From: <nl...@us...> - 2007-02-01 18:27:15
|
Revision: 351 http://svn.sourceforge.net/obo/?rev=351&view=rev Author: nlw Date: 2007-02-01 10:27:15 -0800 (Thu, 01 Feb 2007) Log Message: ----------- more with css Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/about/index.shtml phenote/trunk/doc/phenote-website/css/style.css Modified: phenote/trunk/doc/phenote-website/content/about/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 18:14:55 UTC (rev 350) +++ phenote/trunk/doc/phenote-website/content/about/index.shtml 2007-02-01 18:27:15 UTC (rev 351) @@ -55,7 +55,7 @@ <h3><a name="collaborations">Collaborations</a></h3> This software is being developed in collaboration with several organizations: -<table border="0" class="collab_table"> +<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> Modified: phenote/trunk/doc/phenote-website/css/style.css =================================================================== --- phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 18:14:55 UTC (rev 350) +++ phenote/trunk/doc/phenote-website/css/style.css 2007-02-01 18:27:15 UTC (rev 351) @@ -111,12 +111,16 @@ clear: right; /*border: 1px solid brown;*/ -#main_content .collab_table{ +#main_content table{ align: center; col {width: 100;} td {align: center; } } +#main_content td{ + align: center; +} + /* ---------- "copyright" class. ---------- */ /**/ This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-02-01 23:15:41
|
Revision: 356 http://svn.sourceforge.net/obo/?rev=356&view=rev Author: mgibson Date: 2007-02-01 15:15:42 -0800 (Thu, 01 Feb 2007) Log Message: ----------- -c -> -i which updates config files instead of wipes it out Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp phenote/trunk/doc/phenote-website/phenote-zfin.jnlp Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-02-01 23:14:14 UTC (rev 355) +++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-02-01 23:15:42 UTC (rev 356) @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-c</argument> + <argument>-i</argument> <argument>/flybase.cfg</argument> </application-desc> </jnlp> Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-02-01 23:14:14 UTC (rev 355) +++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-02-01 23:15:42 UTC (rev 356) @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-c</argument> + <argument>-i</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: <mg...@us...> - 2007-02-06 19:21:58
|
Revision: 360 http://svn.sourceforge.net/obo/?rev=360&view=rev Author: mgibson Date: 2007-02-06 11:21:59 -0800 (Tue, 06 Feb 2007) Log Message: ----------- woops -i should be -c for release Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp phenote/trunk/doc/phenote-website/phenote-human.jnlp phenote/trunk/doc/phenote-website/phenote-zfin.jnlp Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-02-06 19:15:49 UTC (rev 359) +++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-02-06 19:21:59 UTC (rev 360) @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-i</argument> + <argument>-c</argument> <argument>/flybase.cfg</argument> </application-desc> </jnlp> Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-02-06 19:15:49 UTC (rev 359) +++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-02-06 19:21:59 UTC (rev 360) @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-i</argument> + <argument>-c</argument> <argument>/human.cfg</argument> </application-desc> </jnlp> Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-02-06 19:15:49 UTC (rev 359) +++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-02-06 19:21:59 UTC (rev 360) @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" -codebase="http://toy.lbl.gov:9010/phenote/1.1/" +codebase="http://toy.lbl.gov:9010/phenote/1.0/" href="phenote-zfin.jnlp"> <information> - <title>Phenote 1.1</title> + <title>Phenote 1.0</title> <vendor>BBOP</vendor> <description>Phenote standalone app via webstart</description> <!-- Declares that the application can run without @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-i</argument> + <argument>-c</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: <mg...@us...> - 2007-02-08 16:32:03
|
Revision: 366 http://svn.sourceforge.net/obo/?rev=366&view=rev Author: mgibson Date: 2007-02-08 08:31:43 -0800 (Thu, 08 Feb 2007) Log Message: ----------- change jnlps to new command line param -i to -u Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp phenote/trunk/doc/phenote-website/phenote-human.jnlp phenote/trunk/doc/phenote-website/phenote-zfin.jnlp Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-02-07 23:05:32 UTC (rev 365) +++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-02-08 16:31:43 UTC (rev 366) @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-c</argument> + <argument>-u</argument> <argument>/flybase.cfg</argument> </application-desc> </jnlp> Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-02-07 23:05:32 UTC (rev 365) +++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-02-08 16:31:43 UTC (rev 366) @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-c</argument> + <argument>-u</argument> <argument>/human.cfg</argument> </application-desc> </jnlp> Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-02-07 23:05:32 UTC (rev 365) +++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-02-08 16:31:43 UTC (rev 366) @@ -38,7 +38,7 @@ <jar href="jars/log4j-1.2.13.jar" /> </resources> <application-desc main-class="phenote.main.Phenote"> - <argument>-c</argument> + <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...> - 2007-02-16 21:34:50
|
Revision: 373 http://svn.sourceforge.net/obo/?rev=373&view=rev Author: nlw Date: 2007-02-16 13:34:45 -0800 (Fri, 16 Feb 2007) Log Message: ----------- adding in a software download page, and listing "development" versions of phenote Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/howtos/index.shtml phenote/trunk/doc/phenote-website/content/info/index.shtml phenote/trunk/doc/phenote-website/ssi/navi_about.html phenote/trunk/doc/phenote-website/ssi/navi_home.html phenote/trunk/doc/phenote-website/ssi/navi_howtos.html phenote/trunk/doc/phenote-website/ssi/navi_info.html Added Paths: ----------- phenote/trunk/doc/phenote-website/content/software/ phenote/trunk/doc/phenote-website/content/software/index.shtml Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-16 21:15:57 UTC (rev 372) +++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-16 21:34:45 UTC (rev 373) @@ -12,13 +12,17 @@ <p> By clicking any of links below, Phenote will use Webstart to launch the java application from the web. Simply clicking on a link below will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software. If a newer version of the software is detected on the server, the newest version will replace your old version and then run.</p> <p> -Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities: +Three configurations of Phenote 1.0 have been created to include the ontologies most appropriate for use by those communities: <ul> <li><a href="/phenote/1.0/phenote-flybase.jnlp">Fly</a></li> <li><a href="/phenote/1.0/phenote-zfin.jnlp">Zebrafish</a></li> <li><a href="/phenote/1.0/phenote-human.jnlp">Human</a></li> </ul> + +Phenote can also be launched from our <a href="/content/software/">Downloads</a> page. There you will also find any newer versions under development. </p> + + <h4>Configuring your browser for Webstart</h4> <p> You must have Java 1.5 or later installed on your computer. Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-02-16 21:15:57 UTC (rev 372) +++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-02-16 21:34:45 UTC (rev 373) @@ -30,6 +30,10 @@ </li> </ul> +<p> +Visit our <a href="/content/software/">Downloads</a> page to get the latest version of Phenote. +</p> + <h3><a name="web_users">Websites Utilizing Phenote Software Components</a></h3> <p>The Dictyostelium Genome Database, <a href="http://dictybase.org"> DictyBase</a>, has a web-based Added: phenote/trunk/doc/phenote-website/content/software/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/software/index.shtml (rev 0) +++ phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-02-16 21:34:45 UTC (rev 373) @@ -0,0 +1,40 @@ +<!--#include virtual="/ssi/header.html" --> + +<div id="page_body"> + +<!--#include virtual="/ssi/navi_home.html" --> + +<div id="main_content"> + +<h2>Phenote Software</h2> + +<h3>Current Release: 1.0</h3> +Three configurations of Phenote have been created to include the ontologies most appropriate for use by those communities. The following are the webstart versions for the most current stable release: +<ul> +<li><a href="/phenote/1.0/phenote-flybase.jnlp">Fly</a></li> +<li><a href="/phenote/1.0/phenote-zfin.jnlp">Zebrafish</a></li> +<li><a href="/phenote/1.0/phenote-human.jnlp">Human</a></li> +</ul> + +<h3><a name="annotation">Development Versions</a></h3> +Note that these versions have not been fully tested and might contain bugs. Please report any bugs you find on our <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">tracker</a> +<ul> +<li><a href="/phenote/1.1/phenote-flybase.jnlp">Fly</a></li> +<li><a href="/phenote/1.1/phenote-zfin.jnlp">Zebrafish</a></li> +<li><a href="/phenote/1.1/phenote-human.jnlp">Human</a></li> +</ul> +<p> +You can also <a href="http://obo.svn.sourceforge.net/*checkout*/obo/phenote/trunk/">checkout</a> the latest Development version of Phenote from sourceforge. +</p> +<p> +For instructions on running Phenote, or downloading the sourcecode, visit our <a href="/content/howtos">How-to pages</a>. +</p> + + + +<br /> +</p> +</div> +</div> + +<!--#include virtual="/ssi/footer.shtml" --> Modified: phenote/trunk/doc/phenote-website/ssi/navi_about.html =================================================================== --- phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-02-16 21:15:57 UTC (rev 372) +++ phenote/trunk/doc/phenote-website/ssi/navi_about.html 2007-02-16 21:34:45 UTC (rev 373) @@ -11,7 +11,7 @@ <a href="/content/info/">Software Info</a> </li> <li> - <a href="/content/under_construction.shtml">Downloads</a> + <a href="/content/software/">Downloads</a> </li> <li> <a href="/content/howtos/">How-tos</a> Modified: phenote/trunk/doc/phenote-website/ssi/navi_home.html =================================================================== --- phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-02-16 21:15:57 UTC (rev 372) +++ phenote/trunk/doc/phenote-website/ssi/navi_home.html 2007-02-16 21:34:45 UTC (rev 373) @@ -11,7 +11,7 @@ <a href="/content/info/">Software Info</a> </li> <li> - <a href="/content/under_construction.shtml">Downloads</a> + <a href="/content/software/">Downloads</a> </li> <li> <a href="/content/howtos/">How-tos</a> Modified: phenote/trunk/doc/phenote-website/ssi/navi_howtos.html =================================================================== --- phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-16 21:15:57 UTC (rev 372) +++ phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-16 21:34:45 UTC (rev 373) @@ -11,7 +11,7 @@ <a href="/content/info/">Software Info</a> </li> <li> - <a href="/content/under_construction.shtml">Downloads</a> + <a href="/content/software/">Downloads</a> </li> <li> <a href="/phenote/content/howtos/">How-tos</a> Modified: phenote/trunk/doc/phenote-website/ssi/navi_info.html =================================================================== --- phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-02-16 21:15:57 UTC (rev 372) +++ phenote/trunk/doc/phenote-website/ssi/navi_info.html 2007-02-16 21:34:45 UTC (rev 373) @@ -27,7 +27,7 @@ </ul> </li> <li> - <a href="/content/under_construction.shtml">Downloads</a> + <a href="/content/software/">Downloads</a> </li> <li> <a href="/content/howtos/">How-tos</a> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-02-21 01:42:27
|
Revision: 375 http://svn.sourceforge.net/obo/?rev=375&view=rev Author: nlw Date: 2007-02-20 17:42:26 -0800 (Tue, 20 Feb 2007) Log Message: ----------- adding content on adding a custom config file Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/howtos/index.shtml phenote/trunk/doc/phenote-website/ssi/navi_howtos.html Added Paths: ----------- phenote/trunk/doc/phenote-website/content/howtos/customize.html Added: phenote/trunk/doc/phenote-website/content/howtos/customize.html =================================================================== --- phenote/trunk/doc/phenote-website/content/howtos/customize.html (rev 0) +++ phenote/trunk/doc/phenote-website/content/howtos/customize.html 2007-02-21 01:42:26 UTC (rev 375) @@ -0,0 +1,48 @@ +<!--#include virtual="/ssi/header.html" --> + +<div id="page_body"> + +<!--#include virtual="/ssi/navi_howtos.html" --> + +<div id="main_content"> + + +<h1><a name="config">How-To: Customize Phenote</a></h1> +<p> +Phenote can be customized in the following ways: +</p> +<ul> + <li><a href="#input">specify input fields</a> and their types</li> + <li><a href="#data_adapter">adding a custom data adapter</a></li> + <li><a href="#ontologies">specify ontologies</a></li> + <li><a href="#post-comp">specify if an ontology field allows for post-composition</a></li> + <li><a href="#ontology-updating">turn on/off ontology-updating</a></li> +</ul> + +<p> +Some basics on customizing phenote: +</p> +<p>Make sure you've already tried running the webstart edition of phenote. Running this once should leave a directory on your computer called ".phenote". On a PC this will be under C:/Documents and Settings/UserName/.phenote. On a mac it will be in your home dir (easiest to get to via a terminal window). +</p> +<p> +Open up the file "my-phenote.cfg" from ".phenote/conf/". It should have one line of text that says "zfin-standalone.cfg". If it doesn't, change this to the name of the file that contains your custom phenote configuration. +</p> +<p> +Next, copy your custom configuration file into the ".phenote/conf/" directory. +</p> +<p>To get a custom ontology that is local and not on SF, you'll have to copy it into ".phenote/obo-files/". Any reference to this ontology within your configuration file must match the filename. +</p> +<p> +Then, you should be able to start phenote with the same webstart link as before, but it should load with this new configuration. you can also start it by double-clicking on the java icon that downloaded to your desktop called "phenote-zfin" or somesuch. +</p> + +<p>More info to come...</p> +<h2>Location of your configuation file</h2> +<h2>Location to put your personal obo files</h2> +<h2>Anatomy of the config file</h2> +<h2>Fields, types</h2> +<h2>Making edits to a config file</h2> +</div> +</div> + +<!--#include virtual="/ssi/footer.shtml" --> Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-16 21:52:49 UTC (rev 374) +++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-21 01:42:26 UTC (rev 375) @@ -44,12 +44,14 @@ </p> -<h4><a name="config">Customizing Input</a></h4> +<h4><a name="customize">Customizing Phenote</a></h4> <p> -Phenote can be customized for data entry fields, and the ontologies that are desired to be included. +Phenote can be customized to allow data entry fields of your choosing, as well as the ontologies that are desired to be included for any of those fields. </p> +<p> +At the moment it requires hand editing of a file, which is fairly painless. If you are interested in configuring your version of Phenote, please read our <a href="/content/howtos/customize.html">Instructions on how to edit the configuration file.</a> In the future, we plan to have an easy-to-use GUI that will allow you to achieve the same results. +</p> - <h3><a name="annotation">Making Annotations</a></h3> <p> </p> Modified: phenote/trunk/doc/phenote-website/ssi/navi_howtos.html =================================================================== --- phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-16 21:52:49 UTC (rev 374) +++ phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-21 01:42:26 UTC (rev 375) @@ -14,12 +14,15 @@ <a href="/content/software/">Downloads</a> </li> <li> - <a href="/phenote/content/howtos/">How-tos</a> + <a href="/content/howtos/">How-tos</a> <ul> <li> <a href="#software">Software</a> </li> <li> + <a href="/content/howtos/customize.html">Customization</a> + </li> + <li> <a href="#annotation">Annotation</a> </li> </ul> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-02-21 01:47:04
|
Revision: 377 http://svn.sourceforge.net/obo/?rev=377&view=rev Author: nlw Date: 2007-02-20 17:47:05 -0800 (Tue, 20 Feb 2007) Log Message: ----------- changing filename of customize links Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/howtos/index.shtml phenote/trunk/doc/phenote-website/ssi/navi_howtos.html Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-21 01:44:50 UTC (rev 376) +++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-02-21 01:47:05 UTC (rev 377) @@ -49,7 +49,7 @@ Phenote can be customized to allow data entry fields of your choosing, as well as the ontologies that are desired to be included for any of those fields. </p> <p> -At the moment it requires hand editing of a file, which is fairly painless. If you are interested in configuring your version of Phenote, please read our <a href="/content/howtos/customize.html">Instructions on how to edit the configuration file.</a> In the future, we plan to have an easy-to-use GUI that will allow you to achieve the same results. +At the moment it requires hand editing of a file, which is fairly painless. If you are interested in configuring your version of Phenote, please read our <a href="/content/howtos/customize.shtml">Instructions on how to edit the configuration file.</a> In the future, we plan to have an easy-to-use GUI that will allow you to achieve the same results. </p> <h3><a name="annotation">Making Annotations</a></h3> Modified: phenote/trunk/doc/phenote-website/ssi/navi_howtos.html =================================================================== --- phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-21 01:44:50 UTC (rev 376) +++ phenote/trunk/doc/phenote-website/ssi/navi_howtos.html 2007-02-21 01:47:05 UTC (rev 377) @@ -20,7 +20,7 @@ <a href="#software">Software</a> </li> <li> - <a href="/content/howtos/customize.html">Customization</a> + <a href="/content/howtos/customize.shtml">Customization</a> </li> <li> <a href="#annotation">Annotation</a> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-03-02 00:03:45
|
Revision: 384 http://svn.sourceforge.net/obo/?rev=384&view=rev Author: mgibson Date: 2007-03-01 16:03:45 -0800 (Thu, 01 Mar 2007) Log Message: ----------- woops forgot to update to 1.1 from 1.0 Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp phenote/trunk/doc/phenote-website/phenote-human.jnlp phenote/trunk/doc/phenote-website/phenote-zfin.jnlp Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-03-01 23:56:22 UTC (rev 383) +++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-03-02 00:03:45 UTC (rev 384) @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" -codebase="http://toy.lbl.gov:9010/phenote/1.0/" +codebase="http://toy.lbl.gov:9010/phenote/1.1" href="phenote-flybase.jnlp"> <information> - <title>Phenote 1.0</title> + <title>Phenote 1.1</title> <vendor>BBOP</vendor> <description>Phenote standalone app via webstart</description> <!-- Declares that the application can run without Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-03-01 23:56:22 UTC (rev 383) +++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-03-02 00:03:45 UTC (rev 384) @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" -codebase="http://toy.lbl.gov:9010/phenote/1.0/" +codebase="http://toy.lbl.gov:9010/phenote/1.1/" href="phenote-human.jnlp"> <information> - <title>Phenote 1.0</title> + <title>Phenote 1.1</title> <vendor>BBOP</vendor> <description>Phenote standalone app via webstart</description> <!-- Declares that the application can run without Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-03-01 23:56:22 UTC (rev 383) +++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-03-02 00:03:45 UTC (rev 384) @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" -codebase="http://toy.lbl.gov:9010/phenote/1.0/" +codebase="http://toy.lbl.gov:9010/phenote/1.1/" href="phenote-zfin.jnlp"> <information> - <title>Phenote 1.0</title> + <title>Phenote 1.1</title> <vendor>BBOP</vendor> <description>Phenote standalone app via webstart</description> <!-- Declares that the application can run without This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-03-08 00:17:04
