834&atid=887913">1633287</a>]</li>
-
- <li>bugfix: Ontology chooser reflects current term</li>
-
- <li>bugfix: phenosyntax reader broken [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1684591&group_id=76834&atid=887913">1684591</a>]</li>
-
- <li>bugfix: post-composed terms not loading [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661728&group_id=76834&atid=887913">1661728</a>]</li>
-
-</ul>
-
-
-
-<h1>1.0</h1>
-
-
-
-<h2>02.06.2007, version <a href="phenote/1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a></h2>
-
-
-
-<h2>01.12.2007, version1.0,
-<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby
-Phenote(components used by Zfin)</a></h2>
-
-<ul>
- <li>change: refactoring of the data model to allow addition of any
-field desired, not just E,Q,GC,GT,Pub. Stage, Evidence, Description,
-Abnormal, and Absent have been added through this new mechanism in the
-newest configurations. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1574912&group_id=76834&atid=887913">1574912</a>]</li>
-
- <li>change: Webby phenote is now using JSP and Spring.</li>
-
- <li>change: There has been some recent work with UVictoria for ontology graph
-visualization. This is coming along well and hopefully will be seen in
-the next release.</li>
-
- <li>bugfix: absent fields not displaying in human 1.03 [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1661973&group_id=76834&atid=887913">1661973</a>]</li>
-
-</ul>
-
-
-
-<h1>0.9</h1>
-
-<h2>11.15.2006, version <a href="phenote/0.9/phenote-flybase.jnlp">0.9-fly</a>,
-<a href="phenote/0.9/phenote-zfin.jnlp">0.9-zfin</a>,
-<a href="http://165.124.152.194/web/html/interface.html">DictyBase
-webby phenote</a></h2>
-
-<h2>11.09.2006, version 0.9</h2>
-
-
-
-<ul>
-
-
-
- <li>feature: Undo - can step backward through previous actions</li>
-
- <li>feature: Quartz scheduler used to schedule when to check for new obo files. Added by Christian Pich of Zfin. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588669&group_id=76834&atid=887913">1588669</a>]</li>
-
- <li>change: upgraded PhenoteServlet to Spring framework. Added by Christian Pich [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1588670&group_id=76834&atid=887913">1588670</a>]</li>
-
- <li>feature: Synonyms are displayed from autocomplete with [syn]; when
-selected the term name (not the synonym) goes into the field and table (webby & standalone)</li>
-
- <li>feature: obsoletes are displayed from autocomplete with [obs]</li>
-
- <li>feature: Bulk update & copy in standalone. [<a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579885&group_id=76834&atid=887913">1579885</a>, <a href="https://sourceforge.net/tracker/index.php?func=detail&aid=1579882&group_id=76834&atid=887913">1579882</a>] </li>
-
- <li>change: search types interface changed from radio buttons to checkboxes (j. balhoff)</li>
-
- <li>bugfix: file-save button changed to say "save" not "load"</li>
-
- <li>feature: file-save recognizes and chooses appropriate data
-adapter based on file extension (.psx for phenosyntax and .xml for
-phenoxml)</li>
-
- <li>change: Single quotes escaped for javascript fns.</li>
-
-</ul>
-
-
-
-<h1>0.8</h1>
-
-
-<h2>10.02.2006, version <a href="phenote/0.8/phenote-flybase.jnlp">0.8-fly</a>,
-<a href="phenote/0.8/phenote-zfin.jnlp">0.8-zfin</a>,
-<a href="http://165.124.152.194/web/html/interface.html">DictyBase
-webby phenote</a></h2>
-<ul>
-
- <li>feature: Added post composition to standalone phenote. </li>
-
- <li>feature: Actions are logged for both webby/servlet & standalone.</li>
-
- <li>feature: Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml
-writer (does pub & genetic context)</li>
-
- <li> feature: Command line reading & writing of phenoxml & phenosyntax.</li>
-
- <li>feature: Application exits on window exit (unless servlet)</li>
-
- <li>feature: Can filter out stage terms from zfin anatomy</li>
-
-</ul>
-
-
-
-
-<h1>0.7</h1>
-
-
-
-<h2>08.23.2007, version <a href="phenote/0.7/phenote-flybase.jnlp">0.7-fly.</a>,
-<a href="0.7/phenote-zfin.jnlp">0.7-zfin</a></h2>
-
-<ul>
- <li>feature: entity chooser (web)</li>
-
- <li>feature: can configure to check for new obo files and load
-them. (These are installed at zfin, if anyone would like to see them
-publicly let me know).</li>
-
- <li>feature: entity field and term info installed into zfin (web)
-phenotype site. Term info & completion are scrollable.</li>
-
- <li>feature: standalone version can read & write pheno-syntax with ids & term names in comments</li>
-
- <li>feature: standalone entity chooser</li>
-
- <li>feature: added pub field</li>
-
- <li>feature: added 'use term' button in term info</li>
-
- <li>feature: can sort table by any field in forward order by clicking on headers</li>
-
- <li>change: personal config file gets copied out of jar</li>
-
- <li>change: directory for file load/save remembered</li>
-
- <li>change: layout fixed</li>
-
- <li>bugfix: paste for mac fixed</li>
-
-</ul>
-
-
-
-<h1>0.6</h1>
-
-
-
-<h2>07.28.2006, version <a href="phenote/0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="phenote/0.6/phenote-zfin.jnlp">0.6-zfin</a>,
-<a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote
-(0.6)</a></h2>
-<ul>
- <li>new: webbified phenote. This is in its extremely early stages
-(very little functionality and buggy). At this point it only does
-Entity and Quality fields and term info and thats it, and even thats
-buggy, but more coming soon! </li>
-
- <li> feature: writing pheno-xml format, and uses the latest
-PATO ontology (as of July 28, 2006).</li>
-</ul>
-
-<h1>0.5</h1>
-
-<h2>05.12.2006, version <a href="phenote/0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="phenote/0.5/phenote-zfin.jnlp">0.5-ZFIN</a></h2>
-<p>
-No new additions to the gui here. In preparation for my visit to
-Cambridge/FlyBase, I worked on a FlyBase dataadapter. This is phenote
-first data adapter so I also laid down the foundations for data
-adapters. The FlyBase data adapter simply cuts and pastes phenotype
-character objects to the system clipboard. The idea is that FlyBase's
-Proforma java application will also cut and paste to the clipboard.
-This is a simple way to pass objects between applications, to get us
-off the ground. Proforma is not there yet so this has not been
-tested yet with Proforma, but it works in the test suite. Added special
-FlyBase character wrappers that do the parsing and creating of Proforma
-character strings.</p>
-
-
-<h1>0.4</h1>
-<h2>04.26.2006, version <a href="phenote/0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="phenote/0.4/phenote-zfin.jnlp">0.4-zfin</a></h2>
-
-<ul>
-
- <li>feature: Added Genetic Context field.</li>
-
- <li>feature: Parent & child terms in term info are now clickable/navigable.</li>
-
- <li>feature: HTML Links in descriptions are clickable (should bring up default browser)</li>
-
- <li>feature: configuration files to configure ontologies & fields. This is
-currently at a devloper level (xml file) not a user level(gui - todo).
-There is a command line argument for which configuration file to use.
-This allows for having separate zf & fb releases without having to
-change the code to do it (like was done for the ctol release). The
-configuration for now is for developers (internal xml file), on the
-todo is to have a gui configuration for users.</li>
-
- <li>bugfix: can't delete to 0 rows</li>
-
- <li>bugfix: synonym search duplicates removed</li>
-
- <li>Development: Refactored for configuration & adding field.