|
Revision: 390 http://svn.sourceforge.net/obo/?rev=390&view=rev Author: mgibson Date: 2007-03-07 16:17:04 -0800 (Wed, 07 Mar 2007) Log Message: ----------- developer docs - maybe its silly to put this under phenote-website? Added Paths: ----------- phenote/trunk/doc/phenote-website/developer-docs/ phenote/trunk/doc/phenote-website/developer-docs/dataadapter.html Added: phenote/trunk/doc/phenote-website/developer-docs/dataadapter.html =================================================================== --- phenote/trunk/doc/phenote-website/developer-docs/dataadapter.html (rev 0) +++ phenote/trunk/doc/phenote-website/developer-docs/dataadapter.html 2007-03-08 00:17:04 UTC (rev 390) @@ -0,0 +1,130 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + + + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> + + + <title>Creating a phenote data adapter - developer docs</title> +</head> + + +<body> + +<h1 style="text-decoration: underline; text-align: center;">Creating a Phenote Data Adapter</h1> + +First off if youve just downloaded phenote from sourceforge obo svn, +the (latest) source is located in phenote/trunk/src/java. The most +important subdirectories under src/java for creating a data adapter are +phenote/dataadapter and phenote/datamodel. <br> +<br> +A good example data adapter to check out is phenote.dataadapter.phenosyntax.PhenoSyntaxFileAdapter<br> +<br> + +The interface that a phenote data adapter implements is phenote.dataadapter.DataAdapterI, and here is what it looks like:<br> + +<br> + +public interface DataAdapterI {<br> + +<br> + + public void load();<br> + + public CharacterListI load(File f);<br> + +<br> + + public void commit(CharacterListI charList);<br> + + public void commit(CharacterListI charList, File f);<br> + +<br> + + /** Set value to use for loading or writeback, for a file adapter this would be<br> + + the file name */<br> + + public void setAdapterValue(String adapterValue);<br> + + public List<String> getExtensions();<br> + + public String getDescription();<br> + +}<br> + +<br> +The most important methods are load() and commit(charList). + load() will be called by phenote to load up a +phenote.datamodel.CharacterListI. A CharacterListI is just a list of +phenote.datamodel.Characters. A Character is basically a phenotypic +statement (relating E,Q,genotype, etc...). So basically what a data +adapter needs to produce is a list of characters. <br> +<br> +A Character is just a set of tag-value fields, where the tag is the +name of the field (Entity, Quality, Genotype...), and value is the +value of the field. The actual names of the fields come from the +phenote configuration. (link to nicoles doc on phenote config), in +other words the phenote datamodel is proscribed by its configuration +file. This means that either a data adapter needs to be able to read +and write any tag-values that come at it, a dataadapter only handles a +certain subset of a configuration, or a configuration is in tune with a +data adapter. If the set of fields in configuration is completely +different than the fields a data adapter is expecting than the data +adapter wont be able to get/load the data it expects. The upshot is in +addition to making a data adapter you need to make a configuration that +fits with it (or make sure it fits with an existing configuration).<br> +<br> + To set a field in a character use:<br> +setValue(CharField cf, String valueString) which throws a +phenote.datamodel.TermNotFoundException if the valueString is not found +in the ontologies associated with the CharField(via configuration)<br> +where phenote.datamodel.CharField is an object that represents a field in a character. To get a char field you can call <br> +getCharFieldForName(String fieldName) which throws a +phenote.datamodel.CharFieldException if you give it a string that is +not from the configuration. Ok even better I just combined this into +one convenience method:<br> +setValue(String fieldString, String valueString) throws TermNotFoundException, CharFieldException.<br> +For fields with ontologies (with term completion) the valueString has to be the id for the term (not the term name)<br> +<br> +So thats basically it for making characters. Some code might look like this:<br> +<br> +try {<br> + Character c = new Character();<br> + c.setValue("Entity","GO:123");<br> + c.setValue("Quality","PATO:345");<br> + c.setValue("Genotype","somegenotypehere");<br> + ....<br> +} <br> +catch (CharFieldException e) {...} // may want to do this per field - error msg?<br> +catch (TermNotFoundException e) {...} // perhaps per field - error message?<br> +<br> +and for CharacterLists just add the characters made above to it:<br> +CharacterList cl = new CharacterList();<br> +cl.add(character1);<br> +cl.add(character2);<br> +...<br> +<br> +Ok I just noticed that currently only load(file) and +commit(charList,file) are being called via the LoadSaveManager - I will +fix this pronto.<br> +<br> +<br> +<br> +<br> +<br> +ToDo:<br> +So load & save from file menu has been directed to LoadSaveManager +which is hardwired to files(Jim Balhoffs work for phenoxml,syntax, +& nexus adapters - which are all file based - we havent had +non-file yet). This wont work for database adapters and needs a +refactoring - I will get on this! <br> +<br> +Add method to Character for setting a field with just strings:<br> +setValue(String field, String value)<br> +<br> +<br> +(dev note: Im wondering if the file stuff in DataAdapterI should be refactored) +</body> +</html> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-03-28 16:34:12
|
Revision: 426 http://svn.sourceforge.net/obo/?rev=426&view=rev Author: mgibson Date: 2007-03-28 09:34:06 -0700 (Wed, 28 Mar 2007) Log Message: ----------- 1.1 notes & webstart Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-release-notes.html phenote/trunk/doc/phenote-website/phenote.html Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-03-28 16:07:26 UTC (rev 425) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-03-28 16:34:06 UTC (rev 426) @@ -2,159 +2,247 @@ <html> <head> + + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> + + <title>Phenote Release Notes</title> </head> <body> + <h1>Phenote Release Notes</h1> -1.1 -will probably come out in February<br> + +1.2 +will probably come out in May<br> + +<h2><span style="text-decoration: underline;">1.1</span></h2> +<a href="1.1/phenote.jnlp">Phenote 1.1</a><br> <br> +March 28, 2007<br> +<br> +Phenote will merge its default configuration with users configuration, +preserving users changes as well as adding anything new from phenote +upgrade.<br> +User can select configuration they want to use at initialization or +subsequently from file menu + (currently requires phenote restart).<br> +Tab delimited data adapter - thank you nicole!<br> +Beginnings of term history - thank you nicole!<br> +Tabbed main panel if more than 12 fields.<br> +QueryableDataAdapter interface for adding a database data adapter that +can be queried. The data adapter specifies queryable fields, which get +a retrieve button.<br> +Improvements to uvic graphics (still not ready for prime time)<br> +Layout improved<br> +Can now search ALL ontologies of a field<br> +Retrieve obo from web if more up to date or no local found<br> +Refactored code for field guis<br> +Ontology chooser reflects current term (bug fix) <h2><span style="text-decoration: underline;">1.0</span></h2> + <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> + <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> + <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase webby phenote</a><br> + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> + <br> + January 12, 2007<br> + <br> + The main improvement here is the ability to add any field you like, not just E,Q,GC,GT,Pub. In the configured webstarts Stage, Evidence, Description, Abnormal, and Absent have been added through this new mechanism. This entailed a refactoring of the datamodel.<br> + <br> + Webby phenote is now using JSP and Spring.<br> + <br> + 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. <h2><span style="text-decoration: underline;">0.9</span></h2> + <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br> + <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + mid November 2006<br> + <br> + Undo<br> + Christian Pich(Zfin) has added a Quartz scheduler to phenote, which zfin takes advantage of, to schedule when to check for new obo files.<br> + Also Christian Pich upgraded the PhenoteServlet to the Spring framework - much nicer!<br> + Synonyms are now returned from auto complete with [syn] and when selected the term goes in the field (webby & standalone), obsoletes hits with [obs]<br> + Bulk update & copy in standalone.<br> + Jim Balhoff(Nescent) changed radio buttons to checkboxes, and file saver says save not load and recognizes adapter by file extensions, psx->phenosyntax, .xml -> phenoxml <br> + Single quotes escaped for javascript fns.<br> + <h2><span style="text-decoration: underline;">0.8</span></h2> + <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br> + <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + 10/2/06<br> + Added post composition to standalone phenote. Logging for both webby/servlet & standalone.<br> + Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml writer (does pub & genetic context)<br> + Command line reading & writing of phenoxml & phenosyntax.<br> + Application exits on window exit (unless servlet)<br> + Can filter out stage terms from zfin anatomy<br> + <h2><span style="text-decoration: underline;">0.7</span></h2> + <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br> + <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + Web: entity chooser, 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). Entity field and term info installed into zfin phenotype site. term info & completion are scrollable.<br> + Standalone: can read & write pheno-syntax with ids & term names in comments, entity chooser, pub field, use button in term info, sort table by clicking on headers, personal config file gets copied out of jar, paste mac bug fixed, file load/save remembered,layout fixed<br> + <br> + <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.6</span></span></h2> + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote (0.6)</a><br> + <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br> + <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br> + <br> + The main feature of release 0.6 is a webby 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! <br> + <br> + Not much new in the stand alone phenote (as Ive been working on the webby phenote). Mainly it can write pheno-xml, and it uses the latest pato (as of July 28, 2006).<br> + <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.5</span></span></h2> + <br> + <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br> + <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br> + <br> + 5/12/06<br> + 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 @@ -167,22 +255,31 @@ FlyBase character wrappers that do the parsing and creating of Proforma character strings.<br> + <h2><span style="text-decoration: underline;">0.4</span></h2> + <a href="0.4/phenote-flybase.jnlp">0.4 flybase webstart</a><br> + <a href="0.4/phenote-zfin.jnlp">0.4 zfin webstart</a><br> + <br> + 4/26/06<br> + Added Genetic Context field.<br> + Parent & child terms in term info are now clickable/navigable.<br> + Links in descriptions are clickable (should bring up default browser)<br> + Added configuration 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. @@ -191,13 +288,17 @@ configuration for now is for developers (internal xml file), on the todo is to have a gui configuration for users.<br> + Minor bugs: cant delete to 0 rows anymore, synonym search duplicates taken out<br> + <br> + Dev stuff:<br> + 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 @@ -205,131 +306,188 @@ 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.<br> + Renamed Phenotype to Character. Added Character interface CharacterI.<br> + Added tests to test suite.<br> + <br> + <h2><span style="text-decoration: underline;">0.3.1 (CToL)<br> + </span></h2> + <a href="0.3.1/phenote-webstart.jnlp">0.3.1 phenote webstart (for CToL)</a><br> + <br> + 4/7/06<br> + 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<br> + 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.<br> + <h2><span style="text-decoration: underline;">0.3</span></h2> + <a href="0.3/phenote-webstart.jnlp">0.3 phenote webstart</a><br> + <br> + 4/7/06<br> + 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.<br> + <br> + Completion terms now sorted alphabeitcally.<br> + Obsolete is now in addition to regular terms, not in lieu of.<br> + Filtering out attribute values (todo: change to actually filter in values)<br> + Html formatting of term info (todo: make terms selectable)<br> + Children relations are in term info<br> + Term info layout greatly improved<br> + Term info in scroller<br> + Border with label around term info<br> + Put definition at end of term info<br> + <br> + Fixed bugs:<br> + Backspace in ontology combo box<br> + Selection of item in comp list causing exception, not going in term box<br> + No terms with just 1 char<br> + Popup was staying up after selection<br> + <br> + Dev stuff:<br> + Test suite added! (todo: add more tests)<br> + Migrated to jdk 1.5 (which caused some of the bugs above)<br> + Ant file made build.xml.<br> + CompletionList refactored into Ontology (prompted by sorting)<br> + <br> + <br> + <h2><span style="text-decoration: underline;">0.2</span></h2> + <a href="0.2/phenote-webstart.jnlp">0.2 phenote webstart</a><br> + <br> + 3/27/06<br> + Added the ability to do term completion on Synonyms, Definitions, and Obsoletes. Also can mouse over a term in a completion list and get information about it in the term info text area. <br> + <br> + The term info area needs a lot of work.<br> + TODO:<br> + layout, scrollbar, border w title, ordering & lumping parents & children, formatting. <br> + Also perhaps have children & parents be clickable in some fashion either html-like clickable text or as buttons.<br> + Theres also bugs in term completion boxes. If you start backspacing it gets wacky for instance.<br> + <br> + <a href="0.2/phenote-webstart.jnlp"><br> + </a> <h2><span style="text-decoration: underline;">0.1</span></h2> + <a href="0.1/phenote-webstart.jnlp">0.1 phenote webstart</a><br> + <br> + 3/1/06<br> + 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 @@ -337,15 +495,21 @@ 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.<br> + <br> + <a href="0.2/phenote-webstart.jnlp"></a><br> + <br> + <br> + <a href="phenote.html">Phenote main page</a><br> + </body> </html> Modified: phenote/trunk/doc/phenote-website/phenote.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote.html 2007-03-28 16:07:26 UTC (rev 425) +++ phenote/trunk/doc/phenote-website/phenote.html 2007-03-28 16:34:06 UTC (rev 426) @@ -6,22 +6,26 @@ + + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> + + <title>Phenote</title> </head> @@ -32,24 +36,28 @@ + <h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br> + </h1> + <br> + Phenote is a tool to annotate phenotypes using the Entity Quality paradigm. It takes advantage of ontologies. It uses term completion to allow curators quick access to @@ -59,59 +67,30 @@ -<br> - - - -<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> - - - - - <br> -<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> - - - - - +<a href="1.1/phenote.jnlp">Phenote 1.1</a><br> <br> +After phenote downloads the java jar files (takes a while) it wil ask +you what configuration you would like to use, fly, zfin, human,worm....<br> -<a href="1.0/phenote-zfin.jnlp"></a><a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br> - - <br> -To be clear the above webstart links for zfin & fly were made via -configuration not hard wired code. Thus one could in theory configure -phenote for ones own purposes.<br> - - - - -<br> - - - - - Recent addditions include the ability to add any field you like, post compose terms, bulk update, undo, spring framework, and synonyms now are shown in the completion list.<br> @@ -120,12 +99,14 @@ + <br> + Zebrafish requires components of phenote(to plug into their non-public website), not a full web app. Here is a proof of concept of some of @@ -136,12 +117,14 @@ + <br> + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> @@ -149,12 +132,14 @@ + <br> + Webby phenote is a collaboration with Sohel Merchant at dictyBase. Here is what they have done:<br> @@ -162,12 +147,14 @@ + <br> + <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase webby phenote</a><br> @@ -175,18 +162,21 @@ + <br> + <br> + We are doing these releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug tracker</a>) and let us know what you @@ -196,30 +186,37 @@ + <br> + In development - the bleeding edge if you will:<br> + <br> -<a href="1.1/phenote.jnlp">Phenote 1.1</a><br> +<a href="1.1/phenote.jnlp">Phenote 1.2</a><br> + + <h4>Phenote links:<br> + </h4> + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote email list</a><br> @@ -227,6 +224,7 @@ + <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote bug tracker</a><br> @@ -234,6 +232,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug tracker email list</a><br> @@ -241,6 +240,7 @@ + <a href="https://sourceforge.net/svn/?group_id=76834">Phenote source code (obo sourceforge svn)</a><br> @@ -248,6 +248,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote svn commit email list</a><br> @@ -255,6 +256,7 @@ + <a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty webby phenote wiki developer docs</a><br> @@ -262,20 +264,24 @@ + <a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote ncbo internal wiki (ncbo folk only)</a><br> + <a href="developer-docs/dataadapter.html">Phenote dataadapter developer doc</a><br> + <br> + <a href="phenote-release-notes.html">Phenote Release Notes and old webstart releases</a><br> @@ -283,12 +289,14 @@ + <br> + If the Phenote webstart link fails to do anything, then there are probably problems with webstart and/or java(has to be jdk 1.5). Take a look at the <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br> @@ -297,18 +305,21 @@ + page.<br> + <br> + Click here for <a href="phenote-java-requirements.html">phenote java requirements</a><br> @@ -316,160 +327,204 @@ + <br> + <br> + <br> + Old releases: <br> + +<a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> + + + + + + +<a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> + + + + + +<a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br> + + + <br> + <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br> + <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br> + <br> + <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br> + <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br> + <br> + <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br> + <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br> + <br> + <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br> + <br> + <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br> + <br> + <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br> + <br> + <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br> + <br> + <a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br> + <br> + <a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br> + <br> + <a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a> (a special release for the CToL group that uses fish taxonomy)<br> @@ -478,53 +533,62 @@ + <br> + <a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br> + <br> + <a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br> + <br> + <a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br> + <br> + <br> + </body> </html> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-03-28 16:39:46
|
Revision: 427 http://svn.sourceforge.net/obo/?rev=427&view=rev Author: mgibson Date: 2007-03-28 09:39:45 -0700 (Wed, 28 Mar 2007) Log Message: ----------- 1.1 docs Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-release-notes.html phenote/trunk/doc/phenote-website/phenote.html Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-03-28 16:34:06 UTC (rev 426) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-03-28 16:39:45 UTC (rev 427) @@ -36,7 +36,7 @@ (currently requires phenote restart).<br> Tab delimited data adapter - thank you nicole!<br> Beginnings of term history - thank you nicole!<br> -Tabbed main panel if more than 12 fields.<br> +Tabbed main field panel if more than 12 fields.<br> QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.<br> Modified: phenote/trunk/doc/phenote-website/phenote.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote.html 2007-03-28 16:34:06 UTC (rev 426) +++ phenote/trunk/doc/phenote-website/phenote.html 2007-03-28 16:39:45 UTC (rev 427) @@ -76,7 +76,7 @@ <a href="1.1/phenote.jnlp">Phenote 1.1</a><br> <br> -After phenote downloads the java jar files (takes a while) it wil ask +After phenote downloads the java jar files (takes a while) it will ask you what configuration you would like to use, fly, zfin, human,worm....<br> @@ -85,13 +85,10 @@ <br> - - - - - - -Recent addditions include the ability to add any field you like, post compose terms, bulk +Recent addditions include the ability to update config while preserving +your changes, change config, tab delimited format, tabbed field panel, +retrieve ontologies from web, retrieve from field to database, search +ALL ontols, add any field you like, post compose terms, bulk update, undo, spring framework, and synonyms now are shown in the completion list.<br> @@ -188,21 +185,13 @@ <br> +[In development - the bleeding edge if you will:<a href="1.1/phenote.jnlp"> Phenote 1.2</a> coming soon]<br> -In development - the bleeding edge if you will:<br> -<br> -<a href="1.1/phenote.jnlp">Phenote 1.2</a><br> - - - - - - <h4>Phenote links:<br> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-02 23:49:21
|
Revision: 457 http://svn.sourceforge.net/obo/?rev=457&view=rev Author: nlw Date: 2007-04-02 16:49:18 -0700 (Mon, 02 Apr 2007) Log Message: ----------- fixed bad link on homepage rearranged order of "features" Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/info/index.shtml phenote/trunk/doc/phenote-website/content/software/index.shtml phenote/trunk/doc/phenote-website/index.shtml Modified: phenote/trunk/doc/phenote-website/content/info/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-04-02 23:25:14 UTC (rev 456) +++ phenote/trunk/doc/phenote-website/content/info/index.shtml 2007-04-02 23:49:18 UTC (rev 457) @@ -22,12 +22,16 @@ </li> <li>Bulk copy/edit/delete/sort of phenotype-genotype character entries </li> - <li>Two output formats: phenosyntax and phenoxml + <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> <p> Modified: phenote/trunk/doc/phenote-website/content/software/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-04-02 23:25:14 UTC (rev 456) +++ phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-04-02 23:49:18 UTC (rev 457) @@ -8,19 +8,19 @@ <h2>Phenote Software</h2> -<h3><a name="current">Current Release: 1.1</a><a href="http://toy.lbl.gov:9010/phenote/1.1/phenote.jnlp">Webstart</a> -<a href="http://obo.svn.sourceforge.net/*checkout*/obo/phenote/tags/release-1.1/">Download</a></h3> +<h3><a name="current">Current Release: 1.1</a> [<a href="http://toy.lbl.gov:9010/phenote/1.1/phenote.jnlp">Webstart</a>] [ +<a href="http://obo.svn.sourceforge.net/*checkout*/obo/phenote/tags/release-1.1/">Download</a>]</h3> Newest Features: <ul> -<li>Phenote will merge its default configuration with users' configuration. This preserves user's additions as well as adding anything new from phenote upgrades.</li> -<li>User can select configuration they want to use at initialization or subsequently from file menu (currently requires phenote restart). </li> +<li>Can now search ALL ontologies of a field without having to change the pull-down menu</li> +<li>User can choose to update their local copy of an OBO ontology from sourceforge (can also retrieve if no local file found)</li> <li>Tab delimited data adapter</li> <li>Beginnings of term history</li> +<li>User can select configuration they want to use at initialization or subsequently from file menu (currently requires phenote restart). </li> +<li>Phenote merges its default configuration with users' configuration. This preserves user's additions as well as adds anything new from phenote upgrades.</li> +<li>QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.</li> +<li>Improved layout</li> <li>Tabbed main data-entry panel if more than 12 fields are present. Note that all fields will be displayed in the lower display table without scrolling</li> -<li>QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.</li> -<li>Layout improved</li> -<li>Can now search ALL ontologies of a field without having to change the pull-down menu</li> -<li>User can choose to update their local copy of an OBO ontology from sourceforge (can also retrieve if no local file found)</li> <li>Refactored code for field guis</li> <li>Ontology chooser reflects current term (bug fix)</li> <li>Improvements to uvic graphics (still not ready for prime time)</li> Modified: phenote/trunk/doc/phenote-website/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/index.shtml 2007-04-02 23:25:14 UTC (rev 456) +++ phenote/trunk/doc/phenote-website/index.shtml 2007-04-02 23:49:18 UTC (rev 457) @@ -13,7 +13,7 @@ <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 OBO ontology with qualities (such as from <a href="http://www.bioontology.org/wiki/index.php/PATO:About">PATO</a>). </p> -<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. Check out our <a href="/info/">Info</a> page to learn more.</p> +<p>The software can be used as a complete package, or individual compontents can be downloaded and plugged in to your desired application. Check out our <a href="/content/info/">Info</a> page to learn more.</p> <p>This tool is being developed by the <a href="http://berkeleybop.org/">Bioinformatics Core</a> of the <a href="http://www.bioontology.org">National Center for Biomedical Ontology</a>. </p> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-04 05:41:09
|
Revision: 462 http://svn.sourceforge.net/obo/?rev=462&view=rev Author: nlw Date: 2007-04-03 22:41:07 -0700 (Tue, 03 Apr 2007) Log Message: ----------- took out notes about "uvic graphics" due to hesitation by uvic people Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/software/index.shtml phenote/trunk/doc/phenote-website/phenote-release-notes.html Modified: phenote/trunk/doc/phenote-website/content/software/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-04-04 00:01:12 UTC (rev 461) +++ phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-04-04 05:41:07 UTC (rev 462) @@ -23,7 +23,6 @@ <li>Tabbed main data-entry panel if more than 12 fields are present. Note that all fields will be displayed in the lower display table without scrolling</li> <li>Refactored code for field guis</li> <li>Ontology chooser reflects current term (bug fix)</li> -<li>Improvements to uvic graphics (still not ready for prime time)</li> </ul> <p> See the <a href="http://www.phenote.org/phenote-release-notes.html">Release Notes</a> for more information or back-versions. Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-04-04 00:01:12 UTC (rev 461) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-04-04 05:41:07 UTC (rev 462) @@ -40,7 +40,6 @@ QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.<br> -Improvements to uvic graphics (still not ready for prime time)<br> Layout improved<br> Can now search ALL ontologies of a field<br> Retrieve obo from web if more up to date or no local found<br> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-06 17:52:35
|
Revision: 467 http://svn.sourceforge.net/obo/?rev=467&view=rev Author: nlw Date: 2007-04-06 10:50:51 -0700 (Fri, 06 Apr 2007) Log Message: ----------- edited JNLPs to get rid of the BBOP language for the splash screen. Changed to NCBO. Modified 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-zfin.jnlp phenote/trunk/doc/phenote-website/phenote.jnlp Modified: phenote/trunk/doc/phenote-website/phenote-flybase.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-04-05 18:00:01 UTC (rev 466) +++ phenote/trunk/doc/phenote-website/phenote-flybase.jnlp 2007-04-06 17:50:51 UTC (rev 467) @@ -5,7 +5,7 @@ href="phenote-flybase.jnlp"> <information> <title>Phenote 1.1</title> - <vendor>BBOP</vendor> + <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 --> Modified: phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp 2007-04-05 18:00:01 UTC (rev 466) +++ phenote/trunk/doc/phenote-website/phenote-go-function-process.jnlp 2007-04-06 17:50:51 UTC (rev 467) @@ -5,7 +5,7 @@ href="phenote-go-function-process.jnlp"> <information> <title>Phenote-for-GO 1.1</title> - <vendor>BBOP</vendor> + <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 --> Modified: phenote/trunk/doc/phenote-website/phenote-human.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-04-05 18:00:01 UTC (rev 466) +++ phenote/trunk/doc/phenote-website/phenote-human.jnlp 2007-04-06 17:50:51 UTC (rev 467) @@ -5,7 +5,7 @@ href="phenote-human.jnlp"> <information> <title>Phenote 1.1</title> - <vendor>BBOP</vendor> + <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 --> Modified: phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp 2007-04-05 18:00:01 UTC (rev 466) +++ phenote/trunk/doc/phenote-website/phenote-mp-xp.jnlp 2007-04-06 17:50:51 UTC (rev 467) @@ -5,7 +5,7 @@ href="phenote-mp-xp.jnlp"> <information> <title>Phenote-for-GO 1.1</title> - <vendor>BBOP</vendor> + <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 --> Modified: phenote/trunk/doc/phenote-website/phenote-zfin.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-04-05 18:00:01 UTC (rev 466) +++ phenote/trunk/doc/phenote-website/phenote-zfin.jnlp 2007-04-06 17:50:51 UTC (rev 467) @@ -5,7 +5,7 @@ href="phenote-zfin.jnlp"> <information> <title>Phenote 1.1</title> - <vendor>BBOP</vendor> + <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 --> Modified: phenote/trunk/doc/phenote-website/phenote.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-04-05 18:00:01 UTC (rev 466) +++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-04-06 17:50:51 UTC (rev 467) @@ -5,7 +5,7 @@ href="phenote.jnlp"> <information> <title>Phenote 1.1</title> - <vendor>BBOP</vendor> + <vendor>National Center for Biomedial Ontology</vendor> <description>Phenote standalone app via webstart</description> <!-- Declares that the application can run without access to the server it was downloaded from --> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-24 18:49:56
|
Revision: 492 http://svn.sourceforge.net/obo/?rev=492&view=rev Author: nlw Date: 2007-04-24 11:49:34 -0700 (Tue, 24 Apr 2007) Log Message: ----------- added sample data file to the website so people can download and play with it also updating the webpage with it Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/howtos/index.shtml phenote/trunk/doc/phenote-website/phenote-release-notes.html Added Paths: ----------- phenote/trunk/doc/phenote-website/sample_data.xls Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-04-23 19:59:06 UTC (rev 491) +++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-04-24 18:49:34 UTC (rev 492) @@ -54,6 +54,12 @@ </p> <h3><a name="annotation">Making Annotations</a></h3> <p> +You might find it valuable to see sample annotations. Please download this +<a href="~/sample_data.xls"> sample_data.xls </a> file. You will need to set +up your phenote to the "demo" configuration. Then choose "open" under the +"file" menu. Select this file from your download location. The data should +load into the spreadsheet. You can play around and manipulate the annotations. + </p> Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-04-23 19:59:06 UTC (rev 491) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-04-24 18:49:34 UTC (rev 492) @@ -23,6 +23,16 @@ 1.2 will probably come out in May<br> +Features: +Can post-compose with >2 terms <br> +Term history display can be toggled on/off <br> +Synonym types display in term info<br> +Obsolete replacements displayed in term info<br> +Search filters moved into menu <br> +Loading splash screen <br> + +Bug Fixes: + <h2><span style="text-decoration: underline;">1.1</span></h2> <a href="1.1/phenote.jnlp">Phenote 1.1</a><br> <br> Added: phenote/trunk/doc/phenote-website/sample_data.xls =================================================================== --- phenote/trunk/doc/phenote-website/sample_data.xls (rev 0) +++ phenote/trunk/doc/phenote-website/sample_data.xls 2007-04-24 18:49:34 UTC (rev 492) @@ -0,0 +1,85 @@ +Pub Genotype Genetic Context ID Genetic Context Name Entity ID Entity Name Quality ID Quality Name Add'l Entity ID Add'l Entity Name Time Count Unit ID Unit Name Abnormal ID Abnormal Name Description + OMIM602229 - HSCR FMA:7199 Intestine PATO:0000648 obstructed intestinal obstruction in neonates + OMIM602229 - HSCR GO:0007588 excretion PATO:0000911 decreased rate constipation in adults + OMIM602229 - HSCR FMA:14544 Rectum PATO:0001557 lacking physical part FMA:5884 Ganglion short segment HSCR - aganglionic tract in rectum+sigmoid colon + OMIM602229 - HSCR FMA:14548 Sigmoid colon PATO:0001557 lacking physical part FMA:5884 Ganglion short segment HSCR - aganglionic tract in rectum+sigmoid colon + OMIM602229 - WS GO:0007605 sensory perception of sound PATO:0000762 impaired hearng loss (sensorineural deafness) + OMIM602229 - WS FMA:77832 Stria vascularis of cochlear duct PATO:0001557 lacking physical part CL:0000148 melanocyte absence of melanocytes from stria vascularis of the inner ear + OMIM602229 - WS GO:0043473 pigmentation PATO:0000460 abnormal pigmentary abnormalities + OMIM602229 - WS FMA:45618 Hindgut PATO:0001557 lacking physical part FMA:84048 Ganglion cell absence of intrinsic ganglion cells of the terminal hindgut +PMID:10973953 OMIM602229.0001 GO:0016563 transcriptional activator activity PATO:0001624 decreased functionality dominant-negative repression of MITF expression +PMID:10973953 OMIM602229.0001 FMA:67257 Protein PATO:0000468 decreased ***endogenous MITF protein levels reduced +PMID:10973953 OMIM602229.0001 PM:0000003 dominant GO:0016566 specific transcriptional repressor activity PATO:0001559 having extra function acts as a dominant-negative repressor of MITF expression +PMID:9462749 OMIM602229.0001 SO:1000062 nonsense_codon_change_in_transcript PATO:0000467 present E189X stop codon mutation +PMID:9722528 OMIM602229.0001 GO:0065004 protein-DNA complex assembly PATO:0000461 normal ***SOX10mut formed protein-DNA complexes despite mutation +PMID:9722528 OMIM602229.0001 GO:0008104 protein localization PATO:0001032 position GO:0005634 nucleus PATO:0000461 normal protein localization to the nucleus +PMID:12668617 OMIM602229.0001 GO:0016563 transcriptional activator activity PATO:0001508 abolished ***Sox10 ability to activate transcription eliminated +PMID:12668617 OMIM602229.0001 GO:0016563 transcriptional activator activity PATO:0001508 abolished ***Pax3 ability to enhance transcription activity eliminated +PMID:9462749 OMIM602229.0002 SO:1000062 nonsense_codon_change_in_transcript PATO:0001632 anterior to SO:0000330 conserved_region Y83X stop codon mutation before HMG domain +PMID:9722528 OMIM602229.0002 GO:0065004 protein-DNA complex assembly PATO:0001511 non-functional ***SOX10mut failed to form protein-DNA complexes +PMID:9722528 OMIM602229.0002 GO:0008104 protein localization PATO:0000628 mislocalised GO:0005829 cytosol PATO:0000460 abnormal protein mislocalization to the cytosol +PMID:9462749 OMIM602229.0003 SO:1000034^located_in(SO:0000330) nucleotide_insertion^located_in(conserved_region) PATO:0000467 present 6-bp insertion in middle of HMG domain +PMID:9722528 OMIM602229.0003 GO:0065004 protein-DNA complex assembly PATO:0001511 non-functional ***SOX10mut failed to form protein-DNA complexes +PMID:9722528 OMIM602229.0003 GO:0008104 protein localization PATO:0001032 position GO:0005634 nucleus PATO:0000461 normal protein localization to the nucleus +PMID:12668617 OMIM602229.0003 GO:0016563 transcriptional activator activity PATO:0001508 abolished ***Sox10 ability to activate transcription eliminated +PMID:12668617 OMIM602229.0003 GO:0016563 transcriptional activator activity PATO:0001508 abolished ***Pax3 ability to enhance transcription activity eliminated +PMID:9462749 OMIM602229.0004 SO:1000065 frameshift_mutation PATO:0000467 present 2-bp deletion causes frameshift, introduces premature termination codon +PMID:9462749 OMIM602229.0004 SO:1000033 nucleotide_deletion PATO:0000467 present 2-bp deletion causes frameshift, introduces premature termination codon +PMID:9462749 OMIM602229.0004 SO:0000319 stop_codon PATO:0001476 decreased position 2-bp deletion causes frameshift, introduces premature termination codon +PMID:9722528 OMIM602229.0004 GO:0065004 protein-DNA complex assembly PATO:0000461 normal ***SOX10mut formed protein-DNA complexes despite mutation +PMID:9722528 OMIM602229.0004 GO:0008104 protein localization PATO:0001032 position GO:0005634 nucleus PATO:0000461 normal protein localization to the nucleus +PMID:12668617 OMIM602229.0005 GO:0016563 transcriptional activator activity PATO:0001508 abolished ***Sox10 ability to activate transcription eliminated +PMID:12668617 OMIM602229.0005 GO:0003713 transcription coactivator activity PATO:0000467 present ***Sox10 ability to coactivate transcription (with Pax3) present +PMID:9722528 OMIM602229.? GO:0016563 transcriptional activator activity PATO:0001511 non-functional deficient in activity as a transcriptional activator +PMID:11734543 OMIM602229.? FMA:62983 Myelin sheath PATO:0001617 deformed myelin defects +PMID:11734543 