-Made the internal code much more generic for adding new fields from
-configuration, got rid of a lot of hard wiring. Part of this was
-instituring model-view-controller in some places where views were
-improperly talking to other views. In theory this should also make it
-easier to plop a web gui on top of the current phenote model &
-controller.</li>
-
- <li>Development: Renamed Phenotype to Character. Added Character interface CharacterI.</li>
-
- <li>Development: Added tests to test suite.</li>
-
-</ul>
-
-
-<h1>0.3</h1>
-
-
-
-<h2>04.07.2006, version <a href="phenote/0.3/phenote-webstart.jnlp">0.3</a>, <a href="phenote/0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a></h2>
-
-<p>Note: 0.3.1 is identical to 0.3 except that it has ontologies for CToL
-(fish evolution group). In particular it uses a fish taxonomy
-ontology for the id (in this taxonomy) choosing. On the todo is the
-ability to configure ontologies, but not there yet, so for now need to
-hardwire with seaparate jar file. This clearly makes the todo item a
-bit more pressing.</p>
-<p> Release for NESCent fish eveolution meeting. No major new functionality
-here. Cleaned up and fixed a lot of the bugs in 0.2, which was rather
-buggy.</p>
-
-<ul>
-
- <li>feature: Completion terms now sorted alphabeitcally.</li>
-
- <li>feature: Obsoletes are now in addition to regular terms, not in lieu of.</li>
-
- <li>feature: Filtering out attribute values (todo: change to actually filter in
-values)</li>
-
- <li>change: Html formatting of term info (todo: make terms selectable)</li>
-
- <li>feature: Children relations are in term info</li>
-
- <li>change: Term info layout greatly improved</li>
-
- <li>change: Term info in scroller</li>
-
- <li>change: Border with label around term info</li>
-
- <li>change: Put definition at end of term info</li>
-
- <li>bugfix: Backspace in ontology combo box</li>
-
- <li>bugfix: Selection of item in comp list causing exception, not going in term box</li>
-
- <li>bugfix: No terms with just 1 char</li>
-
- <li>bugfix: Popup was staying up after selection</li>
-
- <li>development: Test suite added! (todo: add more tests)</li>
-
- <li>development: Migrated to jdk 1.5 (which caused some of the bugs above)</li>
-
- <li>development: Ant file made build.xml.</li>
-
- <li>development: CompletionList refactored into Ontology (prompted by sorting)</li>
-
-</ul>
-
-
-
-
-<h1>0.2</h1>
-
-<h2>03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a></h2>
-<ul>
-
- <li>feature: term completion on Synonyms, Definitions and Obsoletes</li>
-
- <li>feature: mouse-over on term in completion list displays info in 'term info' text area</li>
-
- <li>Todo: layout, scrollbar, border w title, ordering & lumping
-parents
-& children, formatting. Also perhaps have children & parents be
-clickable in some fashion either html-like clickable text or as buttons.</li>
-
- <li>known bugs: If you hit backspace in term completion fields it gets wacky </li>
-
-</ul>
-
-<h1>0.1</h1>
-
-<h2>03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a></h2>
-<p> 0.1 was the initial phenote release (known briefly as the plumper at
-the time). It just had a genotype, anatomy and pato fields, where
-anatomy and pato did term completion (just on term names) with there
-ontologies in a drop down list. There was also the phenotype table that
-tracked phenotype instances being edited in the above fields. This very
-limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.</p>
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
-</body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/resources.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/resources.shtml~ 2008-02-20 20:24:24 UTC (rev 1543)
+++ phenote/trunk/doc/phenote-website/resources.shtml~ 2008-02-20 21:12:40 UTC (rev 1544)
@@ -1,71 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Ontology Resources
- </div>
- <p>You can find out more about available ontologies for use during
- annotation with Phenote software:<p>
- <h3>
- <a href="http://www.bioontology.org/ncbo/faces/pages/ontology_list.xhtml">
- NCBO Bioportal
- </a>
- </h3>
- <p>
- On this page you can find a listing of biomedical ontologies
- that have been submitted to the NCBO. From there you can link
- to their project websites, download the ontology files, and search
- their contents.
- </p>
-
- <h3>
- <a href="http://www.obofoundry.org">OBO Foundry
- </a>
- </h3>
- <p>
- The OBO Foundry is an open, inclusive, and collaborative core of
- interoperable ontologies developed by the research community.
- The goal is to facilitate the creation of consistent, compatible,
- and unambiguous ontologies thereby supporting the biomedical
- research community. The contributors are those biological
- researchers and ontology developers who have agreed to work
- together on an evolving set of design principles that can
- foster interoperability of ontologies, and ensure a gradual
- improvement of quality and formal rigor in ontologies, in ways
- designed to meet the increasing needs of data and information
- integration in the biomedical domain.
- </p>
-
- <h3>
- <a href="http://www.ebi.ac.uk/ontology-lookup/">
- Ontology Lookup Service (OLS)
- </a>
- </h3>
- <p>
- The Ontology Lookup Service is a spin-off of the PRIDE project,
- which required a centralized query interface for ontology and
- controlled vocabulary lookup. While many of the ontologies
- queriable by the OLS are available online, each has its own
- query interface and output format. The OLS provides a web
- service interface to query multiple ontologies from a single
- location with a unified output format.
- </p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/screenshots.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/screenshots.shtml~ 2008-02-20 20:24:24 UTC (rev 1543)
+++ phenote/trunk/doc/phenote-website/screenshots.shtml~ 2008-02-20 21:12:40 UTC (rev 1544)
@@ -1,26 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Phenote Screenshots
- </div>
- <div class="clearall"></div>
- <p><img src="http://www.phenote.org/images/phenote_screenshot.jpg" title="Phenote in action" alt="Phenote screenshot" width="100%"/></p>
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/team.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/team.shtml~ 2008-02-20 20:24:24 UTC (rev 1543)
+++ phenote/trunk/doc/phenote-website/team.shtml~ 2008-02-20 21:12:40 UTC (rev 1544)
@@ -1,78 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote: The Team</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Project Team
- </div>
- <h2 class="bio"><a name="exec" id="exec"></a>
- Development</h2>
- <div class="third_bio">
- <p><img src="http://www.bioontology.org/images/team/gibson.jpg" title="Mark Gibson" alt="Mark Gibson" height="130"/></p>
- <p><a href="http://www.berkeleybop.org/content/about/people/" title="Mark Gibson">Mark Gibson</a>, MSE</p>
- </div>
- <div class="third_bio">
- <p><img src="http://www.bioontology.org/images/team/washington.jpg" title="Nicole Washington" alt="Nicole Washington" height="130" /> </p>
- <p><a href="http://berkeleybop.org/content/about/people/nlwashington/" title="Nicole Washington">Nicole Washington</a>, PhD </p>
- </div>
- <div class="third_bio">
- <p><img src="http://www.bioontology.org/images/team/mungall.jpg" title="Chris Mungall" alt="Chris Mungall" height="130" /></p>
- <p><a href="http://www.fruitfly.org/%7Ecjm/" title="Chris Mungall">Chris Mungall</a>, BSc</p>
- </div>
- <div class="clearall"></div>
-
- <div class="third_bio">
- <p><img src="http://www.bioontology.org/images/team/lewis.jpg" title="Suzanna Lewis" alt="Suzanna Lewis" height="130" /> </p>
- <p><a href="http://www.berkeleybop.org/content/about/people/" title="Suzanna Lewis">Suzanna Lewis</a>, MS</p>
- </div>
- <div class="clearall"></div>
-
- <h1>Affiliations</h1>
-
- <h3>
- <a href="http://bioontology.org/">
- National Center for Biomedical Ontology (NCBO)
- </a>
- </h3>
- <p>
- The NCBO is a consortium of leading biologists, clinicians,
- informaticians, and ontologists who develop innovative
- technology and methods that allow scientists to create,
- disseminate, and manage biomedical information and knowledge
- in machine-processable form.
- </p>
-
- <h3>
- <a href="http://www.berkeleybop.org/">
- Berkeley Bioinformatics and Ontologies Project (BBOP)
- </a>
- </h3>
- <p>
- The BBOP is located at the Lawrence Berkeley National Labs,
- is a diverse group of scientific researchers and software
- engineers dedicated to developing tools and applying
- computational technologies to solve biological
- problems. Members of the group contribute to a number of
- projects, including The Gene Ontology, The National Center
- for Biomedical Ontology, the Model Organism Encyclopedia
- of DNA Elements (modENCODE), and the Generic Model Organism
- Database Project.