OMIM602229.? GO:0016563 transcriptional activator activity PATO:0000462 absent ***SOX10 failed to transactivate the CX32 promoter +PMID:11734543 OMIM602229.? GO:0008134^located_in(SO:0000167) transcription factor binding^located_in(promoter) PATO:0000462 absent ***SOX10 failed to transactivate the CX32 promoter +PMID:9462749 [OMIM602229.0001/+] GO:0007605 sensory perception of sound PATO:0000468 decreased bilateral profound hearing loss +PMID:9462749 [OMIM602229.0001/+] FMA:53667 Hair PATO:0000323 white white hair color +PMID:9462749 [OMIM602229.0001/+] FMA:58611 Iridial part of retina PATO:0000318 blue blue irides with grey speckles +PMID:9462749 [OMIM602229.0001/+] FMA:63846^located_in(FMA:7163) Cell pigment^located_in(Skin) PATO:0001608 patchy depigmented skin patches +PMID:9462749 [OMIM602229.0001/+] FMA:63846 Cell pigment PATO:0000460 abnormal pigmentary abnormalities (detailed with other entries) +PMID:9462749 [OMIM602229.0001/+] FMA:7199 Intestine PATO:0000648 obstructed intestinal obstruction in neonates +PMID:9462749 [OMIM602229.0001/+] GO:0007588 excretion PATO:0000911 decreased rate constipation in adults +PMID:9462749 [OMIM602229.0001/+] FMA:14544 Rectum PATO:0001557 lacking physical part FMA:5884 Ganglion short segment HSCR - aganglionic tract in rectum+sigmoid colon +PMID:9462749 [OMIM602229.0001/+] FMA:14548 Sigmoid colon PATO:0001557 lacking physical part FMA:5884 Ganglion short segment HSCR - aganglionic tract in rectum+sigmoid colon +PMID:9462749 [OMIM602229.0001/+] FMA:58611 Iridial part of retina PATO:0001533 multi-colored blue irides with grey speckles +PMID:9462749 [OMIM602229.0001/+] FMA:58611 Iridial part of retina PATO:0000950 grey blue irides with grey speckles +PMID:9462749 [OMIM602229.0002/+] GO:0007605 sensory perception of sound PATO:0000468 decreased bilateral profound hearing loss +PMID:9462749 [OMIM602229.0002/+] FMA:53667 Hair PATO:0000665 light fair hair color +PMID:9462749 [OMIM602229.0002/+] FMA:58611 Iridial part of retina PATO:0001265 bright blue vivid blue eyes +PMID:9462749 [OMIM602229.0002/+] FMA:7199 Intestine PATO:0001624 decreased functionality bowel problems +PMID:9462749 [OMIM602229.0002/+] FMA:5884^located_in(FMA:14544) Ganglion^located_in(Rectum) PATO:0000419 decreased number number of ganglia was dramatically reduced +PMID:9462749 [OMIM602229.0003/+] GO:0007605 sensory perception of sound PATO:0000468 decreased deafness +PMID:9462749 [OMIM602229.0003/+] FMA:14544 Rectum PATO:0001557 lacking physical part FMA:5884 Ganglion short segment HSCR - aganglionic tract in rectum+sigmoid colon +PMID:9462749 [OMIM602229.0003/+] FMA:14548 Sigmoid colon PATO:0001557 lacking physical part FMA:5884 Ganglion short segment HSCR - aganglionic tract in rectum+sigmoid colon +PMID:9462749 [OMIM602229.0004/+] PM:0000019 penetrance_incomplete GO:0007605 sensory perception of sound PATO:0000468 decreased deafness +PMID:9462749 [OMIM602229.0004/+] PM:0000023 expressivity_incomplete FMA:63846^contained_in(FMA:61695) Cell pigment^contained_in(Body surface) PATO:0000468 decreased hypopigmentation +PMID:9462749 [OMIM602229.0004/+] FMA:7199 Intestine PATO:0001557 lacking physical part FMA:84048 Ganglion cell HSCR +PMID:9462749 [OMIM602229.0004/+] PM:0000023 expressivity_incomplete FMA:53667 Hair PATO:0000323 white white hair color +PMID:9462749 [OMIM602229.0004/+] PM:0000019 penetrance_incomplete FMA:7199 Intestine PATO:0001571 dilated megacolon +PMID:10441344 OMIM602229.0005 SO:1000061 nonconservative_missense_codon_change_in_transcript PATO:0000467 present SER135THR mutation +PMID:10441344 OMIM602229.0005 SO:1000061 nonconservative_missense_codon_change_in_transcript PATO:0000467 present SER135THR mutation +PMID:2280978 Yemenite deaf-blind hypopigmentation syndrome FMA:63846^located_in(FMA:7163) Cell pigment^located_in(Skin) PATO:0001608 patchy hypo and hyperpigmented skin +PMID:2280978 Yemenite deaf-blind hypopigmentation syndrome FMA:58238 Cornea PATO:0000587 decreased size microcornea +PMID:2280978 Yemenite deaf-blind hypopigmentation syndrome FMA:54448 Eye MP:0005262 coloboma coloboma +PMID:2280978 Yemenite deaf-blind hypopigmentation syndrome PM:0000019 penetrance_incomplete GO:0007605 sensory perception of sound PATO:0000468 decreased severe hearing loss +PMID:10441344 OMIM602229.0005 FMA:63846^located_in(FMA:7163) Cell pigment^located_in(Skin) PATO:0001608 patchy hypo and hyperpigmented skin +PMID:10441344 OMIM602229.0005 PM:0000019 penetrance_incomplete GO:0007605 sensory perception of sound PATO:0000468 decreased severe hearing loss +PMID:10482261 OMIM602229.0008 FMA:62983 Myelin sheath PATO:0001617 deformed leukodystrophy - progressive degeneration development of the myelin sheath +PMID:10482261 OMIM602229.0008 FMA:7199 Intestine PATO:0000648 obstructed intestinal obstruction in neonates +PMID:10482261 OMIM602229.0008 FMA:7199 Intestine PATO:0001557 lacking physical part FMA:5884 Ganglion long segment HSCR - aganglionic tract in entire colon +PMID:10482261 OMIM602229.0008 FMA:63846^located_in(FMA:58237) Cell pigment^located_in(Left iris) PATO:0000616 asymmetrical FMA:63846^located_in(FMA:58236) Cell pigment^located_in(Right iris) heterochromia iridis - one eye is different color (intensity) than the other +PMID:10482261 OMIM602229.0008 PM:0000022 expressivity_complete GO:0007605 sensory perception of sound PATO:0000468 decreased profound hearing loss +PMID:10482261 OMIM602229.0008 FMA:59516 Root of nose PATO:0000600 increased width broad nasal root +PMID:10482261 OMIM602229.0008 FMA:59324 Medial angle of left eye PATO:0000374 increased distance FMA:59323 Medial angle of right eye dystopia canthorum - inner corners of the eyes (canthi) are spaced farther apart than normal +PMID:10482261 OMIM602229.0008 GO:0048589^has_participant(FMA:20394) developmental growth^has_participant(Body) PATO:0000911 decreased rate developmental delay +PMID:10482261 OMIM602229.0008 FMA:20394 Body MP:0000754 partial paralysis spastic quadraplegia +PMID:10482261 OMIM602229.0008 FMA:9721 Tendon PATO:0001568 having decreased function GO:0060004 reflex loss of deep tendon reflexes +PMID:10482261 OMIM602229.0008 PM:0000022 expressivity_complete GO:0007600 sensory perception PATO:0000468 decreased sensory dullness +PMID:10482261 OMIM602229.0008 FMA:9903 Peripheral nervous system PATO:0001624 decreased functionality peripheral neuropathy +PMID:10482261 OMIM602229.0008 FMA:5867 Motor nerve PATO:0001585 conduction ***decreased conductive velocity +PMID:10482261 OMIM602229.0008 FMA:30316^contained_in(FMA:7182) Muscle^contained_in(Limb) PATO:0001623 atrophied muscles in all limbs were severely atrophic +PMID:10482261 OMIM602229.0008 FMA:67257^contained_in(FMA:20935) Protein^contained_in(Cerebrospinal fluid) PATO:0001162 increased concentration Protein in the cerebrospinal fluid was elevated +PMID:10482261 OMIM602229.0008 GO:0008038^contained_in(FMA:79876) neuron recognition^contained_in(Brainstem) PATO:0000468 decreased GO:0007605 sensory perception of sound no auditory brainstem response bilaterally +PMID:10482261 OMIM602229.0008 FMA:62983^located_in(FMA:50801) Myelin sheath^located_in(Brain) PATO:0000468 decreased prominent deficiency of myelination in the entire brain This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-24 20:52:42
|
Revision: 494 http://svn.sourceforge.net/obo/?rev=494&view=rev Author: nlw Date: 2007-04-24 13:52:44 -0700 (Tue, 24 Apr 2007) Log Message: ----------- adding documentation on config customization... testing pic links Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/howtos/customize.shtml Added Paths: ----------- phenote/trunk/doc/phenote-website/images/config-data-adapter.png Modified: phenote/trunk/doc/phenote-website/content/howtos/customize.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/howtos/customize.shtml 2007-04-24 18:51:07 UTC (rev 493) +++ phenote/trunk/doc/phenote-website/content/howtos/customize.shtml 2007-04-24 20:52:44 UTC (rev 494) @@ -54,6 +54,18 @@ <p>To get a custom ontology that is local and not on SF, you'll have to copy it into ".phenote/obo-files/". Any reference to this ontology within your configuration file must match the filename. </p> <h2>Anatomy of the config file</h2> +You can download a sample configuration file <a href="/demo.cfg">here</a>. Descriptive images on this page are taken from this demo.cfg configuration file. +<h3>Data Adapters</h3> +<img src="/images/config-data-adapter.png" align="right" caption="Figure 1"> +<p> +The first customizable items in the configuration file are the Data Adapters (see Figure 1). Any developer can write their own data adapter and plug it into the configuration for use during file loading and saving, or for database retrieval. If you are interested in writing your own data adapter, please read the <a href="/developer-docs/dataadapter.html"> Data Adapter developer documentation</a>. <p> +<p> +You can add your customized data adapter at the top of the file. Additionally you can specify if it is "enabled". Enabling a data adapter makes it available during load/save functions. In the case of the example in Figure 1, the PhenoXML and NEXUS data adapters are disabled, while the phenosyntax and delimited adapters are enabled. </p> +<p> WARNING: Be sure to enable at least one data adapter, otherwise you will be unable to save your annotations.</p> + +<h3>Uvic-graph, term-history</h3> +These items are currently under development. By default they are disabled for the typical user. + <h2>Fields, types</h2> <h2>Making edits to a config file</h2> </div> Added: phenote/trunk/doc/phenote-website/images/config-data-adapter.png =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/images/config-data-adapter.png ___________________________________________________________________ Name: svn:mime-type + application/octet-stream This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-30 20:54:09
|
Revision: 516 http://svn.sourceforge.net/obo/?rev=516&view=rev Author: nlw Date: 2007-04-30 13:54:09 -0700 (Mon, 30 Apr 2007) Log Message: ----------- adding an irc_chat instruction page, along with the applicable js Added Paths: ----------- phenote/trunk/doc/phenote-website/irc_chat.shtml phenote/trunk/doc/phenote-website/irc_script.js Added: phenote/trunk/doc/phenote-website/irc_chat.shtml =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat.shtml (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat.shtml 2007-04-30 20:54:09 UTC (rev 516) @@ -0,0 +1,36 @@ +<!--#include virtual="/ssi/header.html" --> + <script language="JavaScript" src="/irc_script.js"><!-- --></script> +<div id="page_body"> + +<!--#include virtual="/ssi/navi_home.html" --> + +<div id="main_content"> +<h2>Phenote Working Group IRC Chat</h2> + +When: First Tuesday of every month; 8:30am <br/> + +<p>You will need an IRC client to visit our chats. You can download any number of free clients to do this. You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p> + +<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. </p> + + <form method="post" name="launcher"> + <table style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" width="100%"> +<tbody> + <tr> + <td colspan="1" rowspan="1" width="156">IRC Nickname</td> + <td style="width: 327px;"><input size="40" name="username"></td> + </tr> + <tr> + <td colspan="2" rowspan="1" style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0); "onclick="startApplets()" type="button"><br> + </td> + </tr> + +</tbody> +</table> +</form> + +</div> +</div> + +<!--#include virtual="/ssi/footer.shtml" --> + Added: phenote/trunk/doc/phenote-website/irc_script.js =================================================================== --- phenote/trunk/doc/phenote-website/irc_script.js (rev 0) +++ phenote/trunk/doc/phenote-website/irc_script.js 2007-04-30 20:54:09 UTC (rev 516) @@ -0,0 +1,37 @@ +var ircwindow = null; +var vncwindow = null; + +function startApplets() { + + if (ircwindow != null) { + ircwindow.close(); + ircwindow = null; + } + + if (vncwindow != null) { + vncwindow.close(); + vncwindow = null; + } + + // vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800"); + ircwindow = window.open("about:blank", "My window", "scrollbars=no,status=no,width=510,height=430"); + + var html = ""; + + html += "<html><body>\n"; + html += "<applet code=\"IRCApplet.class\" archive=\"irc.jar,pixx.jar\" width=475 height=400>\n"; + html += "<param name=\"CABINETS\" value=\"irc.cab,securedirc.cab,pixx.cab\">\n"; + html += "<param name=\"nick\" value='"+document.forms["launcher"].username.value+"'>\n"; + html += "<param name=\"fullname\" value='"+document.forms["launcher"].username.value+"'>\n"; + + html += "<param name=\"alternatenick\" value=\"Anon???\">\n"; + html += "<param name=\"host\" value=\"irc.sf.net\">\n"; + html += "<param name=\"command1\" value=\"/join #phenote\">\n"; + html += "<param name=\"gui\" value=\"pixx\">\n"; + html += "</applet>\n"; + html += "</body></html>"; + +// alert(html); + ircwindow.document.writeln(html); + ircwindow.document.close(); +} This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-30 21:13:19
|
Revision: 519 http://svn.sourceforge.net/obo/?rev=519&view=rev Author: nlw Date: 2007-04-30 14:13:21 -0700 (Mon, 30 Apr 2007) Log Message: ----------- adding the other files for irc chat Added Paths: ----------- phenote/trunk/doc/phenote-website/irc-unsigned.jar phenote/trunk/doc/phenote-website/irc.cab phenote/trunk/doc/phenote-website/irc.jar phenote/trunk/doc/phenote-website/securedirc-unsigned.cab phenote/trunk/doc/phenote-website/securedirc.cab Added: phenote/trunk/doc/phenote-website/irc-unsigned.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc-unsigned.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc.cab =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc.cab ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/securedirc-unsigned.cab =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/securedirc-unsigned.cab ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/securedirc.cab =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/securedirc.cab ___________________________________________________________________ Name: svn:mime-type + application/octet-stream This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-30 21:34:46
|
Revision: 520 http://svn.sourceforge.net/obo/?rev=520&view=rev Author: nlw Date: 2007-04-30 14:34:47 -0700 (Mon, 30 Apr 2007) Log Message: ----------- ok, i removed some of the irc files i added b/c it didn't work. instead, i'm adding john's old webinar folder...pretty much in its entirety. there's probably some stuff that shouldn't be here, but i'll figure that out after i get it working Added Paths: ----------- phenote/trunk/doc/phenote-website/irc_chat/ phenote/trunk/doc/phenote-website/irc_chat/EIRC-gfx.jar phenote/trunk/doc/phenote-website/irc_chat/EIRC.jar phenote/trunk/doc/phenote-website/irc_chat/IRCApplet.class phenote/trunk/doc/phenote-website/irc_chat/background.gif phenote/trunk/doc/phenote-website/irc_chat/blank.html phenote/trunk/doc/phenote-website/irc_chat/chat/ phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.cab phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.jar phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.cab phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.jar phenote/trunk/doc/phenote-website/irc_chat/chat/index.html phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/ phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boink.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boooh.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boop.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Click.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Clock.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Drip.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Hit.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Magic.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Pipe.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Pouet.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Rifle.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Ringin.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Squish.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Train.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Warning.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Whistle.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Whoosh.au phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Yoo.au phenote/trunk/doc/phenote-website/irc_chat/contact.html phenote/trunk/doc/phenote-website/irc_chat/eirc.html phenote/trunk/doc/phenote-website/irc_chat/english.lng phenote/trunk/doc/phenote-website/irc_chat/etiquette.html phenote/trunk/doc/phenote-website/irc_chat/first.html phenote/trunk/doc/phenote-website/irc_chat/french.lng phenote/trunk/doc/phenote-website/irc_chat/gizmo.html phenote/trunk/doc/phenote-website/irc_chat/images/ phenote/trunk/doc/phenote-website/irc_chat/images/splash.jpg phenote/trunk/doc/phenote-website/irc_chat/index.html phenote/trunk/doc/phenote-website/irc_chat/irc-unsigned.jar phenote/trunk/doc/phenote-website/irc_chat/irc.cab phenote/trunk/doc/phenote-website/irc_chat/irc.html phenote/trunk/doc/phenote-website/irc_chat/irc.jar phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml phenote/trunk/doc/phenote-website/irc_chat/irc_script.js phenote/trunk/doc/phenote-website/irc_chat/junk.html phenote/trunk/doc/phenote-website/irc_chat/pbtn3.2.zip phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng phenote/trunk/doc/phenote-website/irc_chat/pixx-french.lng phenote/trunk/doc/phenote-website/irc_chat/pixx-readme.txt phenote/trunk/doc/phenote-website/irc_chat/pixx.cab phenote/trunk/doc/phenote-website/irc_chat/pixx.jar phenote/trunk/doc/phenote-website/irc_chat/pjirc.cfg phenote/trunk/doc/phenote-website/irc_chat/pjirc_2_2_1_bin.zip phenote/trunk/doc/phenote-website/irc_chat/script.js phenote/trunk/doc/phenote-website/irc_chat/securedirc-unsigned.cab phenote/trunk/doc/phenote-website/irc_chat/securedirc.cab phenote/trunk/doc/phenote-website/irc_chat/style.css phenote/trunk/doc/phenote-website/irc_chat/technologies.html phenote/trunk/doc/phenote-website/irc_chat/vnc.html Removed Paths: ------------- phenote/trunk/doc/phenote-website/IRCApplet.class phenote/trunk/doc/phenote-website/irc.cab phenote/trunk/doc/phenote-website/irc.jar phenote/trunk/doc/phenote-website/irc_chat.shtml phenote/trunk/doc/phenote-website/irc_script.js phenote/trunk/doc/phenote-website/securedirc-unsigned.cab phenote/trunk/doc/phenote-website/securedirc.cab Deleted: phenote/trunk/doc/phenote-website/IRCApplet.class =================================================================== (Binary files differ) Deleted: phenote/trunk/doc/phenote-website/irc.cab =================================================================== (Binary files differ) Deleted: phenote/trunk/doc/phenote-website/irc.jar =================================================================== (Binary files differ) Added: phenote/trunk/doc/phenote-website/irc_chat/EIRC-gfx.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/EIRC-gfx.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/EIRC.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/EIRC.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/IRCApplet.class =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/IRCApplet.class ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/background.gif =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/background.gif ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/blank.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/blank.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/blank.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,44 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + <meta http-equiv="content-type" + content="text/html; charset=ISO-8859-1"> + <title>OBO-Edit Webinar Overview</title> + <link type="text/css" href="style.css" rel="stylesheet"> + <script language="JavaScript" src="script.js"> +</head> +<body> +<input><input> <br> +<table style="width: 780px; height: 619px;" cellpadding="10" + cellspacing="0"> + <tbody> + <tr> + <td + style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img + style="width: 200px; height: 138px;" alt="OBO-Edit Logo" + src="images/splash.jpg"></td> + <td + style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;"> + <font color="white"> + <h1>OBO-Edit +Webinar</h1> + </font> + <h2><font color="white">Under construction</font></h2> + <font color="white"> </font> </td> + </tr> + <tr> + <td + style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;"> + <ul> + </ul> + </td> + <td + style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"><br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"><font size="+2">Coming soon</font><br> + </span></span></td> + </tr> + </tbody> +</table> +</body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.cab =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.cab ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC-cfg.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.cab =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.cab ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/EIRC.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/index.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/chat/index.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/chat/index.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,40 @@ +<HTML><HEAD> +<TITLE>www.coolsmile.net - Chat sympa et gratuit</TITLE> +</HEAD> + +<BODY style="background-color: #000000; margin: 1px; overflow: hidden;"> +<CENTER> +<APPLET name="coolsmile" code="EIRC.class" width="100%" height="100%"> + <PARAM name="archive" value="EIRC.jar,EIRC-cfg.jar"> + <PARAM name="cabbase" value="EIRC.cab,EIRC-cfg.cab"> + <PARAM name="server" value="irc.sf.net"> + <PARAM name="port" value="6667"> + <PARAM name="font_name" value="Helvetica"> + <PARAM name="font_size" value="11"> + <PARAM name="language" value=""> + <PARAM name="mainbg" value="#809BDC"> + <PARAM name="mainfg" value="#000000"> + <PARAM name="textbg" value="#FFFFFF"> + <PARAM name="textfg" value="#000000"> + <PARAM name="selbg" value="#F0F0FF"> + <PARAM name="selfg" value="#000000"> + <PARAM name="join" value="#oboedit"> + <PARAM name="username" value="cool"> + <PARAM name="realname" value="20 H Internet"> + <PARAM name="nickname" value="Hello??????"> + <PARAM name="login" value="1"> + <PARAM name="asl" value="1"> + <PARAM name="spawn_frame" value="0"> + <PARAM name="width" value="700"> + <PARAM name="height" value="500"> + <PARAM name="write_color" value="12"> + <PARAM name="debug_traffic" value="0"> + <PARAM name="boxmessage" value="Please wait while loading chat box..."> + <PARAM name="boxbgcolor" value="blue"> + <PARAM name="boxfgcolor" value="black"> + <PARAM name="progressbar" value="true"> + <PARAM name="progresscolor" value="red"> + <B>You must enable or <A HREF="http://www.java.com">setup Java</A> in your web browser !</B> +</APPLET> +</CENTER> +</BODY></HTML> \ No newline at end of file Added: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boink.au =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boink.au ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boooh.au =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Boooh.au 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on: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Clock.au ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Drip.au =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Drip.au ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Hit.au =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Hit.au ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/chat/sfx/Magic.au 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=================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/contact.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/contact.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,58 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + <meta http-equiv="content-type" + content="text/html; charset=ISO-8859-1"> + <title>OBO-Edit Webinar Contacts</title> + <link type="text/css" href="style.css" rel="stylesheet"> +</head> +<body> +<br> +<table style="width: 780px; height: 619px;" cellpadding="10" + cellspacing="0"> + <tbody> + <tr> + <td + style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img + style="width: 200px; height: 138px;" alt="OBO-Edit Logo" + src="images/splash.jpg"></td> + <td + style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;"> + <font color="white"> + <h1>OBO-Edit +Webinar</h1> + <h2>Contact<br> + </h2> + </font> </td> + </tr> + <tr> + <td + style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;"> + <ul> + <li><a href="index.html">Overview</a></li> + <li><a href="technologies.html">Technologies</a><br> + </li> + <ul> + <li><a href="vnc.html">VNC</a></li> + <li><a href="irc.html">IRC</a></li> + <li><a href="gizmo.html">The Gizmo Project</a></li> + <li><a href="oboedit.html">OBO-Edit</a></li> + </ul> + <li><a href="etiquette.html">Etiquette</a></li> + <li style="color: rgb(255, 255, 255);">Contact</li> + </ul> + </td> + <td + style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"> + <br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);">For more information, +please contact John Day-Richter at <b>joh...@ay...</b>, +or call him on The Gizmo Project with id <b>johnrichter.</b><br> + </span></span><span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"> </span></span></td> + </tr> + </tbody> +</table> +</body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/eirc.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/eirc.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/eirc.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,37 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" + "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> +<html xmlns="http://www.w3.org/1999/xhtml"> + <head> + <title>Eteria IRC Client</title> + </head> + + <body> + <applet code="EIRC" archive="EIRC.jar,EIRC-gfx.jar" width="620" height="400"> + <!-- Uncomment the line below to use signed CABs /--> + <!--param name="cabinets" value="EIRC.cab,EIRC-gfx.cab" /--> + <param name="server" value="irc.diboo.net" > + <!--param name="server" value="eu.undernet.org" /--> + <!--param name="port" value="6667" /--> + <!--param name="mainbg" value="#424242" /--> + <param name="mainbg" value="#C0C0C0" /> + <param name="mainfg" value="#000000" /> + <param name="textbg" value="#FFFFFF" /> + <param name="textfg" value="#000000" /> + <param name="selbg" value="#00007F" /> + <param name="selfg" value="#FFFFFF" /> + <param name="channel" value="#eirc" /> + <param name="titleExtra" value=" - EIRC" /> + <param name="nickname" value="Guest????" /> + <param name="login" value="1" /> + <!--param name="spawn_frame" value="1" /--> + <!--param name="frame_width" value="620" /--> + <!--param name="frame_height" value="400" /--> + <!--param name="language" value="en" /--> + <!--param name="country" value="US" /--> + + <h1>Eteria IRC Client</h1> + <p> + Sorry, but you need a Java 1.1.x enabled browser to use EIRC.</p> + </applet> + </body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/english.lng =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/english.lng (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/english.lng 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,93 @@ +# +# This java file is a part of the +# +# - Plouf's Java IRC Client - +# +# Copyright (C) 2004 Philippe Detournay +# +# This file is licensed under the GPL license +# +# All contacts : the...@ya... +# +# +# Syntax : +# Comments begin with the # character. This character must be the first character of the line. +# A data line has three parts : the data id, the data id description, the data string. +# - Data id : An hexadecimal figure identifying the string. +# - Data description : Begins by [ and ends by ]. The description is not parsed and +# can be any string. +# - Data string : The string itself. Parameters are specified using the %i syntax. +# +# Trailing spaces can be added using the \s escape character. + +0001 [INTERPRETOR_NOT_ON_CHANNEL] Not on a channel +0002 [INTERPRETOR_UNKNOWN_DCC] %1 : unknown dcc subcommand +0003 [INTERPRETOR_INSUFFICIENT_PARAMETERS] %1 : insufficient parameters +0004 [INTERPRETOR_BAD_CONTEXT] %1 : unable to perform in current context +0005 [INTERPRETOR_CANNOT_CTCP_IN_DCCCHAT] Cannot send CTCP codes via DCC Chat +0006 [INTERPRETOR_UNKNOWN_CONFIG] %1 : unknown config subcommand +0007 [INTERPRETOR_TIMESTAMP_ON] Timestamp enabled +0008 [INTERPRETOR_TIMESTAMP_OFF] Timestamp disabled +0009 [INTERPRETOR_SMILEYS_ON] Graphical smileys enabled +000a [INTERPRETOR_SMILEYS_OFF] Graphical smileys disabled +000b [INTERPRETOR_IGNORE_ON] Now ignoring %1 +000c [INTERPRETOR_IGNORE_OFF] Not ignoring %1 anymore +000d [INTERPRETOR_MULTISERVER_DISABLED] Multiserver support is disabled + +0101 [DCC_WAITING_INCOMING] Waiting for incoming connection... +0102 [DCC_UNABLE_TO_OPEN_CONNECTION] Unable to open connection : %1 +0103 [DCC_CONNECTION_ESTABLISHED] DCC Connection established +0104 [DCC_CONNECTION_CLOSED] Connection closed +0105 [DCC_ERROR] Error : %1 +0106 [DCC_UNABLE_TO_SEND_TO] %1 : unable to send to %2 +0107 [DCC_BAD_CONTEXT] Unable to execute command from current context +0108 [DCC_NOT_CONNECTED] Not connected +0109 [DCC_UNABLE_PASSIVE_MODE] Unable to initialize passive mode +010a [CTCP_PING_REPLY] [%1 PING reply] : %2 seconds +010b [DCC_STREAM_CLOSED] Stream closed + +0201 [IDENT_FAILED_LAUNCH] Failed to launch Ident server : %1 +0202 [IDENT_REQUEST] Ident request from %1 +0203 [IDENT_ERROR] Error occurred +0204 [IDENT_REPLIED] Replied %1 +0205 [IDENT_DEFAULT_USER] default user +0206 [IDENT_NO_USER] No user for request +0207 [IDENT_RUNNING_ON_PORT] Ident server running on port %1 +0208 [IDENT_LEAVING] Ident server leaving : %1 +0209 [IDENT_NONE] none +020a [IDENT_UNKNOWN] unknown +020b [IDENT_UNDEFINED] Undefined result + +0301 [FILE_SAVEAS] Save file as + +0401 [ABOUT_ABOUT] About +0402 [ABOUT_PROGRAMMING] Programming +0403 [ABOUT_DESIGN] Design +0404 [ABOUT_THANKS] Thanks to +0405 [ABOUT_SUPPORT] for support, ideas and testing +0406 [ABOUT_GPL] This software is licensed under the GPL license + +0501 [SERVER_UNABLE_TO_CONNECT] Unable to connect : %1 +0502 [SERVER_UNABLE_TO_CONNECT_STILL] Unable to connect to %1 : currently trying to connect to %2 +0503 [SERVER_DISCONNECTING] Disconnecting from %1 +0504 [SERVER_CONNECTING] Connecting... +0505 [SERVER_NOT_CONNECTED] Not connected +0506 [SERVER_LOGIN] Logging in... +0507 [SERVER_DISCONNECTED] Disconnected from %1 +0508 [SERVER_ERROR] Error : %1 +0509 [SERVER_AUTOREJOIN_ATTEMPT] Attempting to rejoin channel %1... +050a [SERVER_AUTOREJOIN_FAILED] Unable to rejoin channel %1 + +071a [GUI_CHANGE_NICK] Change nick to +071b [GUI_COPY_WINDOW] Copy text +071c [GUI_DCC_CHAT_WARNING_TITLE] Warning +071d [GUI_DCC_CHAT_WARNING_TEXT] Do you want to accept DCC chat from %1? + +0801 [ASL_MALE] Boy, %1 years old, %2 +0802 [ASL_FEMALE] Girl, %1 years old, %2 +0803 [ASL_UNKNOWN] %1 years old from %2 + +0901 [REPLY_IDLE] %1 has been idle for %2 +0902 [REPLY_SIGNON] %1 connected on %2 + +ffff [ERROR_NOT_DEFINED] Undefined string Added: phenote/trunk/doc/phenote-website/irc_chat/etiquette.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/etiquette.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/etiquette.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,87 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + <meta http-equiv="content-type" + content="text/html; charset=ISO-8859-1"> + <title>OBO-Edit Webinar +Technologies: OBO-Edit</title> + <link type="text/css" href="style.css" rel="stylesheet"> +</head> +<body> +<br> +<table style="width: 780px; height: 619px;" cellpadding="10" + cellspacing="0"> + <tbody> + <tr> + <td + style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img + style="width: 200px; height: 138px;" alt="OBO-Edit Logo" + src="images/splash.jpg"></td> + <td + style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;"> + <font color="white"> + <h1>OBO-Edit +Webinar</h1> + <h2>Etiquette<br> + </h2> + </font> </td> + </tr> + <tr> + <td + style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;"> + <ul> + <li><a href="index.html">Overview</a></li> + <li><a href="technologies.html">Technologies</a><br> + </li> + <ul> + <li><a href="vnc.html">VNC</a></li> + <li><a href="irc.html">IRC</a></li> + <li><a href="gizmo.html">The Gizmo Project</a></li> + <li><a href="oboedit.html">OBO-Edit</a></li> + </ul> + <li style="color: rgb(255, 255, 255);">Etiquette</li> + <li><a href="contact.html">Contact</a></li> + </ul> + </td> + <td + style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"> + <br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);">This +is a new way of communicating for the Gene Ontology, and we're not sure +how well it will work.<br> + <br> +In order to make the whole process go more smoothly, here are some +etiquette suggestions for the webinar...<br> + <br> + </span></span> + <ol> + <li><b>Please +keep your phone muted. </b>The Gizmo Project teleconferencing software +works well with many users as long as +most users aren't transmitting data. If everyone keeps their phone +except when asking a question, we should be fine.</li> + <li><b>Use +IRC to raise your hand.</b> Before +unmuting your phone, raise your hand in IRC and wait +to be +acknowledged. You can either raise your hand by typing "I have a +question" (or something similar) or by typing "/me raises her hand". +The second version will create a special message like "* Jane raises +her hand"in the IRC room. I'll type "go ahead, Jane" in the IRC +channel, and you can go ahead and ask your question.<br> + </li> + <li><b>Test +your configuration beforehand!</b> +Please make sure that all the tools work for you before we go into this +seminar. We are bound to have technical problems the first +day, but it would be nice to have as few as possible.</li> + </ol> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"> </span></span></span></span></td> + </tr> + </tbody> +</table> +</body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/first.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/first.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/first.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,135 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + <meta http-equiv="content-type" + content="text/html; charset=ISO-8859-1"> + <title>OBO-Edit Webinar Overview</title> + <link type="text/css" href="style.css" rel="stylesheet"> + <script language="JavaScript" src="script.js"> +</head> +<body> +<br> +<table style="width: 780px; height: 619px;" cellpadding="10" + cellspacing="0"> + <tbody> + <tr> + <td + style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img + style="width: 200px; height: 138px;" alt="OBO-Edit Logo" + src="file:///home/jrichter/oboedit_webinar/images/splash.jpg"></td> + <td + style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;"> + <font color="white"> + <h1>OBO-Edit +Webinar</h1> + <h2>Overview</h2> + </font> </td> + </tr> + <tr> + <td + style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;"> + <ul> + <li>Overview</li> + <li><a href="technologies.html">Technologies</a></li> + <ul> + <li><a href="vnc.html">VNC</a></li> + <li><a href="irc.html">IRC</a></li> + <li><a href="gizmo.html">The Gizmo Project</a></li> + <li><a href="oboedit.html">OBO-Edit</a></li> + </ul> + <li><a href="contact.html">Contact</a></li> + </ul> + </td> + <td + style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"> + <table style="width: 517px; height: 420px;"> + <tbody> + <tr> + <td style="width: 67px; vertical-align: top;"><span + style="color: rgb(0, 0, 0); font-weight: bold;">What:</span></td> + <td + style="color: rgb(0, 0, 0); width: 411px; vertical-align: top;">OBO-Edit +Tutorial</td> + </tr> + <tr> + <td style="width: 67px; vertical-align: top;"><span + style="color: rgb(0, 0, 0); font-weight: bold;">When:</span></td> + <td + style="color: rgb(0, 0, 0); width: 411px; vertical-align: top;"><span + style="color: rgb(0, 0, 0);">February 7th - </span><span + style="font-style: italic; color: rgb(0, 0, 0);">9:00AM +- 3:00PM PST</span><br style="color: rgb(0, 0, 0);"> + <span style="color: rgb(0, 0, 0);">February 8th - </span><span + style="font-style: italic; color: rgb(0, 0, 0);">12:00PM +- 3:00PM PST</span></td> + </tr> + <tr> + <td style="width: 67px; vertical-align: top;"><span + style="font-weight: bold; color: rgb(0, 0, 0);">Where:</span></td> + <td style="width: 411px; vertical-align: top;"><span + style="color: rgb(0, 0, 0);">The Internet</span></td> + </tr> + <tr> + <td style="vertical-align: top;"><span + style="font-weight: bold; color: rgb(0, 0, 0);">Signups:</span></td> + <td style="vertical-align: top;"><span + style="color: rgb(0, 0, 0);">Participation is +currently limited to GO Consortium members only</span></td> + </tr> + <tr> + <td style="height: 132px;" colspan="2" rowspan="1"> + <hr><span style="color: rgb(0, 0, 0);"><br> +Participants +should visit the Technologies section to learn how to download and +install the programs you'll need to join the webinar.</span><br + style="color: rgb(0, 0, 0);"> + <br style="color: rgb(0, 0, 0);"> + <span style="color: rgb(0, 0, 0);">IRC +and VNC can be accessed via Java applets. To test your browsers +compatibility with these applets, log in below...<br> + <br> + <hr> </span></td> + </tr> + <tr> + <td style="height: 107px;" colspan="2" rowspan="1"> + <form method="post" action="javascript:launchTest()" + name="launcher"> + <table + style="text-align: left; margin-left: auto; margin-right: auto; width: 363px; height: 102px;"> + <tbody> + <tr> + <td + style="height: 25px; color: rgb(0, 0, 0); width: 143px;">IRC +Nickname</td> + <td + style="height: 25px; width: 204px; color: rgb(0, 0, 0);"><input + name="username" size="30" style="color: rgb(0, 0, 0);"></td> + </tr> + <tr> + <td + style="height: 24px; color: rgb(0, 0, 0); width: 143px;">Full +Name</td> + <td style="height: 24px; width: 204px;"><input + name="fullname" size="30" style="color: rgb(0, 0, 0);"></td> + </tr> + <tr> + <td style="height: 49px; width: 204px;" colspan="2" + rowspan="1" align="center"><input value="Submit" name="submitbutton" + style="color: rgb(0, 0, 0);" type="submit"></td> + </tr> + </tbody> + </table> + </form> + </td> + </tr> + </tbody> + </table> + <br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"><br> + </span></span></td> + </tr> + </tbody> +</table> +</body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/french.lng =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/french.lng (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/french.lng 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,93 @@ +# +# This java file is a part of the +# +# - Plouf's Java IRC Client - +# +# Copyright (C) 2004 Philippe Detournay +# +# This file is licensed under the GPL license +# +# All contacts : the...