- </p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
Deleted: phenote/trunk/doc/phenote-website/users.shtml~
===================================================================
--- phenote/trunk/doc/phenote-website/users.shtml~ 2008-02-20 20:24:24 UTC (rev 1543)
+++ phenote/trunk/doc/phenote-website/users.shtml~ 2008-02-20 21:12:40 UTC (rev 1544)
@@ -1,79 +0,0 @@
-<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
-<html xmlns="http://www.w3.org/1999/xhtml">
- <head>
-
- <!--#include virtual="ssi/head.html" -->
- <title>Phenote</title>
-
- </head>
- <body>
-
- <!--#include virtual="ssi/header.html" -->
-
- <div id="main_container_aux">
- <div id="main_content_aux">
- <div class="catch_phrase">
- Phenote User Community
- </div>
- <h1>Collaborations</h1>
-
- <p>Phenote development is a community effort. We welcome input and feedback from our users. The following groups are using Phenote:</p>
- <table border="0">
- <tr>
- <td><a href="http://flybase.bio.indiana.edu/"> <img src="/images/fly_logo.png" alt="Flybase" /></a>
- </td>
- <td>Flybase</td>
- </tr>
- <tr>
- <td><a href="http://www.zfin.org/"> <img height="50" src="/images/zfin_logo.gif" alt="Zfin" /></a>
- </td>
- <td>Zebrafish Information Network (Zfin)</td>
- </tr>
- <tr>
- <td><a href="http://www.nbirn.net/research/mouse/index.shtm">
- <img src="/images/BIRN_logo.gif" alt="BIRN" /></a>
- </td>
- <td>mouse Biomedical Informatics Research Network (mouseBIRN)</td>
- </tr>
- <tr>
- <td><a href="http://www.dictybase.org/"><img height="50" src="/images/dicty_logo.png" alt="Dictybase" /></a>
- </td>
- <td>Dictyostelium Model Organism Database (Dictybase)</td>
- </tr>
- <tr>
- <td><a href="http://www.geneontology.org/"><img height="50" src="/images/go_logo.gif" alt="GO" /></a>
- </td>
- <td>The Gene Ontology</td>
- </tr>
- <tr>
- <td><a href="http://www.wormbase.org/"><img src="/images/worm_logo.jpg" height="50" alt="WB" /></a>
- </td>
- <td>The <i>C. elegans</i> Genome Database (Wormbase)</td>
- </tr>
- <tr>
- <td><a href="http://www.nescent.org/">
- <img src="/images/nescent_logo.gif" height="50" alt="Nescent" /></a>
- </td>
- <td>National Evolutionary Synthesis Center (NESCent)</td>
- </tr>
- <tr>
- <td><a href="http://www.pharmgkb.org/"><img src="/images/pgkb_logo.png" height="50" alt="PharmGKB" /></a>
- </td>
- <td>PharmacoGenomics KnowledgeBase (PharmGKB)</td>
- </tr>
- <tr>
- <td><a href="http://www.xenbase.org/"><img src="/images/xenbase_logo.gif" height="50" alt="Xenbase" /></a>
- </td>
- <td>Xenopus Model Organism Database (Xenbase)</td>
- </tr>
-</table>
-
- <p>If you are an active user and would like to be listed on our webpage, please <a href="contact.shtml">contact us</a>.</p>
-
- </div>
- </div>
-
- <!--#include virtual="ssi/footer.html" -->
-
- </body>
-</html>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
![http://www.phenote.org/images/phenote_screenshot.jpg"](http://www.phenote.org/images/phenote_screenshot.jpg"){kind=link}
![http://www.bioontology.org/images/team/gibson.jpg"](http://www.bioontology.org/images/team/gibson.jpg"){kind=link}
![http://www.bioontology.org/images/team/washington.jpg"](http://www.bioontology.org/images/team/washington.jpg"){kind=link}
![http://www.bioontology.org/images/team/mungall.jpg"](http://www.bioontology.org/images/team/mungall.jpg"){kind=link}
![http://www.bioontology.org/images/team/lewis.jpg"](http://www.bioontology.org/images/team/lewis.jpg"){kind=link}
|
From: <nl...@us...> - 2008-03-04 22:08:24
|
Revision: 1586
http://obo.svn.sourceforge.net/obo/?rev=1586&view=rev
Author: nlw
Date: 2008-03-04 14:08:23 -0800 (Tue, 04 Mar 2008)
Log Message:
-----------
moved the old jnlps to the attic/ dir, so that there's only a couple left
Added Paths:
-----------
phenote/trunk/doc/phenote-website/attic/
phenote/trunk/doc/phenote-website/attic/phenote-flybase.jnlp
phenote/trunk/doc/phenote-website/attic/phenote-go-function-process.jnlp
phenote/trunk/doc/phenote-website/attic/phenote-human.jnlp
phenote/trunk/doc/phenote-website/attic/phenote-mp-xp.jnlp
phenote/trunk/doc/phenote-website/attic/phenote-so-xp.jnlp
phenote/trunk/doc/phenote-website/attic/phenote-zfin.jnlp
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp
phenote/trunk/doc/phenote-website/phenote-human.jnlp
phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp
phenote/trunk/doc/phenote-website/phenote-so-xp.jnlp
phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
Copied: phenote/trunk/doc/phenote-website/attic/phenote-flybase.jnlp (from rev 1582, phenote/trunk/doc/phenote-website/phenote-flybase.jnlp)
===================================================================
--- phenote/trunk/doc/phenote-website/attic/phenote-flybase.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/attic/phenote-flybase.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
+href="phenote-flybase.jnlp">
+<information>
+ <title>Phenote @@phenote.version@@</title>
+ <vendor>National Center for Biomedical Ontology</vendor>
+ <description>Phenote standalone app via webstart</description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-u</argument>
+ <argument>/flybase.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
Copied: phenote/trunk/doc/phenote-website/attic/phenote-go-function-process.jnlp (from rev 1582, phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp)
===================================================================
--- phenote/trunk/doc/phenote-website/attic/phenote-go-function-process.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/attic/phenote-go-function-process.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
+href="phenote-go-function-process.jnlp">
+<information>
+ <title>Phenote-for-GO @@phenote.version@@</title>
+ <vendor>National Center for Biomedical Ontology</vendor>
+ <description>Phenote demo for </description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-u</argument>
+ <argument>/go-function-process.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
Copied: phenote/trunk/doc/phenote-website/attic/phenote-human.jnlp (from rev 1582, phenote/trunk/doc/phenote-website/phenote-human.jnlp)
===================================================================
--- phenote/trunk/doc/phenote-website/attic/phenote-human.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/attic/phenote-human.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
+href="phenote-human.jnlp">
+<information>
+ <title>Phenote @@phenote.version@@</title>
+ <vendor>National Center for Biomedical Ontology</vendor>
+ <description>Phenote standalone app via webstart</description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-u</argument>
+ <argument>/human.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
Copied: phenote/trunk/doc/phenote-website/attic/phenote-mp-xp.jnlp (from rev 1582, phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp)
===================================================================
--- phenote/trunk/doc/phenote-website/attic/phenote-mp-xp.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/attic/phenote-mp-xp.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
+href="phenote-mp-xp.jnlp">
+<information>
+ <title>Phenote-for-GO @@phenote.version@@</title>
+ <vendor>National Center for Biomedical Ontology</vendor>
+ <description>Phenote demo for </description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-u</argument>
+ <argument>/mp-xp.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
Copied: phenote/trunk/doc/phenote-website/attic/phenote-so-xp.jnlp (from rev 1582, phenote/trunk/doc/phenote-website/phenote-so-xp.jnlp)
===================================================================
--- phenote/trunk/doc/phenote-website/attic/phenote-so-xp.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/attic/phenote-so-xp.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://www.berkeleybop.org/ontologies/phenote/latest/"
+href="phenote-so-xp.jnlp">
+<information>
+ <title>Phenote-for-GO (TEST)</title>
+ <vendor>National Center for Biomedical Ontology</vendor>
+ <description>Phenote demo for </description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-u</argument>
+ <argument>/so-xp.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
Copied: phenote/trunk/doc/phenote-website/attic/phenote-zfin.jnlp (from rev 1582, phenote/trunk/doc/phenote-website/phenote-zfin.jnlp)
===================================================================
--- phenote/trunk/doc/phenote-website/attic/phenote-zfin.jnlp (rev 0)
+++ phenote/trunk/doc/phenote-website/attic/phenote-zfin.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<jnlp
+spec="1.0+"
+codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
+href="phenote-zfin.jnlp">
+<information>
+ <title>Phenote @@phenote.version@@</title>
+ <vendor>National Center for Biomedical Ontology</vendor>
+ <description>Phenote standalone app via webstart</description>
+ <!-- Declares that the application can run without
+ access to the server it was downloaded from -->
+ <offline-allowed />
+</information>
+<security>
+ <!-- Request that the application be given full
+ access to the local (executing) machine,
+ as if it were a regular Java application.
+ Requires that all JAR files be signed
+ by a trusted party -->
+ <all-permissions />
+</security>
+<resources>
+ <!-- Specify the versions of the Java Runtime Environment
+ (JRE) that are supported by the application.
+ Multiple entries of this kind are allowed, in which
+ case they are considered to be in order of preference -->
+ <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
+ <jar href="jars/phenote.jar" />
+ <jar href="jars/oboedit.jar" />
+ <jar href="jars/org.geneontology.jar" />
+ <jar href="jars/BrowserLauncher2-10rc4.jar" />
+ <jar href="jars/jsr173_1.0_api.jar" />
+ <jar href="jars/phenoxmlbeans.jar" />
+ <jar href="jars/phenoteconfigbeans.jar" />
+ <jar href="jars/tomcat-servlet.jar" />
+ <jar href="jars/xbean.jar" />
+ <jar href="jars/te-common.jar" />
+ <jar href="jars/log4j-1.2.13.jar" />
+</resources>
+<application-desc main-class="phenote.main.Phenote">
+ <argument>-u</argument>
+ <argument>/zfin-standalone.cfg</argument>
+</application-desc>
+</jnlp>
+
+
+
Deleted: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2008-03-04 21:47:17 UTC (rev 1585)
+++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<jnlp
-spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
-href="phenote-flybase.jnlp">
-<information>
- <title>Phenote @@phenote.version@@</title>
- <vendor>National Center for Biomedical Ontology</vendor>
- <description>Phenote standalone app via webstart</description>
- <!-- Declares that the application can run without
- access to the server it was downloaded from -->
- <offline-allowed />
-</information>
-<security>
- <!-- Request that the application be given full
- access to the local (executing) machine,
- as if it were a regular Java application.
- Requires that all JAR files be signed
- by a trusted party -->
- <all-permissions />
-</security>
-<resources>
- <!-- Specify the versions of the Java Runtime Environment
- (JRE) that are supported by the application.
- Multiple entries of this kind are allowed, in which
- case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote.jar" />
- <jar href="jars/oboedit.jar" />
- <jar href="jars/org.geneontology.jar" />
- <jar href="jars/BrowserLauncher2-10rc4.jar" />
- <jar href="jars/jsr173_1.0_api.jar" />
- <jar href="jars/phenoxmlbeans.jar" />
- <jar href="jars/phenoteconfigbeans.jar" />
- <jar href="jars/xbean.jar" />
- <jar href="jars/tomcat-servlet.jar" />
- <jar href="jars/te-common.jar" />
- <jar href="jars/log4j-1.2.13.jar" />
-</resources>
-<application-desc main-class="phenote.main.Phenote">
- <argument>-u</argument>
- <argument>/flybase.cfg</argument>
-</application-desc>
-</jnlp>
-
-
-
Deleted: phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp 2008-03-04 21:47:17 UTC (rev 1585)
+++ phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<jnlp
-spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
-href="phenote-go-function-process.jnlp">
-<information>
- <title>Phenote-for-GO @@phenote.version@@</title>
- <vendor>National Center for Biomedical Ontology</vendor>
- <description>Phenote demo for </description>
- <!-- Declares that the application can run without
- access to the server it was downloaded from -->
- <offline-allowed />
-</information>
-<security>
- <!-- Request that the application be given full
- access to the local (executing) machine,
- as if it were a regular Java application.