@ya... +# +# +# Syntax : +# Comments begin with the # character. This character must be the first character of the line. +# A data line has three parts : the data id, the data id description, the data string. +# - Data id : An hexadecimal figure identifying the string. +# - Data description : Begins by [ and ends by ]. The description is not parsed and +# can contains any string. +# - Data string : The string itself. Parameters are specified using the %i syntax. +# +# Trailing spaces can be added using the \s escape character. + +0001 [INTERPRETOR_NOT_ON_CHANNEL] Pas sur un canal +0002 [INTERPRETOR_UNKNOWN_DCC] %1 : sous-commande dcc inconnue +0003 [INTERPRETOR_INSUFFICIENT_PARAMETERS] %1 : param\xE8tres insuffisants +0004 [INTERPRETOR_BAD_CONTEXT] Impossible d'effectuer %1 ici +0005 [INTERPRETOR_CANNOT_CTCP_IN_DCCCHAT] Impossible d'envoyer des codes CTCP dans un DCC Chat +0006 [INTERPRETOR_UNKNOWN_CONFIG] %1 : sous-commande de configuration inconnue +0007 [INTERPRETOR_TIMESTAMP_ON] Horodateur activ\xE9 +0008 [INTERPRETOR_TIMESTAMP_OFF] Horodateur d\xE9sactiv\xE9 +0009 [INTERPRETOR_SMILEYS_ON] Emoticons activ\xE9s +000a [INTERPRETOR_SMILEYS_OFF] Emoticons d\xE9sactiv\xE9s +000b [INTERPRETOR_IGNORE_ON] Ignore \xE0 pr\xE9sent %1 +000c [INTERPRETOR_IGNORE_OFF] N'ignore plus %1 +000d [INTERPRETOR_MULTISERVER_DISABLED] Le support multiserveur est d\xE9sactiv\xE9 + +0101 [DCC_WAITING_INCOMING] Attente de connexion... +0102 [DCC_UNABLE_TO_OPEN_CONNECTION] Impssible d'ouvrir la connexion : %1 +0103 [DCC_CONNECTION_ESTABLISHED] "Connexion DCC \xE9tablie +0104 [DCC_CONNECTION_CLOSED] Connexion ferm\xE9e +0105 [DCC_ERROR] Erreur : %1 +0106 [DCC_UNABLE_TO_SEND_TO] %1 : impossible d'envoyer \xE0 %2 +0107 [DCC_BAD_CONTEXT] Impossible d'ex\xE9cuter la commande dans le contexte actuel +0108 [DCC_NOT_CONNECTED] Non connect\xE9 +0109 [DCC_UNABLE_PASSIVE_MODE] Impossible d'initialiser le mode passif +010a [CTCP_PING_REPLY] [%1 PING reply] : %2 secondes +010b [DCC_STREAM_CLOSED] Stream ferm\xE9 + +0201 [IDENT_FAILED_LAUNCH] Impossible de lancer le serveur IDENT : %1 +0202 [IDENT_REQUEST] Requ\xEAte ident de %1 +0203 [IDENT_ERROR] Erreur survenue +0204 [IDENT_REPLIED] R\xE9pondu %1 +0205 [IDENT_DEFAULT_USER] utilisateur par d\xE9faut +0206 [IDENT_NO_USER] Aucun utilisateur pour la req\xFBete +0207 [IDENT_RUNNING_ON_PORT] Le serveur Ident s'ex\xE9cute sur le port %1 +0208 [IDENT_LEAVING] Le serveur Ident se termine : %1 +0209 [IDENT_NONE] aucun +020a [IDENT_UNKNOWN] inconnu +020b [IDENT_UNDEFINED] R\xE9sultat ind\xE9termin\xE9 + +0301 [FILE_SAVEAS] Sauver le fichier sous + +0401 [ABOUT_ABOUT] A propos +0402 [ABOUT_PROGRAMMING] Programmation +0403 [ABOUT_DESIGN] Design +0404 [ABOUT_THANKS] Remerciements +0405 [ABOUT_SUPPORT] pour leur support, leurs id\xE9es et les tests +0406 [ABOUT_GPL] Ce programme est sous license GPL + +0501 [SERVER_UNABLE_TO_CONNECT] Impossible de se connecter : %1 +0502 [SERVER_UNABLE_TO_CONNECT_STILL] Impossible de se connecter \xE0 %1, d\xE9j\xE0 en train d'essayer de se connecter \xE0 %2 +0503 [SERVER_DISCONNECTING] D\xE9connexion de %1 +0504 [SERVER_CONNECTING] Connexion... +0505 [SERVER_NOT_CONNECTED] Non connect\xE9 +0506 [SERVER_LOGIN] Enregistrement... +0507 [SERVER_DISCONNECTED] D\xE9connect\xE9 de %1 +0508 [SERVER_ERROR] Erreur : %1 +0509 [SERVER_AUTOREJOIN_ATTEMPT] Tentative de retour sur le canal %1... +050a [SERVER_AUTOREJOIN_FAILED] Impossible de rejoindre le canal %1 + +071a [GUI_CHANGE_NICK] Modifier le nick +071b [GUI_COPY_WINDOW] Copier le texte +071c [GUI_DCC_CHAT_WARNING_TITLE] Attention +071d [GUI_DCC_CHAT_WARNING_TEXT] Voulez-vous accepter une connection DCC-chat en provenance de %1? + +0801 [ASL_MALE] Gar\xE7on, %1 ans, %2 +0802 [ASL_FEMALE] Fille, %1 ans, %2 +0803 [ASL_UNKNOWN] %1 ans de %2 + +0901 [REPLY_IDLE] %1 est inactif depuis %2 +0902 [REPLY_SIGNON] %1 s'est connect\xE9(e) le %2 + +ffff [ERROR_NOT_DEFINED] Texte non d\xE9fini Added: phenote/trunk/doc/phenote-website/irc_chat/gizmo.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/gizmo.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/gizmo.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,90 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + <meta http-equiv="content-type" + content="text/html; charset=ISO-8859-1"> + <title>OBO-Edit Webinar Technologies: The Gizmo Project</title> + <link type="text/css" href="style.css" rel="stylesheet"> +</head> +<body> +<br> +<table style="width: 780px; height: 619px;" cellpadding="10" + cellspacing="0"> + <tbody> + <tr> + <td + style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img + style="width: 200px; height: 138px;" alt="OBO-Edit Logo" + src="images/splash.jpg"></td> + <td + style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;"> + <font color="white"> + <h1>OBO-Edit +Webinar</h1> + <h2>The Gizmo Project<br> + </h2> + </font> </td> + </tr> + <tr> + <td + style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;"> + <ul> + <li><a href="index.html">Overview</a></li> + <li><a href="technologies.html">Technologies</a><br> + </li> + <ul> + <li><a href="vnc.html">VNC</a></li> + <li><a href="irc.html">IRC</a></li> + <li style="color: rgb(255, 255, 255);">The Gizmo Project</li> + <li><a href="oboedit.html">OBO-Edit</a></li> + </ul> + <li><a href="etiquette.html">Etiquette</a></li> + <li><a href="contact.html">Contact</a></li> + </ul> + </td> + <td + style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"> + <br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);">The OBO-Edit webinar +will use <a href="gizmo.html">The +Gizmo Project</a> to handle Voice +over IP communications.<br> + <br> + </span></span><span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"><a + href="file:///home/jrichter/oboedit_webinar/gizmo.html">The +Gizmo Project</a> is an open source +program similar to Skype. Users can communicate using their computer +speakers and microphone. </span></span><span + style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);"><a + href="file:///home/jrichter/oboedit_webinar/gizmo.html">The +Gizmo Project</a> allows several +dozen users to teleconference at once, which is why this technology has +been chosen.<br> + <br> +Download and install your copy from </span></span><span + style="color: rgb(0, 0, 0);"><span style="color: rgb(0, 0, 0);">h<a + href="http://www.gizmoproject.com">ttp://www.gizmoproject.com</a></span></span><br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"> <br> +Once the software is installed, you will to complete some initial setup +tasks, such as creating a user id and password, etc. <br> + <br> +To join the conference call, dial <b>1-222-626-3348</b> +in the phone number field near the top of the screen. If you are the +first to join, you'll hear strange demo music and a message saying you +are the first to call.<br> + <br> + <b>IMPORTANT: MUTE YOUR +GIZMO PHONE IF YOU AREN'T TALKING!!!</b> <br> +There is a mute button near the top right corner of the Gizmo window +once you are connected. The Gizmo conference call system degrades +quickly as more people talk, so the only way this will work is if only +one or two people have their mikes unmuted at once.<br> + </span></span></td> + </tr> + </tbody> +</table> +</body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/images/splash.jpg =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/images/splash.jpg ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/index.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/index.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/index.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,133 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + <meta content="text/html; charset=ISO-8859-1" + http-equiv="content-type"> + <title>OBO-Edit Webinar Overview</title> + <link rel="stylesheet" href="style.css" type="text/css"> + <script language="JavaScript" src="script.js"><!-- --></script> +</head> +<body> +<br> +<table style="width: 776px; height: 617px;" cellpadding="10" + cellspacing="0"> + <tbody> + <tr> + <td + style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img + style="width: 200px; height: 138px;" alt="OBO-Edit Logo" + src="images/splash.jpg"></td> + <td + style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;"> + <font color="white"> + <h1>OBO-Edit +Webinar</h1> + <h2>Overview</h2> + </font> </td> + </tr> + <tr> + <td + style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;"> + <ul> + <li style="color: rgb(255, 255, 255);">Overview</li> + <li><a href="technologies.html">Technologies</a></li> + <ul> + <li><a href="vnc.html">VNC</a></li> + <li><a href="irc.html">IRC</a></li> + <li><a href="gizmo.html">The Gizmo Project</a></li> + <li><a href="oboedit.html">OBO-Edit</a></li> + </ul> + <li><a href="etiquette.html">Etiquette</a></li> + <li><a href="contact.html">Contact</a></li> + </ul> + </td> + <td + style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"> + <table height="361" width="491"> + <tbody> + <tr> + <td style="vertical-align: top;"><span + style="color: rgb(0, 0, 0); font-weight: bold;">What:</span></td> + <td style="color: rgb(0, 0, 0); vertical-align: top;">OBO-Edit +Tutorial</td> + </tr> + <tr> + <td style="width: 67px; vertical-align: top;"><span + style="color: rgb(0, 0, 0); font-weight: bold;">When:</span></td> + <td + style="color: rgb(0, 0, 0); width: 411px; vertical-align: top;"><span + style="color: rgb(0, 0, 0);">February 6th - <i>9:00AM - 9:30AM PST</i> +- Technology test<br> +February 7th - </span><span + style="font-style: italic; color: rgb(0, 0, 0);">9:00AM +- 3:00PM PST</span><br style="color: rgb(0, 0, 0);"> + <span style="color: rgb(0, 0, 0);">February 8th - </span><span + style="font-style: italic; color: rgb(0, 0, 0);">1:00PM +- 3:00PM PST (revised time!)</span></td> + </tr> + <tr> + <td style="width: 67px; vertical-align: top;"><span + style="font-weight: bold; color: rgb(0, 0, 0);">Where:</span></td> + <td style="width: 411px; vertical-align: top;"><span + style="color: rgb(0, 0, 0);">The Internet</span></td> + </tr> + <tr> + <td style="vertical-align: top;"><span + style="font-weight: bold; color: rgb(0, 0, 0);">Signups:</span></td> + <td style="vertical-align: top;"><span + style="color: rgb(0, 0, 0);">Participation +is +currently limited to GO Consortium members only</span></td> + </tr> + <tr> + <td style="height: 132px;" colspan="2" rowspan="1"> + <hr><span style="color: rgb(0, 0, 0);"><br> +Participants +should visit the Technologies section to learn how to download and +install the programs you'll need to join the webinar. All of these +technologies can be tested immediately; you do not need to wait until +the webinar begins.</span><br style="color: rgb(0, 0, 0);"> + <br style="color: rgb(0, 0, 0);"> + <span style="color: rgb(0, 0, 0);">Voice chat can be +accessed via The Gizmo Project using phone number <b>1-222-626-3348</b> +(1-222-OBO-EDIT). Don't try to call from a regular phone; it won't work.<br> + <br> +IRC +and VNC can be accessed via Java applets. The VNC password is <b>oboedit_vnc</b>.<br> + <br> + </span> + <form method="post" name="launcher"> + <table + style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" + width="100%"> + <tbody> + <tr> + <td colspan="1" rowspan="1" width="156">IRC +Nickname</td> + <td style="width: 327px;"><input size="40" + name="username"></td> + </tr> + <tr> + <td colspan="2" rowspan="1" + style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input + name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0);" + onclick="startApplets()" type="button"><br> + </td> + </tr> + </tbody> + </table> + </form> + <span style="color: rgb(0, 0, 0);"> + <hr> </span></td> + </tr> + </tbody> + </table> + <br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"><br> + </span></span></td> + </tr> + </tbody> +</table> +</body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/irc-unsigned.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/irc-unsigned.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/irc.cab =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/irc.cab ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/irc.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/irc.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/irc.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,96 @@ +<!DOCTYPE html PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"> +<html> +<head> + <meta http-equiv="content-type" + content="text/html; charset=ISO-8859-1"> + <title>OBO-Edit Webinar Technologies: IRC</title> + <link type="text/css" href="style.css" rel="stylesheet"> +</head> +<body> +<br> +<table style="width: 780px; height: 619px;" cellpadding="10" + cellspacing="0"> + <tbody> + <tr> + <td + style="width: 200px; height: 149px; background-color: rgb(109, 150, 202); direction: ltr;"><img + style="width: 200px; height: 138px;" alt="OBO-Edit Logo" + src="images/splash.jpg"></td> + <td + style="text-align: center; width: 568px; height: 149px; background-color: rgb(109, 150, 202); font-family: Helvetica,Arial,sans-serif;"> + <font color="white"> + <h1>OBO-Edit +Webinar</h1> + <h2>IRC</h2> + </font> </td> + </tr> + <tr> + <td + style="vertical-align: top; background-color: rgb(109, 150, 202); height: 454px;"> + <ul> + <li><a href="index.html">Overview</a></li> + <li><a href="technologies.html">Technologies</a><br> + </li> + <ul> + <li><a href="vnc.html">VNC</a></li> + <li style="color: rgb(255, 255, 255);">IRC</li> + <li><a href="gizmo.html">The Gizmo Project</a></li> + <li><a href="oboedit.html">OBO-Edit</a></li> + </ul> + <li><a href="etiquette.html">Etiquette</a></li> + <li><a href="contact.html">Contact</a></li> + </ul> + </td> + <td + style="background-color: rgb(198, 203, 228); width: 568px; vertical-align: top; height: 454px;"> + <br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);">The OBO-Edit webinar +will handle live chat over IRC (Internet Relay Chat).<br> + <br> +The best way to connect to the OBO-Edit IRC chat is to use the applet +on the <a href="index.html">front +page</a>. If you decide you'd like +to use your own IRC applet, connect to <b>irc.sf.net</b> +and join the <b>#oboedit</b> +channel.<br> + <br> +There are many, many IRC clients available for every computer platform. +If you'd like to download your own client, consider:<br> + <br> + <br> + <table border="1" height="40" width="500"> + <tbody> + <tr> + <td align="center" width="159"><b>Mac</b></td> + <td align="center" width="159"><b>Windows</b></td> + <td align="center" width="160"><b>Linux</b></td> + </tr> + <tr> + <td align="center" width="159"><a + href="http://homepage.mac.com/philrobin/conversation/">Conversation</a><br> + <a href="http://www.snak.com/Snak.html">Snak</a><br> + <a href="http://www.ircle.com/">ircle</a></td> + <td align="center" width="159"><a + href="http://www.mirc.com/">mIRC</a><br> + <a href="http://www.xircon.com/">Xircon</a><br> + <span style="color: rgb(0, 0, 0);"><span + style="color: rgb(0, 0, 0);"><a href="http://www.xchat.org/">xchat</a></span></span></td> + <td align="center" width="160"><a + href="http://konversation.kde.org/">Konversation</a><br> + <a href="http://www.xchat.org/">xchat</a><br> + <a href="http://www.bitchx.org/">BitchX</a></td> + </tr> + </tbody> + </table> + <br> +Although we won't be using most IRC features during the webinar, there +are dozens and dozens of commands and special IRC features. If you want +to read up, take a look at the IRC primer at <a + href="http://www.irchelp.org/irchelp/ircprimer.html">http://www.irchelp.org/irchelp/ircprimer.html</a><br> + </span></span></td> + </tr> + </tbody> +</table> +</body> +</html> Added: phenote/trunk/doc/phenote-website/irc_chat/irc.jar =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/irc.jar ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/irc_chat.shtml 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,36 @@ +<!--#include virtual="/ssi/header.html" --> + <script language="JavaScript" src="/irc_script.js"><!-- --></script> +<div id="page_body"> + +<!--#include virtual="/ssi/navi_home.html" --> + +<div id="main_content"> +<h2>Phenote Working Group IRC Chat</h2> + +When: First Tuesday of every month; 8:30am <br/> + +<p>You will need an IRC client to visit our chats. You can download any number of free clients to do this. You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p> + +<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. </p> + + <form method="post" name="launcher"> + <table style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" width="100%"> +<tbody> + <tr> + <td colspan="1" rowspan="1" width="156">IRC Nickname</td> + <td style="width: 327px;"><input size="40" name="username"></td> + </tr> + <tr> + <td colspan="2" rowspan="1" style="height: 25px; color: rgb(0, 0, 0); text-align: center; width: 327px;"><input name="appletbutton" value="Start Applets" style="color: rgb(0, 0, 0); "onclick="startApplets()" type="button"><br> + </td> + </tr> + +</tbody> +</table> +</form> + +</div> +</div> + +<!--#include virtual="/ssi/footer.shtml" --> + Added: phenote/trunk/doc/phenote-website/irc_chat/irc_script.js =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/irc_script.js (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/irc_script.js 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,37 @@ +var ircwindow = null; +var vncwindow = null; + +function startApplets() { + + if (ircwindow != null) { + ircwindow.close(); + ircwindow = null; + } + + if (vncwindow != null) { + vncwindow.close(); + vncwindow = null; + } + + vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800"); + ircwindow = window.open("about:blank", "My window", "scrollbars=no,status=no,width=510,height=430"); + + var html = ""; + + html += "<html><body>\n"; + html += "<applet code=\"IRCApplet.class\" archive=\"irc.jar,pixx.jar\" width=475 height=400>\n"; + html += "<param name=\"CABINETS\" value=\"irc.cab,securedirc.cab,pixx.cab\">\n"; + html += "<param name=\"nick\" value='"+document.forms["launcher"].username.value+"'>\n"; + html += "<param name=\"fullname\" value='"+document.forms["launcher"].username.value+"'>\n"; + + html += "<param name=\"alternatenick\" value=\"Anon???\">\n"; + html += "<param name=\"host\" value=\"irc.sf.net\">\n"; + html += "<param name=\"command1\" value=\"/join #phenote\">\n"; + html += "<param name=\"gui\" value=\"pixx\">\n"; + html += "</applet>\n"; + html += "</body></html>"; + +// alert(html); + ircwindow.document.writeln(html); + ircwindow.document.close(); +} Added: phenote/trunk/doc/phenote-website/irc_chat/junk.html =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/junk.html (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/junk.html 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,15 @@ +<html> +<head> +</head> +<body> +<applet code="IRCApplet.class" archive="irc.jar,pixx.jar" width=300 height=300> + <param name="CABINETS" value="irc.cab,securedirc.cab,pixx.cab"> + <param name="nick" value="jrichter"> + <param name="alternatenick" value="Anon???"> + <param name="fullname" value="John Day-Richter"> + <param name="host" value="irc.diboo.net"> + <param name="command1" value="/join #oboedit"> + <param name="gui" value="pixx"> +</applet> +</body> +</html> \ No newline at end of file Added: phenote/trunk/doc/phenote-website/irc_chat/pbtn3.2.zip =================================================================== (Binary files differ) Property changes on: phenote/trunk/doc/phenote-website/irc_chat/pbtn3.2.zip ___________________________________________________________________ Name: svn:mime-type + application/octet-stream Added: phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng (rev 0) +++ phenote/trunk/doc/phenote-website/irc_chat/pixx-english.lng 2007-04-30 21:34:47 UTC (rev 520) @@ -0,0 +1,75 @@ +# +# This java file is a part of the +# +# - Plouf's Java IRC Client - +# +# Copyright (C) 2004 Philippe Detournay +# +# This file is licensed under the GPL license +# +# All contacts : the...@ya... +# +# +# Syntax : +# Comments begin with the # character. This character must be the first character of the line. +# A data line has three parts : the data id, the data id description, the data string. +# - Data id : An hexadecimal figure identifying the string. +# - Data description : Begins by [ and ends by ]. The description is not parsed and +# can be any string. +# - Data string : The string itself. Parameters are specified using the %i syntax. +# +# Trailing spaces can be added using the \s escape character. + +8601 [SOURCE_YOU_KICKED] You've been kicked out of %1... [truncated message content] |