- Requires that all JAR files be signed
- by a trusted party -->
- <all-permissions />
-</security>
-<resources>
- <!-- Specify the versions of the Java Runtime Environment
- (JRE) that are supported by the application.
- Multiple entries of this kind are allowed, in which
- case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote.jar" />
- <jar href="jars/oboedit.jar" />
- <jar href="jars/org.geneontology.jar" />
- <jar href="jars/BrowserLauncher2-10rc4.jar" />
- <jar href="jars/jsr173_1.0_api.jar" />
- <jar href="jars/phenoxmlbeans.jar" />
- <jar href="jars/phenoteconfigbeans.jar" />
- <jar href="jars/xbean.jar" />
- <jar href="jars/tomcat-servlet.jar" />
- <jar href="jars/te-common.jar" />
- <jar href="jars/log4j-1.2.13.jar" />
-</resources>
-<application-desc main-class="phenote.main.Phenote">
- <argument>-u</argument>
- <argument>/go-function-process.cfg</argument>
-</application-desc>
-</jnlp>
-
-
-
Deleted: phenote/trunk/doc/phenote-website/phenote-human.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2008-03-04 21:47:17 UTC (rev 1585)
+++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<jnlp
-spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
-href="phenote-human.jnlp">
-<information>
- <title>Phenote @@phenote.version@@</title>
- <vendor>National Center for Biomedical Ontology</vendor>
- <description>Phenote standalone app via webstart</description>
- <!-- Declares that the application can run without
- access to the server it was downloaded from -->
- <offline-allowed />
-</information>
-<security>
- <!-- Request that the application be given full
- access to the local (executing) machine,
- as if it were a regular Java application.
- Requires that all JAR files be signed
- by a trusted party -->
- <all-permissions />
-</security>
-<resources>
- <!-- Specify the versions of the Java Runtime Environment
- (JRE) that are supported by the application.
- Multiple entries of this kind are allowed, in which
- case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote.jar" />
- <jar href="jars/oboedit.jar" />
- <jar href="jars/org.geneontology.jar" />
- <jar href="jars/BrowserLauncher2-10rc4.jar" />
- <jar href="jars/jsr173_1.0_api.jar" />
- <jar href="jars/phenoxmlbeans.jar" />
- <jar href="jars/phenoteconfigbeans.jar" />
- <jar href="jars/tomcat-servlet.jar" />
- <jar href="jars/xbean.jar" />
- <jar href="jars/te-common.jar" />
- <jar href="jars/log4j-1.2.13.jar" />
-</resources>
-<application-desc main-class="phenote.main.Phenote">
- <argument>-u</argument>
- <argument>/human.cfg</argument>
-</application-desc>
-</jnlp>
-
-
-
Deleted: phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp 2008-03-04 21:47:17 UTC (rev 1585)
+++ phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<jnlp
-spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
-href="phenote-mp-xp.jnlp">
-<information>
- <title>Phenote-for-GO @@phenote.version@@</title>
- <vendor>National Center for Biomedical Ontology</vendor>
- <description>Phenote demo for </description>
- <!-- Declares that the application can run without
- access to the server it was downloaded from -->
- <offline-allowed />
-</information>
-<security>
- <!-- Request that the application be given full
- access to the local (executing) machine,
- as if it were a regular Java application.
- Requires that all JAR files be signed
- by a trusted party -->
- <all-permissions />
-</security>
-<resources>
- <!-- Specify the versions of the Java Runtime Environment
- (JRE) that are supported by the application.
- Multiple entries of this kind are allowed, in which
- case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote.jar" />
- <jar href="jars/oboedit.jar" />
- <jar href="jars/org.geneontology.jar" />
- <jar href="jars/BrowserLauncher2-10rc4.jar" />
- <jar href="jars/jsr173_1.0_api.jar" />
- <jar href="jars/phenoxmlbeans.jar" />
- <jar href="jars/phenoteconfigbeans.jar" />
- <jar href="jars/xbean.jar" />
- <jar href="jars/tomcat-servlet.jar" />
- <jar href="jars/te-common.jar" />
- <jar href="jars/log4j-1.2.13.jar" />
-</resources>
-<application-desc main-class="phenote.main.Phenote">
- <argument>-u</argument>
- <argument>/mp-xp.cfg</argument>
-</application-desc>
-</jnlp>
-
-
-
Deleted: phenote/trunk/doc/phenote-website/phenote-so-xp.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-so-xp.jnlp 2008-03-04 21:47:17 UTC (rev 1585)
+++ phenote/trunk/doc/phenote-website/phenote-so-xp.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<jnlp
-spec="1.0+"
-codebase="http://www.berkeleybop.org/ontologies/phenote/latest/"
-href="phenote-so-xp.jnlp">
-<information>
- <title>Phenote-for-GO (TEST)</title>
- <vendor>National Center for Biomedical Ontology</vendor>
- <description>Phenote demo for </description>
- <!-- Declares that the application can run without
- access to the server it was downloaded from -->
- <offline-allowed />
-</information>
-<security>
- <!-- Request that the application be given full
- access to the local (executing) machine,
- as if it were a regular Java application.
- Requires that all JAR files be signed
- by a trusted party -->
- <all-permissions />
-</security>
-<resources>
- <!-- Specify the versions of the Java Runtime Environment
- (JRE) that are supported by the application.
- Multiple entries of this kind are allowed, in which
- case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote.jar" />
- <jar href="jars/oboedit.jar" />
- <jar href="jars/org.geneontology.jar" />
- <jar href="jars/BrowserLauncher2-10rc4.jar" />
- <jar href="jars/jsr173_1.0_api.jar" />
- <jar href="jars/phenoxmlbeans.jar" />
- <jar href="jars/phenoteconfigbeans.jar" />
- <jar href="jars/xbean.jar" />
- <jar href="jars/tomcat-servlet.jar" />
- <jar href="jars/te-common.jar" />
- <jar href="jars/log4j-1.2.13.jar" />
-</resources>
-<application-desc main-class="phenote.main.Phenote">
- <argument>-u</argument>
- <argument>/so-xp.cfg</argument>
-</application-desc>
-</jnlp>
-
-
-
Deleted: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2008-03-04 21:47:17 UTC (rev 1585)
+++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2008-03-04 22:08:23 UTC (rev 1586)
@@ -1,47 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<jnlp
-spec="1.0+"
-codebase="http://toy.lbl.gov:9010/phenote/@@phenote.version@@"
-href="phenote-zfin.jnlp">
-<information>
- <title>Phenote @@phenote.version@@</title>
- <vendor>National Center for Biomedical Ontology</vendor>
- <description>Phenote standalone app via webstart</description>
- <!-- Declares that the application can run without
- access to the server it was downloaded from -->
- <offline-allowed />
-</information>
-<security>
- <!-- Request that the application be given full
- access to the local (executing) machine,
- as if it were a regular Java application.
- Requires that all JAR files be signed
- by a trusted party -->
- <all-permissions />
-</security>
-<resources>
- <!-- Specify the versions of the Java Runtime Environment
- (JRE) that are supported by the application.
- Multiple entries of this kind are allowed, in which
- case they are considered to be in order of preference -->
- <j2se version="1.5+" initial-heap-size="64m" max-heap-size="500m" />
- <jar href="jars/phenote.jar" />
- <jar href="jars/oboedit.jar" />
- <jar href="jars/org.geneontology.jar" />
- <jar href="jars/BrowserLauncher2-10rc4.jar" />
- <jar href="jars/jsr173_1.0_api.jar" />
- <jar href="jars/phenoxmlbeans.jar" />
- <jar href="jars/phenoteconfigbeans.jar" />
- <jar href="jars/tomcat-servlet.jar" />
- <jar href="jars/xbean.jar" />
- <jar href="jars/te-common.jar" />
- <jar href="jars/log4j-1.2.13.jar" />
-</resources>
-<application-desc main-class="phenote.main.Phenote">
- <argument>-u</argument>
- <argument>/zfin-standalone.cfg</argument>
-</application-desc>
-</jnlp>
-
-
-
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-03-04 22:43:24
|
Revision: 1587
http://obo.svn.sourceforge.net/obo/?rev=1587&view=rev
Author: nlw
Date: 2008-03-04 14:43:26 -0800 (Tue, 04 Mar 2008)
Log Message:
-----------
added links to the newest phenote, phenote-plus apps. updated release
notes.
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2008-03-04 22:08:23 UTC (rev 1586)
+++ phenote/trunk/doc/phenote-website/download.shtml 2008-03-04 22:43:26 UTC (rev 1587)
@@ -15,15 +15,40 @@
<div class="catch_phrase">
</div>
<h2>For Users</h2>
- <p><b><a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Launch Phenote in your browser</a></b></p>
+ <h2>************Important Message*************<h2>
+ <p>For version 1.5 we will be introducing a new look and feel that we
+ call the "plus" edition. We will
+ continue to support the old look-and-feel for a couple more versions.
+ So, if you would like to keep using the original Phenote, continue
+ here. Otherwise, go down the page to the section called "Phenote+"</p>
<p> You can run phenote directly from your web browser without a separate installation by selecting one of the following links:</p>
<ul>
- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5-beta2/phenote.jnlp">1.5 beta2</a></strong></li>
+ <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">1.5 </a></strong></li>
<li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
</p>
+ <h2><strong>Phenote+ beta(v1.5)</strong></h2>
+ <ul>
+ <li>Webstart: <a
+ href="http://www.phenote.org/phenote/1.5/phenote-plus.jnlp">Phenote+
+ webstart</a></li>
+ <li>MacOSX:
+ <ul>
+ <li><a
+ href="http://www.phenote.org/phenote/1.5/phenote1.5.mac.dmg">Download
+ the disc image</a>. This should self-extract. You should see an
+ icon for the "drive" that the Phenote+ aplication is on.</li>
+ <li>Drag the Phenote application icon to your "Applications" folder
+ (or your favorite spot on your hard drive</li>
+ <li>That's it! Double-click the icon and its ready to run.</li>
+ </ul>
+ </li>
+ <li>Windows: Installer coming soon!</li>
+ <li>Linux/Solaris: Installer coming soon! </li>
+ </ul>
+
<h2>For Developers</h2>
Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclipse.shtml">command line or in Eclipse</a>
@@ -49,32 +74,27 @@
<div id="sidebar_content">
<div class="content_box_head_blue">
- Recently added features, version 1.4
+ Recently added features, Phenote+ version 1.5
</div>
<div class="content_box_blue">
- <b>feature</b>: Loading splash more informative about what's going on behind-the-scenes such as which ontologies are loading, if they are being updated, etc.<br />
- <b>feature</b>: obo edit annotation model can now be optionally configured for backend, which will allow for more sophisticated data to be captured (like comparisons)<br />
- <b>feature</b>: Error for obo parse failures to info panel <br />
- <b>feature</b>: Delimited tab adapter uses column headings to map to table, rather than ordering <br />
- <b>feature</b>: Autocompletion optimized with threading, cancels stale requests (min-comp-chars now pase) <br />
- <b>feature</b>: Date created automatically added into data (under the hood) <br />
- <b>feature</b>: If arrow hit with empty input then gets & displays all terms (used to inefficiently pre-load) <br />
- <b>feature</b>: Can sort completion list by ID, needed for zfin stages<br />
- <b>feature</b>: Table preserves user ordering of columns, in addition to column widths.<br />
- <b>feature</b>: Filter search field allows user to narrow down displayed data rows via matching text.<br />
- <b>feature</b>: See actual value in input field when multiple rows are selected and have the same value.<br />
- <b>feature</b>: Copy all taxon names in specimen list as an unresolved Newick tree (for PhenoMap/NESCent)<br />
- <b>feature</b>: Automatically open specimen list and phylogenetic tree files when opening data file (for PhenoMap/NESCent)<br />
- <b>change</b>: Moved test suites in with source to work with eclipse<br />
- <b>change</b>: Took a lot of obos out of webstart jar - less bulky - as they get automatically downloaded<br />
- <b>change</b>: Phenote now follows standard log4j configuration conventions. Pass a custom log configuration to Phenote via the classpath or the system propery "log4j.configuration".<br />
- <b>bugfix</b>: Terms not found are no longer dropped, a dangler is created, and error msg to info, show up in red<br />
- <b>bugfix</b>: if log conf fails use backup default<br />
- <b>bugfix</b>: Input fields now commit changes with either Return or Tab<br />
- <b>bugfix</b>: Native lib is loaded properly for Mac interface on webstart, allowing traversal of aliases in file dialog, as well as user sidebar items in file dialog<br />
- <b>bugfix</b>: Noncontiguous row selection works now on Mac<br />
-</ul>
+ <b>feature:</b> New look and feel with Phenote+ <br />
+ <ul>
+ <li> Ability to move different panels around to customize the user experience. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1729114&group_id=76834&atid=887913">1729114</a>] These panels can be "locked" by going to the Settings->Lock Docking Components menu item. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1882110&group_id=76834&atid=887913">1882110</a>]</li>
+ <li> Panels can be "undocked" so that they can float independently around the screen</li>
+ <li>Phenote can interoperate with some obo-edit components, such as the tree-like dag viewer and the graph editor. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1822371&group_id=76834&atid=887913">1822371</a>]</li>
+ </ul>
+ <b>feature</b>: New ontology-update window shows the user in one place
+ which ontologies need updating. <br />
+ <b>feature</b>: if user changes their annotations since previous save, user is prompted for resave [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1810448&group_id=76834&atid=887913">1810448</a>] <br />
+ <b>feature:</b> "Save" added as menu item to overwrite currently open file [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1803824&group_id=76834&atid=887913">1803824</a>]. A dot in the titlebar will disappear upon save. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1893249&group_id=76834&atid=887913">1893249</a>] <br />
+ <b>feature:</b> Solaris OS now supported for webstart versions <br />
+ <b>feature:</b> addition of the ProtocolEditor as a plug-in to phenote. For more information, please see the <a href="http://users.openmicroscopy.org.uk/~ola/720x540/OMERO.ProtocolEditor-new-omero-movie.mov">Protocol Editor demo</a>. This plugin is being developed by the folks at the <a href="http://openmicroscopy.org/">Open Microscopy Environment</a><br />
+ <b>feature:</b> Term info panel updated with collapsible panes.<br />
+ <b>change:</b> post-compositions are now displayed in multi-line style [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1579357&group_id=76834&atid=887913">1579357</a>]<br />
+ <b>feature:</b>Lookup abstracts from PubMed, if Pub field is configured.This can be tried in the "demo" configuration. <br />
+ <b>bugfix:</b> Field name is now always shown, even if there is only one ontology configured for that field. It used to default to the ontology name in this instance. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1852112&group_id=76834&atid=887913">1852112</a>]<br />
+ <b>bufgix:</b> Phenote can now accomodate empty E/Q fields when mapping to the annotation model [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1894065&group_id=76834&atid=887913">1894065</a>]<br />
</div>
</div>
</div>
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-03-04 22:08:23 UTC (rev 1586)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-03-04 22:43:26 UTC (rev 1587)
@@ -29,6 +29,7 @@
<li>feature: Read-only fields can be configured [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1737572&group_id=76834&atid=887913">1737572</a></li>
<li>feature: "Save" added as menu item to overwrite currently open file [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1803824&group_id=76834&atid=887913">1803824</a>]. A dot in the titlebar will disappear upon save. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1893249&group_id=76834&atid=887913">1893249</a></li>
<li>feature: "Open" and "Save" added as toolbar icons [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1811165&group_id=76834&atid=887913">1811165</a>]</li>
+<li>feature: User can lookup abstracts from PubMed or OMIM for "Pub" fields configured with the PubMedDataAdapter. These can be seen in the "ncbo-test" and "demo" configurations</li>
<li>change: table manipulation actions such as "New", "Delete", and "Duplicate" have been moved to a iconic-toolbar at the top of the table window [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1824391&group_id=76834&atid=887913">1824391</a>]</li>
<li>feature: new data types added for configuration: boolean, ints, FILL ME IN </li>
<li>change: all configurations have been changed to include "terminology definitions" which need to be defined for the new ontology update feature</li>
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-03-04 23:12:47
|
Revision: 1589
http://obo.svn.sourceforge.net/obo/?rev=1589&view=rev
Author: nlw
Date: 2008-03-04 15:12:40 -0800 (Tue, 04 Mar 2008)
Log Message:
-----------
more website changes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/events.shtml
phenote/trunk/doc/phenote-website/index.shtml
Modified: phenote/trunk/doc/phenote-website/events.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/events.shtml 2008-03-04 22:51:31 UTC (rev 1588)
+++ phenote/trunk/doc/phenote-website/events.shtml 2008-03-04 23:12:40 UTC (rev 1589)
@@ -17,11 +17,32 @@
</div>
<h1>Upcoming Events, 2008</h1>
- <h2>February</h2>
+ <h2>March, 2008</h2>
<ul>
- <li>Major release scheduled with new dockable components</li>
+ <li>03.06.2008 - Phenote Users Group, Online
+ </li>
+ <li>03.03.2008 - NEW<a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">Phenote webstart release 1.5</a></li>
+ <li>03.03.2008 - Silent release of <a href="http://www.phenote.org/download.shtml">Phenote+ for Mac OSX</a> </li>
+ <li>03.01.2008 - We'd like to know more about what kind of computer you are using. <a href="http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139" onClick="window.open('http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139', '','toolbar=0,location=0,directories=0,status=0,menubar=0,scrollbars=1,resizable=1,width=700,height=480');return false" ><b>Please take our survey</b></a></li>
+ </ul>
+ <h2>April, 2008</h2>
+ <ul>
+ <li>04.03.2008 - Phenote Users Group, Online</li>
+ <li>04.17-21.2008 <a
+ href="http://www.nescent.org/phenoscape/Main_Page">Phenoscape</a>
+ Jamboree Meeting, <a href="http://www.nescent.org/">NESCent</a>,
+ Durham, NC </li>
+ </ul>
+ <h1>Past News and Events</h1>
+
+ <h2>February, 2008</h2>
+ <ul>
+ <li>02.19.2008 - <a href="/doc/api">API documentation</a> added to website</li>
+ <li>02.07.2008 - With our upcoming release, Phenote will be known at <b>Phenote+</b></li>