From: <nl...@us...> - 2007-04-30 21:57:18
|
Revision: 523 http://svn.sourceforge.net/obo/?rev=523&view=rev Author: nlw Date: 2007-04-30 14:57:20 -0700 (Mon, 30 Apr 2007) Log Message: ----------- making changes to the header Modified Paths: -------------- phenote/trunk/doc/phenote-website/irc_chat/index.shtml phenote/trunk/doc/phenote-website/ssi/header.html Modified: phenote/trunk/doc/phenote-website/irc_chat/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/index.shtml 2007-04-30 21:51:18 UTC (rev 522) +++ phenote/trunk/doc/phenote-website/irc_chat/index.shtml 2007-04-30 21:57:20 UTC (rev 523) @@ -1,5 +1,4 @@ <!--#include virtual="/ssi/header.html" --> - <script language="JavaScript" src="/irc_script.js"><!-- --></script> <div id="page_body"> <!--#include virtual="/ssi/navi_home.html" --> Modified: phenote/trunk/doc/phenote-website/ssi/header.html =================================================================== --- phenote/trunk/doc/phenote-website/ssi/header.html 2007-04-30 21:51:18 UTC (rev 522) +++ phenote/trunk/doc/phenote-website/ssi/header.html 2007-04-30 21:57:20 UTC (rev 523) @@ -14,6 +14,7 @@ <link rel="stylesheet" type="text/css" href="/phenote/css/style.css" title="standard" /> <script type="text/javascript" src="/javascript/obfuscate.js"></script> +<script type="text/javascript" src="/javascript/irc_script.js"></script> <title>Phenote: A Phenotype Annotation Tool using Ontologies</title> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-04-30 22:13:44
|
Revision: 525 http://svn.sourceforge.net/obo/?rev=525&view=rev Author: nlw Date: 2007-04-30 15:13:46 -0700 (Mon, 30 Apr 2007) Log Message: ----------- removed the vnc client applet, and added text to describe changing nickname during chats Modified Paths: -------------- phenote/trunk/doc/phenote-website/irc_chat/index.shtml phenote/trunk/doc/phenote-website/javascript/irc_script.js Modified: phenote/trunk/doc/phenote-website/irc_chat/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/irc_chat/index.shtml 2007-04-30 22:00:15 UTC (rev 524) +++ phenote/trunk/doc/phenote-website/irc_chat/index.shtml 2007-04-30 22:13:46 UTC (rev 525) @@ -10,7 +10,7 @@ <p>You will need an IRC client to visit our chats. You can download any number of free clients to do this. You'll need to connect to the <b>irc.sf.net</b> and join the <b>#phenote</b> channel. </p> -<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. </p> +<p>Alternatively, you can connect to the Phenote IRC chat using the applet at the bottom of this page. Simply enter a name to be used during the chat. If the name you enter is already being used by someone else, an 'anonymous' one will be assigned to you. (but you can change it once you're logged on by typing the command "/nick newname") </p> <form method="post" name="launcher"> <table style="text-align: left; margin-left: auto; margin-right: auto; width: 524px; height: 84px;" width="100%"> Modified: phenote/trunk/doc/phenote-website/javascript/irc_script.js =================================================================== --- phenote/trunk/doc/phenote-website/javascript/irc_script.js 2007-04-30 22:00:15 UTC (rev 524) +++ phenote/trunk/doc/phenote-website/javascript/irc_script.js 2007-04-30 22:13:46 UTC (rev 525) @@ -13,7 +13,7 @@ vncwindow = null; } - vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800"); + // vcnwindow = window.open("http://frizzled.lbl.gov:5801", "VNC", "status=no,width=1100,height=800"); ircwindow = window.open("about:blank", "My window", "scrollbars=no,status=no,width=510,height=430"); var html = ""; This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-05-09 21:03:20
|
Revision: 570 http://svn.sourceforge.net/obo/?rev=570&view=rev Author: mgibson Date: 2007-05-09 14:03:21 -0700 (Wed, 09 May 2007) Log Message: ----------- notes & jnlp for 1.3-beta1 release Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-release-notes.html phenote/trunk/doc/phenote-website/phenote.html phenote/trunk/doc/phenote-website/phenote.jnlp Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-09 20:51:17 UTC (rev 569) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-09 21:03:21 UTC (rev 570) @@ -4,16 +4,20 @@ + + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> + + <title>Phenote Release Notes</title> </head> @@ -22,114 +26,164 @@ + <h1>Phenote Release Notes</h1> + 1.3 will probably come out in June<br> + +<h2><span style="text-decoration: underline;">1.3-beta1</span></h2> + +<a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br> <br> +Added config for birn<br> +Added SAO.obo for birn<br> +Namespace config writes back<br> +Config update/merge bug where fields in wrong order fixed.<br> +Can specify more than one website for ontologies<br> +Empty field shows all terms in ontology rather than none<br> + <h2><span style="text-decoration: underline;">1.2</span></h2> + <a href="1.2/phenote.jnlp">Phenote 1.2</a><br> + <br> + Features: Can post-compose with >2 terms <br> + Term history display can be toggled on/off <br> + Synonym types display in term info<br> + Obsolete replacements displayed in term info<br> + Search filters moved into menu <br> + Loading splash screen <br> + Can configure by namespace for ontologies<br> + Bug Fixes: Free text field text not "sticking" <h2><span style="text-decoration: underline;">1.1</span></h2> + <a href="1.1/phenote.jnlp">Phenote 1.1</a><br> + <br> + March 28, 2007<br> + <br> + Phenote will merge its default configuration with users configuration, preserving users changes as well as adding anything new from phenote upgrade.<br> + User can select configuration they want to use at initialization or subsequently from file menu (currently requires phenote restart).<br> + Tab delimited data adapter - thank you nicole!<br> + Beginnings of term history - thank you nicole!<br> + Tabbed main field panel if more than 12 fields.<br> + QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.<br> + Layout improved<br> + Can now search ALL ontologies of a field<br> + Retrieve obo from web if more up to date or no local found<br> + Refactored code for field guis<br> + Ontology chooser reflects current term (bug fix) <h2><span style="text-decoration: underline;">1.0</span></h2> + <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> + <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> + <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DichtyBase webby phenote</a><br> + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> + <br> + January 12, 2007<br> + <br> + The main improvement here is the ability to add any field you like, not just E,Q,GC,GT,Pub. In the configured webstarts Stage, Evidence, Description, Abnormal, and Absent have been added through this new mechanism. This entailed a refactoring of the datamodel.<br> + <br> + Webby phenote is now using JSP and Spring.<br> + <br> + 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. @@ -137,133 +191,163 @@ + <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br> + <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + mid November 2006<br> + <br> + Undo<br> + Christian Pich(Zfin) has added a Quartz scheduler to phenote, which zfin takes advantage of, to schedule when to check for new obo files.<br> + Also Christian Pich upgraded the PhenoteServlet to the Spring framework - much nicer!<br> + Synonyms are now returned from auto complete with [syn] and when selected the term goes in the field (webby & standalone), obsoletes hits with [obs]<br> + Bulk update & copy in standalone.<br> + Jim Balhoff(Nescent) changed radio buttons to checkboxes, and file saver says save not load and recognizes adapter by file extensions, psx->phenosyntax, .xml -> phenoxml <br> + Single quotes escaped for javascript fns.<br> + <h2><span style="text-decoration: underline;">0.8</span></h2> + <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br> + <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + 10/2/06<br> + Added post composition to standalone phenote. Logging for both webby/servlet & standalone.<br> + Pheno-xml reader (thanks to Jim Balhoff) and improvements to pheno-xml writer (does pub & genetic context)<br> + Command line reading & writing of phenoxml & phenosyntax.<br> + Application exits on window exit (unless servlet)<br> + Can filter out stage terms from zfin anatomy<br> + <h2><span style="text-decoration: underline;">0.7</span></h2> + <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br> + <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br> + <a href="http://165.124.152.194/web/html/interface.html">DichtyBase webby phenote</a><br> + <br> + Web: entity chooser, 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). Entity field and term info installed into zfin @@ -271,6 +355,7 @@ + Standalone: can read & write pheno-syntax with ids & term names in comments, entity chooser, pub field, use button in term info, sort table by clicking on headers, personal config file gets copied out of @@ -278,31 +363,38 @@ + <br> + <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.6</span></span></h2> + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote (0.6)</a><br> + <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br> + <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br> + <br> + The main feature of release 0.6 is a webby 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 @@ -310,40 +402,49 @@ + <br> + Not much new in the stand alone phenote (as Ive been working on the webby phenote). Mainly it can write pheno-xml, and it uses the latest pato (as of July 28, 2006).<br> + <h2><span style="font-weight: bold;"><span style="text-decoration: underline;">0.5</span></span></h2> + <br> + <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br> + <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br> + <br> + 5/12/06<br> + 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 @@ -358,38 +459,47 @@ + <h2><span style="text-decoration: underline;">0.4</span></h2> + <a href="0.4/phenote-flybase.jnlp">0.4 flybase webstart</a><br> + <a href="0.4/phenote-zfin.jnlp">0.4 zfin webstart</a><br> + <br> + 4/26/06<br> + Added Genetic Context field.<br> + Parent & child terms in term info are now clickable/navigable.<br> + Links in descriptions are clickable (should bring up default browser)<br> + Added configuration 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. @@ -400,19 +510,23 @@ + Minor bugs: cant delete to 0 rows anymore, synonym search duplicates taken out<br> + <br> + Dev stuff:<br> + 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 @@ -422,43 +536,53 @@ + Renamed Phenotype to Character. Added Character interface CharacterI.<br> + Added tests to test suite.<br> + <br> + <h2><span style="text-decoration: underline;">0.3.1 (CToL)<br> + </span></h2> + <a href="0.3.1/phenote-webstart.jnlp">0.3.1 phenote webstart (for CToL)</a><br> + <br> + 4/7/06<br> + 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<br> + 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 @@ -466,199 +590,246 @@ + <h2><span style="text-decoration: underline;">0.3</span></h2> + <a href="0.3/phenote-webstart.jnlp">0.3 phenote webstart</a><br> + <br> + 4/7/06<br> + 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.<br> + <br> + Completion terms now sorted alphabeitcally.<br> + Obsolete is now in addition to regular terms, not in lieu of.<br> + Filtering out attribute values (todo: change to actually filter in values)<br> + Html formatting of term info (todo: make terms selectable)<br> + Children relations are in term info<br> + Term info layout greatly improved<br> + Term info in scroller<br> + Border with label around term info<br> + Put definition at end of term info<br> + <br> + Fixed bugs:<br> + Backspace in ontology combo box<br> + Selection of item in comp list causing exception, not going in term box<br> + No terms with just 1 char<br> + Popup was staying up after selection<br> + <br> + Dev stuff:<br> + Test suite added! (todo: add more tests)<br> + Migrated to jdk 1.5 (which caused some of the bugs above)<br> + Ant file made build.xml.<br> + CompletionList refactored into Ontology (prompted by sorting)<br> + <br> + <br> + <h2><span style="text-decoration: underline;">0.2</span></h2> + <a href="0.2/phenote-webstart.jnlp">0.2 phenote webstart</a><br> + <br> + 3/27/06<br> + Added the ability to do term completion on Synonyms, Definitions, and Obsoletes. Also can mouse over a term in a completion list and get information about it in the term info text area. <br> + <br> + The term info area needs a lot of work.<br> + TODO:<br> + layout, scrollbar, border w title, ordering & lumping parents & children, formatting. <br> + Also perhaps have children & parents be clickable in some fashion either html-like clickable text or as buttons.<br> + Theres also bugs in term completion boxes. If you start backspacing it gets wacky for instance.<br> + <br> + <a href="0.2/phenote-webstart.jnlp"><br> + </a> <h2><span style="text-decoration: underline;">0.1</span></h2> + <a href="0.1/phenote-webstart.jnlp">0.1 phenote webstart</a><br> + <br> + 3/1/06<br> + 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 @@ -668,25 +839,31 @@ + <br> + <a href="0.2/phenote-webstart.jnlp"></a><br> + <br> + <br> + <a href="phenote.html">Phenote main page</a><br> + </body> </html> Modified: phenote/trunk/doc/phenote-website/phenote.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote.html 2007-05-09 20:51:17 UTC (rev 569) +++ phenote/trunk/doc/phenote-website/phenote.html 2007-05-09 21:03:21 UTC (rev 570) @@ -9,6 +9,7 @@ + @@ -17,6 +18,7 @@ + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> @@ -26,6 +28,7 @@ + @@ -34,6 +37,7 @@ + <title>Phenote</title> </head> @@ -47,6 +51,7 @@ + <h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br> @@ -56,6 +61,7 @@ + </h1> @@ -65,6 +71,7 @@ + <br> @@ -74,6 +81,7 @@ + Phenote is a tool to annotate phenotypes using the Entity Quality paradigm. It takes advantage of ontologies. It uses term completion to allow curators quick access to @@ -86,6 +94,7 @@ + <br> @@ -94,13 +103,17 @@ + <a href="1.2/phenote.jnlp">Phenote 1.2</a><br> + <br> + <br> + After phenote downloads the java jar files (takes a while) it will ask you what configuration you would like to use, fly, zfin, human,worm....<br> @@ -111,9 +124,11 @@ + <br> + Recent addditions include the ability to update config while preserving your changes, change config, tab delimited format, tabbed field panel, retrieve ontologies from web, retrieve from field to database, search @@ -128,6 +143,7 @@ + <br> @@ -137,6 +153,7 @@ + Zebrafish requires components of phenote(to plug into their non-public website), not a full web app. Here is a proof of concept of some of @@ -150,6 +167,7 @@ + <br> @@ -159,6 +177,7 @@ + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> @@ -169,6 +188,7 @@ + <br> @@ -178,6 +198,7 @@ + Webby phenote is a collaboration with Sohel Merchant at dictyBase. Here is what they have done:<br> @@ -188,6 +209,7 @@ + <br> @@ -197,6 +219,7 @@ + <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase webby phenote</a><br> @@ -207,6 +230,7 @@ + <br> @@ -216,6 +240,7 @@ + <br> @@ -225,6 +250,7 @@ + We are doing these releases to get feedback. Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug tracker</a>) and let us know what you @@ -237,11 +263,13 @@ + <br> -[In development - the bleeding edge if you will:<a href="1.3/phenote.jnlp"> Phenote 1.3</a> coming soon]<br> +In development - the bleeding edge if you will:<br> +<a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br> @@ -249,6 +277,8 @@ + + <h4>Phenote links:<br> @@ -258,6 +288,7 @@ + </h4> @@ -267,6 +298,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote email list</a><br> @@ -277,6 +309,7 @@ + <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote bug tracker</a><br> @@ -287,6 +320,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug tracker email list</a><br> @@ -297,6 +331,7 @@ + <a href="https://sourceforge.net/svn/?group_id=76834">Phenote source code (obo sourceforge svn)</a><br> @@ -307,6 +342,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote svn commit email list</a><br> @@ -317,6 +353,7 @@ + <a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty webby phenote wiki developer docs</a><br> @@ -327,13 +364,16 @@ + <a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote ncbo internal wiki (ncbo folk only)</a><br> + <a href="developer-docs/dataadapter.html">Phenote dataadapter developer doc</a><br> + <a href="developer-docs/developer-docs.html">More developer docs</a><br> @@ -343,6 +383,7 @@ + <br> @@ -352,6 +393,7 @@ + <a href="phenote-release-notes.html">Phenote Release Notes and old webstart releases</a><br> @@ -362,6 +404,7 @@ + <br> @@ -371,6 +414,7 @@ + If the Phenote webstart link fails to do anything, then there are probably problems with webstart and/or java(has to be jdk 1.5). Take a look at the <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br> @@ -382,6 +426,7 @@ + page.<br> @@ -391,6 +436,7 @@ + <br> @@ -400,6 +446,7 @@ + Click here for <a href="phenote-java-requirements.html">phenote java requirements</a><br> @@ -410,6 +457,7 @@ + <br> @@ -419,6 +467,7 @@ + <br> @@ -428,6 +477,7 @@ + <br> @@ -437,6 +487,7 @@ + Old releases: <br> @@ -446,7 +497,9 @@ + <a href="1.1/phenote.jnlp">Phenote 1.1</a><br> + <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> @@ -456,6 +509,7 @@ + <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> @@ -464,12 +518,14 @@ + <a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br> + <br> @@ -479,6 +535,7 @@ + <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br> @@ -488,6 +545,7 @@ + <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br> @@ -496,6 +554,7 @@ + <br> @@ -504,6 +563,7 @@ + <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br> @@ -513,6 +573,7 @@ + <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br> @@ -522,6 +583,7 @@ + <br> @@ -531,6 +593,7 @@ + <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br> @@ -540,6 +603,7 @@ + <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br> @@ -549,6 +613,7 @@ + <br> @@ -558,6 +623,7 @@ + <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br> @@ -567,6 +633,7 @@ + <br> @@ -576,6 +643,7 @@ + <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br> @@ -585,6 +653,7 @@ + <br> @@ -594,6 +663,7 @@ + <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br> @@ -603,6 +673,7 @@ + <br> @@ -612,6 +683,7 @@ + <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br> @@ -621,6 +693,7 @@ + <br> @@ -630,6 +703,7 @@ + <a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br> @@ -639,6 +713,7 @@ + <br> @@ -648,6 +723,7 @@ + <a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br> @@ -657,6 +733,7 @@ + <br> @@ -666,6 +743,7 @@ + <a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a> (a special release for the CToL group that uses fish taxonomy)<br> @@ -677,6 +755,7 @@ + <br> @@ -686,6 +765,7 @@ + <a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br> @@ -695,6 +775,7 @@ + <br> @@ -704,6 +785,7 @@ + <a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br> @@ -713,6 +795,7 @@ + <br> @@ -722,6 +805,7 @@ + <a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br> @@ -731,6 +815,7 @@ + <br> @@ -740,6 +825,7 @@ + <br> @@ -749,5 +835,6 @@ + </body> </html> Modified: phenote/trunk/doc/phenote-website/phenote.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-05-09 20:51:17 UTC (rev 569) +++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-05-09 21:03:21 UTC (rev 570) @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" -codebase="http://toy.lbl.gov:9010/phenote/1.2" +codebase="http://toy.lbl.gov:9010/phenote/1.2-beta1" href="phenote.jnlp"> <information> - <title>Phenote 1.2</title> + <title>Phenote 1.3-beta1</title> <vendor>National Center for Biomedial Ontology</vendor> <description>Phenote standalone app via webstart</description> <!-- Declares that the application can run without This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <nl...@us...> - 2007-05-30 05:43:01