+ <li>02.07.2008 - <b>Developer Articles</b> - A new section was added to this website to store articles for Developers. <a href="developer-docs/">Check it out...</a>. You'll find it under the "Help" menu on this site.</li>
+ <li>02.07.2008 - Phenote Users Group, Online
+ </li>
</ul>
- <h1>Past News and Events</h1>
<h2>January, 2008</h2>
<ul>
<li>January 10, Seminar, <a href="http://www.nescent.org/">NESCent</a>, Duke University, NC</li>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-03-04 22:51:31 UTC (rev 1588)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-03-04 23:12:40 UTC (rev 1589)
@@ -134,12 +134,12 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
+ <p>03.03.2008 - NEW<a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">Phenote webstart release 1.5</a></p>
+ <p>03.03.2008 - Silent release of <a href="http://www.phenote.org/download.shtml">Phenote+ for Mac OSX</a> </p>
<p>03.01.2008 - We'd like to know more about what kind of computer you are using. <a href="http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139" onClick="window.open('http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139', '','toolbar=0,location=0,directories=0,status=0,menubar=0,scrollbars=1,resizable=1,width=700,height=480');return false" ><b>Please take our survey</b></a></p>
<p>02.19.2008 - <a href="/doc/api">API documentation</a> added to website</p>
<p>02.07.2008 - With our upcoming release, Phenote will be known at <b>Phenote+</b></p>
<p>02.07.2008 - <b>Developer Articles</b> - A new section was added to this website to store articles for Developers. <a href="developer-docs/">Check it out...</a>. You'll find it under the "Help" menu on this site.</p>
- <p>01.10.2008 - Seminar presentation at <a href="http://www.nescent.org/">NESCent</a></p>
- <p>12.20.2007 - <b>New Phenote Beta Release - <a href="http://www.phenote.org/download.shtml">version 1.5-beta2</a></b></p>
<!--
<h3>Event Title</h3>
<ul class="events">
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <nl...@us...> - 2008-03-05 21:55:48
|
Revision: 1602
http://obo.svn.sourceforge.net/obo/?rev=1602&view=rev
Author: nlw
Date: 2008-03-05 13:46:54 -0800 (Wed, 05 Mar 2008)
Log Message:
-----------
edits to webpages for release
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/features.shtml
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/screenshots.shtml
Added Paths:
-----------
phenote/trunk/doc/phenote-website/images/screenshots/
phenote/trunk/doc/phenote-website/images/screenshots/phenote-plus.png
phenote/trunk/doc/phenote-website/images/screenshots/phenote_screenshot.png
Removed Paths:
-------------
phenote/trunk/doc/phenote-website/images/phenote_screenshot.png
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2008-03-05 20:01:00 UTC (rev 1601)
+++ phenote/trunk/doc/phenote-website/download.shtml 2008-03-05 21:46:54 UTC (rev 1602)
@@ -23,8 +23,7 @@
here. Otherwise, go down the page to the section called "Phenote+"</p>
<p> You can run phenote directly from your web browser via "webstart" without a separate installation by selecting one of the following links:</p>
<ul>
- <li><strong>Beta release: <a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">1.5 </a></strong></li>
- <li><strong>Stable release: <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp">1.4</a> </strong></li>
+ <li><strong>NEW release: <a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">1.5</a> </strong></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
@@ -34,19 +33,18 @@
<li>Webstart: <a
href="http://www.phenote.org/phenote/1.5/phenote-plus.jnlp">Phenote+
webstart</a></li>
- <li>MacOSX:
- <ol>
- <li><a
- href="http://www.phenote.org/phenote/1.5/phenote1.5.mac.dmg">Download
- the disc image</a>. This should self-extract. You should see an
+ <li>Platform-specific installers:
+ <a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_macosx_installer.dmg">MacOS X</a> |
+ <a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_windows_installer.exe">Windows</a> |
+ <a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_linux_installer.rpm">Linux</a> |
+ <a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_unix_installer.sh">Unix</a>
+ <ol>
+ <li>Download your platform-specific package. (For MacOS, this should self-extract into a disk image. If it doesn't, double-click on the file. You should see an
icon for the "drive" that the Phenote+ application is on.</li>
- <li>Drag the Phenote application icon to your "Applications" folder
- (or your favorite spot on your hard drive)</li>
- <li>That's it! Double-click the icon and its ready to run.</li>
+ <li>Double-click on the Phenote installer icon. This will open up the installer software. You will be asked a few questions, such as the installation location.</li>
+ <li>When its finished installing, you are ready to go! Double-click the Phenote application icon and its ready to run.</li>
</ol>
</li>
- <li>Windows: Installer coming soon!</li>
- <li>Linux/Solaris: Installer coming soon! </li>
</ul>
<h2>For Developers</h2>
Modified: phenote/trunk/doc/phenote-website/features.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/features.shtml 2008-03-05 20:01:00 UTC (rev 1601)
+++ phenote/trunk/doc/phenote-website/features.shtml 2008-03-05 21:46:54 UTC (rev 1602)
@@ -52,9 +52,9 @@
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp"
+ <a href="http://www.phenote.org/phenote/1.5/phenote.jnlp"
title="Lauch Phenote via Webstart">
- Launch Phenote v1.4-beta3
+ Launch Phenote v1.5
</a> via webstart
</p>
<p class="quick_link">
Deleted: phenote/trunk/doc/phenote-website/images/phenote_screenshot.png
===================================================================
(Binary files differ)
Added: phenote/trunk/doc/phenote-website/images/screenshots/phenote-plus.png
===================================================================
(Binary files differ)
Property changes on: phenote/trunk/doc/phenote-website/images/screenshots/phenote-plus.png
___________________________________________________________________
Name: svn:mime-type
+ application/octet-stream
Copied: phenote/trunk/doc/phenote-website/images/screenshots/phenote_screenshot.png (from rev 1599, phenote/trunk/doc/phenote-website/images/phenote_screenshot.png)
===================================================================
(Binary files differ)
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-03-05 20:01:00 UTC (rev 1601)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-03-05 21:46:54 UTC (rev 1602)
@@ -60,7 +60,7 @@
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.phenote.org/phenote/1.4/phenote.jnlp"
+ <a href="http://www.phenote.org/phenote/1.5/phenote.jnlp"
title="Lauch Phenote via Webstart">
Launch Phenote via Webstart
</a>
@@ -134,8 +134,8 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
- <p>03.03.2008 - NEW<a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">Phenote webstart release 1.5</a></p>
- <p>03.03.2008 - Silent release of <a href="http://www.phenote.org/download.shtml">Phenote+ for Mac OSX</a> </p>
+ <p>03.04.2008 - NEW<a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">Phenote webstart release 1.5</a></p>
+ <p>03.04.2008 - Release of <a href="http://www.phenote.org/download.shtml">Phenote+</a> with platform-specific installers.</p>
<p>03.01.2008 - We'd like to know more about what kind of computer you are using. <a href="http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139" onClick="window.open('http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139', '','toolbar=0,location=0,directories=0,status=0,menubar=0,scrollbars=1,resizable=1,width=700,height=480');return false" ><b>Please take our survey</b></a></p>
<p>02.19.2008 - <a href="/doc/api">API documentation</a> added to website</p>
<p>02.07.2008 - With our upcoming release, Phenote will be known at <b>Phenote+</b></p>
Modified: phenote/trunk/doc/phenote-website/screenshots.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/screenshots.shtml 2008-03-05 20:01:00 UTC (rev 1601)
+++ phenote/trunk/doc/phenote-website/screenshots.shtml 2008-03-05 21:46:54 UTC (rev 1602)
@@ -16,8 +16,12 @@
Phenote Screenshots
</div>
<div class="clearall"></div>
- <p><img src="http://www.phenote.org/images/phenote_screenshot.png" title="Phenote in action" alt="Phenote screenshot" width="100%"/></p>
- </div>
+ <p>Introducing Phenote+</p>
+ <p><img src="http://www.phenote.org/images/screenshots/phenote-plus.png" title="Phenote Plus" alt="Phenote screenshot" width="100%"/></p>
+ <p>Original Phenote Screenshot</p>
+ <p><img src="http://www.phenote.org/images/screenshots/phenote_screenshot.png" title="Phenote in action" alt="Phenote screenshot" width="100%"/></p>
+
+ </div>
</div>
<!--#include virtual="ssi/footer.html" -->
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
![http://www.phenote.org/images/phenote_screenshot.png"](http://www.phenote.org/images/phenote_screenshot.png"){kind=link}
![http://www.phenote.org/images/screenshots/phenote-plus.png"](http://www.phenote.org/images/screenshots/phenote-plus.png"){kind=link}
![http://www.phenote.org/images/screenshots/phenote_screenshot.png"](http://www.phenote.org/images/screenshots/phenote_screenshot.png"){kind=link}
|
From: <nl...@us...> - 2008-04-16 22:28:23
|
Revision: 1736
http://obo.svn.sourceforge.net/obo/?rev=1736&view=rev
Author: nlw
Date: 2008-04-16 15:28:14 -0700 (Wed, 16 Apr 2008)
Log Message:
-----------
adding details about the new sourceforge distribution of the releases.
also updated the release notes
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/download.shtml
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
phenote/trunk/doc/phenote-website/ssi/header.html
Modified: phenote/trunk/doc/phenote-website/download.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/download.shtml 2008-04-16 18:53:23 UTC (rev 1735)
+++ phenote/trunk/doc/phenote-website/download.shtml 2008-04-16 22:28:14 UTC (rev 1736)
@@ -15,29 +15,22 @@
<div class="catch_phrase">
</div>
<h2>For Users</h2>
- <h2>************Important Message*************</h2>
- <p>For version 1.5 we will be introducing a new look and feel that we
- call the "plus" edition. We will
- continue to support the old look-and-feel for a couple more versions.
- So, if you would like to keep using the original Phenote, continue
- here. Otherwise, go down the page to the section called "Phenote+"</p>
- <p> You can run phenote directly from your web browser via "webstart" without a separate installation by selecting one of the following links:</p>
+ <h3>Phenote and Phenote+ webstart edition</h3>
<ul>
- <li><strong>NEW release: <a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">1.5</a> </strong></li>
+ <li>1.6-beta4 release: <a href="http://www.phenote.org/phenote/1.6-beta4/phenote.jnlp">Phenote</a> | <a href="http://www.phenote.org/phenote/1.6-beta4/phenote-plus.jnlp">Phenote+</a></li>
+ <li>1.5 stable release: <a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">Phenote</a> | <a href="http://www.phenote.org/phenote/1.5/phenote-plus.jnlp">Phenote+</a></li>
<li><a href="http://www.phenote.org/phenote/phenote.html">Older releases</a></li>
</ul>
<p> You may be prompted to sign a certificate and allow the download. This will take a few minutes the first time you do this.
</p>
- <h2><strong>Phenote+ (beta) v1.5</strong></h2>
+ <h3>Phenote+ installer edition</h3>
<ul>
- <li>Webstart: <a
- href="http://www.phenote.org/phenote/1.5/phenote-plus.jnlp">Phenote+
- webstart</a></li>
- <li>Platform-specific installers:
+ <li>Platform-specific installers are available for Phenote+ v1.5 at<a href="https://sourceforge.net/project/showfiles.php?group_id=76834">sourceforge</a> or here:
<a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_macos_installer.dmg">MacOS X</a> |
<a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_windows_installer.exe">Windows</a> |
<a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_linux_installer.rpm">Linux</a> |
<a href="http://www.phenote.org/phenote/1.5/Phenote+_1_5_unix_installer.sh">Unix</a>
+ </li>
<ol>
<li>Download your platform-specific package. (For MacOS, this should self-extract into a disk image. If it doesn't, double-click on the file. You should see an
icon for the "drive" that the Phenote+ application is on.</li>
@@ -46,7 +39,17 @@
</ol>
</li>
</ul>
+ <p>Phenote+ v1.6: We will be distributing Phenote+ using the Sourceforge download system. You can now find Phenote <a href="https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=270424">betas</a> and <a href="https://sourceforge.net/project/showfiles.php?group_id=76834&package_id=272237">releases</a> by visiting their pages. </p>
+ <p> We will continue to post links to major releases on this website, but you are invited to download the software by directly connecting to the <a href="https://sourceforge.net/project/showfiles.php?group_id=76834">Phenote Sourceforge Project page</a></p>
+
+ <h3>Important Message</h3>
+ <p>For version 1.5 we will be introducing a new look and feel that we
+ call the "plus" edition. We will
+ continue to support the old look-and-feel for a couple more versions.
+ So, if you would like to keep using the original Phenote, launch
+ the webstart edition through the link above.</p>
+
<h2>For Developers</h2>
Check out our special documentation for running either on the <a href="developer-docs/getting-source-code-in-eclipse.shtml">command line or in Eclipse</a>
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-04-16 18:53:23 UTC (rev 1735)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-04-16 22:28:14 UTC (rev 1736)
@@ -102,7 +102,7 @@
<li class="events">
<p class="quick_link">
<img src="images/star.gif" alt="" class="icon_green"/>
- <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, March 6, 8:30am, Online
+ <a href="http://www.bioontology.org/wiki/index.php/Phenote:Main_Page#Phenote_Working_Group">User's Group Monthly Meeting</a>, May 1, 8:30am, Online
</p>
</li>
</ul>
@@ -134,6 +134,8 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
+ <p>04.15.2008 - Phenote 1.6-beta4 <a href="http://www.phenote.org/phenote/1.6-beta4/phenote.jnlp">Phenote webstart release 1.6-beta4</a></p>
+ <p>04.15.2008 - <a href="https://sourceforge.net/project/showfiles.php?group_id=76834">Phenote sourceforge page</a> introducted to house beta releases</p>
<p>03.04.2008 - NEW<a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">Phenote webstart release 1.5</a></p>
<p>03.04.2008 - Release of <a href="http://www.phenote.org/download.shtml">Phenote+</a> with platform-specific installers.</p>
<p>03.01.2008 - We'd like to know more about what kind of computer you are using. <a href="http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139" onClick="window.open('http://FreeOnlineSurveys.com/rendersurvey.asp?sid=bf1bbbvdppbjw56402139', '','toolbar=0,location=0,directories=0,status=0,menubar=0,scrollbars=1,resizable=1,width=700,height=480');return false" ><b>Please take our survey</b></a></p>
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-04-16 18:53:23 UTC (rev 1735)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-04-16 22:28:14 UTC (rev 1736)
@@ -20,6 +20,41 @@
Phenote Release Notes
</div>
+<h1>1.6</h1>
+<h2>04.15.2008, version <a href="phenote/1.6-beta4/phenote-plus.jnlp">1.6 - beta4</a></h2>
+<ul>
+<li>feature: in-table editing added [<a href="</li>
+<li>feature: large text fields can now be viewed/edited in separate panel when configured [<a
+href="http://sourceforge.net/tracker/index.php?func=detail&aid=1873002&group_id=76834&atid=887913">1873002</a>
+| <a
+href="http://sourceforge.net/tracker/index.php?func=detail&aid=1610324&group_id=76834&atid=887913">1610324</a>]</li>
+<li>feature: ontology tree browser is a new component, and all ontologies can
+be browsed. terms can be dragged/dropped from the tree to the editor [<a
+href="http://sourceforge.net/tracker/index.php?func=detail&aid=1933810&group_id=76834&atid=887913"<1933810</a>]</li>
+<li>change: configurations birn, worm, ncbo, etc., were all updated with the
+"big text box" for the "description" field</li>
+<li>bugfix: layouts/perspectives are no longer automatically overwritten at
+application close [<a
+href="http://sourceforge.net/tracker/index.php?func=detail&aid=1909013&group_id=76834&atid=887913">1909013</a>]</li>
+<li>bugfix: post-composition window is no longer automatically displaying terms
+in their intersection style when selected</li>
+<li>bugfix: a strange bug where a change to the configuration with the "select
+config" option in phenote was not preserving the change with the new
+windows-installer. this was a specific problem to the ncbo.cfg
+configuration. this originated with a bug in the configuration file, and has
+now been remedied. [<a
+href="http://sourceforge.net/tracker/index.php?func=detail&aid=1911327&group_id=76834&atid=887913">1911327</a>]</li>
+<li>bugfix: column content was being sorted with case-sensitivity. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1890712&group_id=76834&atid=887913">1890712</a>]</li>
+<li>bugfix: selection of a row in the annotation table is preserved when
+sorting on different columns. [<a
+href="http://sourceforge.net/tracker/index.php?func=detail&aid=1922443&group_id=76834&atid=887913">1922443</a>]</li>
+<li>bugfix: field widths in editor panel are maxed to the size of the panel so
+that scrolling horizontally won't have to happen. [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1922353&group_id=76834&atid=887913">1922353</a>]</li>
+<li>bugfix: terms from the autocompletion pick-list were not
+highlighted in the genotype maker
+[<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1909007&group_id=76834&atid=887913">1909007</a>]</li>
+</ul>
+
<h1>1.5</h1>
<h2>03.03.2008, version <a href="phenote/1.5-release/phenote.jnlp">1.5 - release</a></h2>
<p>With the release of version 1.5, we are transitioning over to a new interface. We will continue to support the webstart version of phenote for a couple of releases, but will ultimately switch to the standalone version that is debuting in this release. The new 'Phenote+' will have at least the same capabilities as the original Phenote, but new components will be only added to the new interface. Be sure to choose the proper phenote (or phenote plus) when entering bug reports</p>
Modified: phenote/trunk/doc/phenote-website/ssi/header.html
===================================================================
--- phenote/trunk/doc/phenote-website/ssi/header.html 2008-04-16 18:53:23 UTC (rev 1735)
+++ phenote/trunk/doc/phenote-website/ssi/header.html 2008-04-16 22:28:14 UTC (rev 1736)
@@ -52,6 +52,10 @@
title="Phenote Software Download Page">Download</a>
</li>
<li>
+ <a href="https://sourceforge.net/project/showfiles.php?group_id=76834"
+ title="Betas on Sourceforge">Betas on Sourceforge</a>
+ </li>
+ <li>
<a href="http://www.phenote.org/phenote-release-notes.shtml"
title="Phenote Release Notes">Release Notes</a>
</li>
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|
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From: <nl...@us...> - 2008-04-16 22:55:39
|
Revision: 1737
http://obo.svn.sourceforge.net/obo/?rev=1737&view=rev
Author: nlw
Date: 2008-04-16 15:55:42 -0700 (Wed, 16 Apr 2008)
Log Message:
-----------
couple more ganges to website
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/index.shtml
phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
Modified: phenote/trunk/doc/phenote-website/index.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/index.shtml 2008-04-16 22:28:14 UTC (rev 1736)
+++ phenote/trunk/doc/phenote-website/index.shtml 2008-04-16 22:55:42 UTC (rev 1737)
@@ -134,6 +134,7 @@
<!--No news is good news!-->
<!-- Do not destry the following event template -->
+ <p>04.16.2008 - Phenote will receive a "Google Summer of Code" student through our hosting organization, NESCent. Welcome Michael Wallinga to our team for the summer. You can find a description of his project <a href="http://www.nescent.org/wg_phyloinformatics/Phyloinformatics_summer_of_Code_2008#Matrix_display_of_phenotype_annotations_using_ontologies_in_Phenote">here</a></p>
<p>04.15.2008 - Phenote 1.6-beta4 <a href="http://www.phenote.org/phenote/1.6-beta4/phenote.jnlp">Phenote webstart release 1.6-beta4</a></p>
<p>04.15.2008 - <a href="https://sourceforge.net/project/showfiles.php?group_id=76834">Phenote sourceforge page</a> introducted to house beta releases</p>
<p>03.04.2008 - NEW<a href="http://www.phenote.org/phenote/1.5/phenote.jnlp">Phenote webstart release 1.5</a></p>
Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.shtml
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-04-16 22:28:14 UTC (rev 1736)
+++ phenote/trunk/doc/phenote-website/phenote-release-notes.shtml 2008-04-16 22:55:42 UTC (rev 1737)
@@ -23,7 +23,7 @@
<h1>1.6</h1>
<h2>04.15.2008, version <a href="phenote/1.6-beta4/phenote-plus.jnlp">1.6 - beta4</a></h2>
<ul>
-<li>feature: in-table editing added [<a href="</li>
+<li>feature: in-table editing added, complete with auto-completion </li>
<li>feature: large text fields can now be viewed/edited in separate panel when configured [<a
href="http://sourceforge.net/tracker/index.php?func=detail&aid=1873002&group_id=76834&atid=887913">1873002</a>
| <a
@@ -37,7 +37,7 @@
application close [<a
href="http://sourceforge.net/tracker/index.php?func=detail&aid=1909013&group_id=76834&atid=887913">1909013</a>]</li>
<li>bugfix: post-composition window is no longer automatically displaying terms
-in their intersection style when selected</li>
+in their intersection style when selected [<a href="http://sourceforge.net/tracker/index.php?func=detail&aid=1927441&group_id=76834&atid=887913">1927441</a>] </li>
<li>bugfix: a strange bug where a change to the configuration with the "select
config" option in phenote was not preserving the change with the new
windows-installer. this was a specific problem to the ncbo.cfg
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From: <mg...@us...> - 2008-04-17 17:21:08
|
Revision: 1743
http://obo.svn.sourceforge.net/obo/?rev=1743&view=rev
Author: mgibson
Date: 2008-04-17 10:20:56 -0700 (Thu, 17 Apr 2008)
Log Message:
-----------
postgres jar for worm adapter
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-plus.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-plus.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-04-17 16:09:37 UTC (rev 1742)
+++ phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-04-17 17:20:56 UTC (rev 1743)
@@ -67,6 +67,8 @@
<jar href="jars/wsdl4j-1.5.1.jar"/>
<jar href="jars/owlapi-api.jar"/>
<jar href="jars/piccolo.jar"/>
+ <!-- for worm adapter -->
+ <jar href="jars/postgresql-8.2-504.jdbc3.jar"/>
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2008-04-17 16:09:37 UTC (rev 1742)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2008-04-17 17:20:56 UTC (rev 1743)
@@ -59,6 +59,9 @@
<jar href="jars/wsdl4j-1.5.1.jar"/>
<jar href="jars/axis.jar"/>
<jar href="jars/owlapi-api.jar"/>
+ <!-- for worm adapter -->
+ <jar href="jars/postgresql-8.2-504.jdbc3.jar"/>
+
<!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
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|
|
From: <mg...@us...> - 2008-06-13 20:57:13
|
Revision: 1855
http://obo.svn.sourceforge.net/obo/?rev=1855&view=rev
Author: mgibson
Date: 2008-06-13 13:56:30 -0700 (Fri, 13 Jun 2008)
Log Message:
-----------
fun fun
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2008-06-13 20:45:06 UTC (rev 1854)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2008-06-13 20:56:30 UTC (rev 1855)
@@ -58,6 +58,7 @@
<jar href="jars/saaj.jar"/>
<jar href="jars/jaxrpc.jar"/>
<jar href="jars/wsdl4j-1.5.1.jar"/>
+ <jar href="jars/macify-1.1.jar"/>
<!-- for soap adapter to ckb -->
<jar href="jars/jsr181-api.jar"/>
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2008-06-13 20:45:06 UTC (rev 1854)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2008-06-13 20:56:30 UTC (rev 1855)
@@ -62,6 +62,7 @@
<!-- for worm adapter -->
<jar href="jars/postgresql-8.2-504.jdbc3.jar"/>
+ <jar href="jars/macify-1.1.jar"/>
<!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <mg...@us...> - 2008-06-13 21:13:00
|
Revision: 1856
http://obo.svn.sourceforge.net/obo/?rev=1856&view=rev
Author: mgibson
Date: 2008-06-13 14:06:25 -0700 (Fri, 13 Jun 2008)
Log Message:
-----------
jars
Modified Paths:
--------------
phenote/trunk/doc/phenote-website/phenote-plus.jnlp
phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
phenote/trunk/doc/phenote-website/phenote.jnlp
Modified: phenote/trunk/doc/phenote-website/phenote-plus.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-06-13 20:56:30 UTC (rev 1855)
+++ phenote/trunk/doc/phenote-website/phenote-plus.jnlp 2008-06-13 21:06:25 UTC (rev 1856)
@@ -56,6 +56,7 @@
<jar href="jars/commons-logging-1.0.4.jar"/>
<jar href="jars/saaj.jar"/>
<jar href="jars/jaxrpc.jar"/>
+
<!-- for phenote+ (formerly phenote2) only -->
<jar href="jars/macify-1.1.jar"/>
<jar href="jars/tablelayout.jar"/>
Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2008-06-13 20:56:30 UTC (rev 1855)
+++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2008-06-13 21:06:25 UTC (rev 1856)
@@ -58,7 +58,6 @@
<jar href="jars/saaj.jar"/>
<jar href="jars/jaxrpc.jar"/>
<jar href="jars/wsdl4j-1.5.1.jar"/>
- <jar href="jars/macify-1.1.jar"/>
<!-- for soap adapter to ckb -->
<jar href="jars/jsr181-api.jar"/>
@@ -74,6 +73,18 @@
<jar href="jars/streambuffer.jar"/>
<jar href="jars/saaj-api.jar"/>
+ <!-- plus jars -->
+ <jar href="jars/macify-1.1.jar"/>
+ <jar href="jars/tablelayout.jar"/>
+ <jar href="jars/idw-gpl.jar"/>
+ <jar href="jars/jaxrpc.jar"/>
+ <jar href="jars/axis.jar"/>
+ <jar href="jars/ProtocolEditor.jar"/>
+ <jar href="jars/ols-client.jar"/>
+ <jar href="jars/wsdl4j-1.5.1.jar"/>
+ <jar href="jars/owlapi-api.jar"/>
+ <jar href="jars/piccolo.jar"/>
+
</resources>
<!-- was smart-atlas.cfg, merged into birn.cfg -->
<application-desc main-class="phenote.main.Phenote2">
Modified: phenote/trunk/doc/phenote-website/phenote.jnlp
===================================================================
--- phenote/trunk/doc/phenote-website/phenote.jnlp 2008-06-13 20:56:30 UTC (rev 1855)
+++ phenote/trunk/doc/phenote-website/phenote.jnlp 2008-06-13 21:06:25 UTC (rev 1856)
@@ -62,13 +62,12 @@
<!-- for worm adapter -->
<jar href="jars/postgresql-8.2-504.jdbc3.jar"/>
- <jar href="jars/macify-1.1.jar"/>
-
<!-- jars not needed for webstart(?) axis, commons-beanutils-1.6, commons-discovery,
commons-lang, eutils,jaxrpc, jdom, jebl, jhindexer, jlfgr, jnlp, jsp, jsr
jst, junit, jwf, layouts, libquaqua, macify? -->
- <!-- jars needed for phenote2 but not phenote1? idw-gpl, commons*? -->
+ <!-- jars needed for phenote2 but not phenote1? idw-gpl, commons*? see
+ phenote-plus.jnlp -->
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|
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