|
Revision: 645 http://svn.sourceforge.net/obo/?rev=645&view=rev Author: nlw Date: 2007-05-29 22:42:59 -0700 (Tue, 29 May 2007) Log Message: ----------- added new links to the 'latest' for the website. this will link to v1.3 Modified Paths: -------------- phenote/trunk/doc/phenote-website/content/howtos/index.shtml phenote/trunk/doc/phenote-website/content/software/index.shtml phenote/trunk/doc/phenote-website/phenote-release-notes.html Modified: phenote/trunk/doc/phenote-website/content/howtos/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-05-30 05:26:51 UTC (rev 644) +++ phenote/trunk/doc/phenote-website/content/howtos/index.shtml 2007-05-30 05:42:59 UTC (rev 645) @@ -12,7 +12,7 @@ <p> Phenote is a Java application, which can be launched from the web using "Webstart". Simply click on the link below, and this will download the application to your computer and run. Future clicks on the link should recognize that you've already downloaded the application, and it will simply start the software.</p> <p> -Webstart: <a href="http://toy.lbl.gov:9010/phenote/1.2/phenote.jnlp">Phenote v1.2</a> +Webstart: <a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Phenote v1.2</a> </p> <p> Phenote can also be launched from our <a href="/content/software/">Downloads</a> page. There you will also find any newer versions under development. Modified: phenote/trunk/doc/phenote-website/content/software/index.shtml =================================================================== --- phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-05-30 05:26:51 UTC (rev 644) +++ phenote/trunk/doc/phenote-website/content/software/index.shtml 2007-05-30 05:42:59 UTC (rev 645) @@ -8,28 +8,29 @@ <h2>Phenote Software</h2> -<h3><a name="current">Current Release: 1.2</a> [<a href="http://toy.lbl.gov:9010/phenote/1.2/phenote.jnlp">Webstart</a>] </h3> +<h3><a name="current">Current Release: 1.3</a> [<a href="http://www.phenote.org/phenote/latest/phenote.jnlp">Webstart</a>] </h3> Newest Features: <ul> -<li>Can now search ALL ontologies of a field without having to change the pull-down menu</li> -<li>User can choose to update their local copy of an OBO ontology from sourceforge (can also retrieve if no local file found)</li> -<li>Tab delimited data adapter</li> -<li>Beginnings of term history</li> -<li>User can select configuration they want to use at initialization or subsequently from file menu (currently requires phenote restart). </li> -<li>Phenote merges its default configuration with users' configuration. This preserves user's additions as well as adds anything new from phenote upgrades.</li> -<li>QueryableDataAdapter interface for adding a database data adapter that can be queried. The data adapter specifies queryable fields, which get a retrieve button.</li> -<li>Improved layout</li> -<li>Tabbed main data-entry panel if more than 12 fields are present. Note that all fields will be displayed in the lower display table without scrolling</li> -<li>Refactored code for field guis</li> -<li>Ontology chooser reflects current term (bug fix)</li> +<li>Web-based documentation and Help features</li> +<li>Metadata fields added to configuration. User can name their configuration, add a description, and author</li> +<li>Dialog allows user to back out of exiting from File->Exit</li> +<li>Autocompletion search default settings configurable </li> +<li>Can post-compose with >2 terms </li> +<li>Synonyms delineated by scope in Term Info: Exact, Narrow, Broad, General, Related. </li> +<li>Obsolete replacements or consideration terms are displayed in term info with links.</li> +<li>Can configure by namespace for ontologies</li> +<li>Can automatically update ontologies during startup (configurable)</li> +<li>Added common configuration for OMIM curation for use by NCBO (ncbo.cfg)</li> +<li>Can check for updates to ontology files independently from any URL </li> +<li>Obsolete replacements or consideration terms are displayed in term info with links</li> </ul> <p> -See the <a href="http://www.phenote.org/phenote-release-notes.html">Release Notes</a> for more information or back-versions. +See the <a href="http://www.phenote.org/phenote-release-notes.html">Release Notes</a> for more detailed information. </p> <p> To download this version with subversion, use the command: -svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/release-1.2/ phenote +svn co https://obo.svn.sourceforge.net/svnroot/obo/phenote/tags/1.3/ phenote </p> <h3><a name="devel">Development Version</a></h3> @@ -43,7 +44,7 @@ You can also browse the subversion repository at: <br /> https://obo.svn.sourceforge.net/viewvc/obo/phenote/ </p> <p> -For instructions on running Phenote, or downloading the sourcecode, visit our <a href="/content/howtos">How-to pages</a>. +For instructions on running Phenote, or downloading the sourcecode, visit our <a href="/content/howtos">How-to pages</a> our our new <a href="www.phenote.org/help">HELP</a> pages. </p> Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-30 05:26:51 UTC (rev 644) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-05-30 05:42:59 UTC (rev 645) @@ -17,9 +17,8 @@ <h2>1.3 <hr></h2> +05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a><br> -in development, 1.3-beta2 -> 1.3 release<br> - <ul> <li>feature: Web-based documentation and Help features</li> @@ -54,7 +53,7 @@ </ul> -05.09.2007, version <a href="1.3-beta1/phenote.jnlp">1.3-beta1</a><br> +05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a><br> <ul> @@ -81,7 +80,7 @@ <h2>1.2 <hr></h2> -05.02.2007, version <a href="1.2/phenote.jnlp">1.2</a><br> +05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a><br> <ul> @@ -124,7 +123,7 @@ <h2>1.1 <hr></h2> -04.06.2007, version <a href="1.1/phenote.jnlp">1.1.3</a><br> +04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a><br> <ul> @@ -183,7 +182,7 @@ <h2>1.0 <hr></h2> -02.06.2007, version <a href="1.0/phenote-flybase.jnlp">1.0.5-fly</a>, <a href="1.0/phenote-zfin.jnlp">1.0.5-zfin</a><br> +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><br> 01.12.2007, version1.0, <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby @@ -209,8 +208,8 @@ <h2>0.9 <hr></h2> -11.15.2006, version <a href="0.9/phenote-flybase.jnlp">0.9-fly</a>, -<a href="0.9/phenote-zfin.jnlp">0.9-zfin</a>, +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><br> @@ -246,8 +245,8 @@ <h2>0.8 <hr></h2> -10.02.2006, version <a href="0.8/phenote-flybase.jnlp">0.8-fly</a>, -<a href="0.8/phenote-zfin.jnlp">0.8-zfin</a>, +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><br> @@ -272,7 +271,7 @@ <h2>0.7 <hr></h2> -08.23.2007, version <a href="0.7/phenote-flybase.jnlp">0.7-fly.</a>, +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><br> <ul> @@ -309,7 +308,7 @@ <h2>0.6 <hr></h2> -07.28.2006, version <a href="0.6/phenote-flybase.jnlp">0.6-fly</a>, <a href="0.6/phenote-zfin.jnlp">0.6-zfin</a>, +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><br> @@ -328,7 +327,7 @@ <h2>0.5 <hr></h2> -05.12.2006, version <a href="0.5/phenote-flybase.jnlp">0.5-FlyBase</a>, <a href="0.5/phenote-zfin.jnlp">0.5-ZFIN</a><br> +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><br> <p> No new additions to the gui here. In preparation for my visit to @@ -347,7 +346,7 @@ <h2>0.4 <hr></h2> -04.26.2006, version <a href="0.4/phenote-flybase.jnlp">0.4-flybase</a>, <a href="0.4/phenote-zfin.jnlp">0.4-zfin</a><br> +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><br> <ul> @@ -388,7 +387,7 @@ <h2>0.3 <hr></h2> -04.07.2006, version <a href="0.3/phenote-webstart.jnlp">0.3</a>, <a href="0.3.1/phenote-webstart.jnlp">0.3.1 (for CToL)</a><br> +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><br> <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<br> @@ -445,7 +444,7 @@ <h2>0.2 <hr></h2> -03.27.2006, version <a href="0.2/phenote-webstart.jnlp">0.2</a><br> +03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a><br> <ul> @@ -465,7 +464,7 @@ <h2>0.1 <hr></h2> -03.01.2006, version <a href="0.1/phenote-webstart.jnlp">0.1</a><br> +03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a><br> <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 This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-07-17 19:20:53
|
Revision: 728 http://svn.sourceforge.net/obo/?rev=728&view=rev Author: mgibson Date: 2007-07-17 12:20:55 -0700 (Tue, 17 Jul 2007) Log Message: ----------- webstart for smart atlas updated for 1.4-beta2 release Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote.jnlp Added Paths: ----------- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp Added: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp (rev 0) +++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-17 19:20:55 UTC (rev 728) @@ -0,0 +1,45 @@ +<?xml version="1.0" encoding="UTF-8"?> +<jnlp +spec="1.0+" +codebase="http://phenote.org/phenote/1.4-beta2" +href="phenote.jnlp"> +<information> + <title>Phenote 1.4-beta2</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> +<!-- no cmd line param will ask user for config at initialization --> +<application-desc main-class="phenote.main.Phenote"> + <argument>-u</argument> + <argument>/smart-atlas.cfg</argument> +</application-desc> +</jnlp> Modified: phenote/trunk/doc/phenote-website/phenote.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-17 18:25:25 UTC (rev 727) +++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-17 19:20:55 UTC (rev 728) @@ -1,10 +1,10 @@ <?xml version="1.0" encoding="UTF-8"?> <jnlp spec="1.0+" -codebase="http://phenote.org/phenote/1.3" +codebase="http://phenote.org/phenote/1.4-beta2" href="phenote.jnlp"> <information> - <title>Phenote 1.3</title> + <title>Phenote 1.4-beta2</title> <vendor>National Center for Biomedical Ontology</vendor> <description>Phenote standalone app via webstart</description> <!-- Declares that the application can run without This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |
From: <mg...@us...> - 2007-07-18 18:16:56
|
Revision: 734 http://svn.sourceforge.net/obo/?rev=734&view=rev Author: mgibson Date: 2007-07-18 11:16:56 -0700 (Wed, 18 Jul 2007) Log Message: ----------- jars for jnlp jh.jar release notes, for 1.4-beta2 Modified Paths: -------------- phenote/trunk/doc/phenote-website/phenote-release-notes.html phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp phenote/trunk/doc/phenote-website/phenote.html phenote/trunk/doc/phenote-website/phenote.jnlp Modified: phenote/trunk/doc/phenote-website/phenote-release-notes.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-18 16:53:44 UTC (rev 733) +++ phenote/trunk/doc/phenote-website/phenote-release-notes.html 2007-07-18 18:16:56 UTC (rev 734) @@ -2,350 +2,512 @@ <html> <head> + + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> + + <title>Phenote Release Notes</title> </head> <body> + <h1>Phenote Release Notes</h1> + <h2>1.4 </h2> -<h3>version 1.4beta1 - in development</h3> +<h3>version 1.4-beta2</h3> <ul> + <li>feature: help </li> + <li>feature: RESTful data input for birn's smart atlas</li> + <li>feature: Character Template for nescent/ctol (Jim Balhoff)</li> + <li>feature: Progress on gui for config (in progress)</li> + <li>feature: Progress on field groups (genotype maker, pub querying...)</li> + <li>change: Command line read & write of .tab</li> + <li>change: Not dropping obsolete terms</li> + <li>.... and more...</li> +</ul> +<h3>version 1.4-beta1 - in development</h3> + + +<ul> + <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: '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>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: '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> + </ul> + <h2>1.3</h2> + 05.24.2007, version <a href="phenote/1.3/phenote.jnlp">1.3 release</a><br> + <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> + 05.09.2007, version <a href="phenote/1.3-beta1/phenote.jnlp">1.3-beta1</a><br> + <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> + <h2>1.2 <hr></h2> + 05.02.2007, version <a href="phenote/1.2/phenote.jnlp">1.2</a><br> + <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: 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> + <h2>1.1 <hr></h2> + 04.06.2007, version <a href="phenote/1.1/phenote.jnlp">1.1.3</a><br> + <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> + 03.28.2007, version 1.1.1<br> + <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> + <h2>1.0 <hr></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><br> + 01.12.2007, version1.0, <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> + <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> + <h2>0.9 <hr></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><br> + 11.09.2006, version 0.9<br> + <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> + <h2>0.8 <hr></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><br> + <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> + <h2>0.7 <hr></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><br> + <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> + <h2>0.6 <hr></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><br> + <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> + <h2>0.5 <hr></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><br> + <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 @@ -360,19 +522,26 @@ character strings.</p> + <h2>0.4 <hr></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><br> + <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. @@ -381,10 +550,13 @@ 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 @@ -393,96 +565,134 @@ 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> + <h2>0.3 <hr></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><br> + <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<br> + 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> + <h2>0.2 <hr></h2> + 03.27.2006, version <a href="phenote/0.2/phenote-webstart.jnlp">0.2</a><br> + <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> + <h2>0.1 <hr></h2> + 03.01.2006, version <a href="phenote/0.1/phenote-webstart.jnlp">0.1</a><br> + <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 @@ -491,5 +701,6 @@ limited functionality was demo'd at the cbio meeting 3/3/06 at Stanford.</p> + </body> </html> Modified: phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 16:53:44 UTC (rev 733) +++ phenote/trunk/doc/phenote-website/phenote-smart-atlas.jnlp 2007-07-18 18:16:56 UTC (rev 734) @@ -36,6 +36,7 @@ <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" /> </resources> <!-- no cmd line param will ask user for config at initialization --> <application-desc main-class="phenote.main.Phenote"> Modified: phenote/trunk/doc/phenote-website/phenote.html =================================================================== --- phenote/trunk/doc/phenote-website/phenote.html 2007-07-18 16:53:44 UTC (rev 733) +++ phenote/trunk/doc/phenote-website/phenote.html 2007-07-18 18:16:56 UTC (rev 734) @@ -11,6 +11,7 @@ + @@ -21,6 +22,7 @@ + <meta content="text/html; charset=ISO-8859-1" http-equiv="content-type"> @@ -32,6 +34,7 @@ + @@ -42,6 +45,7 @@ + <title>Phenote</title> </head> @@ -57,6 +61,7 @@ + <h1 style="text-align: left;"><span style="font-weight: bold;"></span>Phenote<br> @@ -68,6 +73,7 @@ + </h1> @@ -79,6 +85,7 @@ + <br> @@ -90,6 +97,7 @@ + Phenote is a tool to annotate phenotypes using the Entity Quality paradigm. It takes advantage of ontologies. It uses term completion to allow curators quick access to @@ -104,7 +112,10 @@ + <br> +<a href="1.4-beta2/phenote.jnlp">Phenote 1.4-beta2</a><br> +<br> @@ -114,16 +125,20 @@ + <a href="1.3/phenote.jnlp">Phenote 1.3</a><br> + <br> + After phenote downloads the java jar files (takes a while) it will ask you what configuration you would like to use, fly, zfin, human,worm,birn....<br> + <br> @@ -135,9 +150,12 @@ + <a href="phenote-release-notes.html">Phenote Release Notes and old webstart releases</a><br> + <br> + Recent addditions include the ability to update config while preserving your changes, change config, tab delimited format, tabbed field panel, retrieve ontologies from web, retrieve from field to database, search @@ -154,6 +172,7 @@ + <br> @@ -165,6 +184,7 @@ + Zebrafish requires components of phenote(to plug into their non-public website), not a full web app. Here is a proof of concept of some of @@ -180,6 +200,7 @@ + <br> @@ -191,6 +212,7 @@ + <a href="http://reaper.lbl.gov/phenote/html/ncbo.html">Webby Phenote(components used by Zfin)</a><br> @@ -203,6 +225,7 @@ + <br> @@ -214,6 +237,7 @@ + Webby phenote is a collaboration with Sohel Merchant at dictyBase, and Christian Pich & Kevin Schaper at zfin. Here is what Dicty has done:<br> @@ -226,6 +250,7 @@ + <br> @@ -237,6 +262,7 @@ + <a href="http://165.124.152.194/db/cgi-bin/dictyBase/curation/phenotypeCuration.pl">DictyBase webby phenote</a><br> @@ -249,6 +275,7 @@ + <br> @@ -260,6 +287,7 @@ + <br> @@ -271,6 +299,7 @@ + We would love to get your feedback! Please report any bugs (ideally through the <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">bug tracker</a>) and let us know what you think (email:<a href="mailto:mg...@be..."> mg...@be...</a>, email list: <a href="mailto:obo...@li...">obo...@li...</a>).<br> @@ -284,6 +313,7 @@ + <br> @@ -295,6 +325,7 @@ + <h4>Phenote links:<br> @@ -306,6 +337,7 @@ + </h4> @@ -317,6 +349,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote">Phenote email list</a><br> @@ -329,6 +362,7 @@ + <a href="https://sourceforge.net/tracker/?group_id=76834&atid=887913">Phenote bug tracker</a><br> @@ -341,6 +375,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-phenote-bug-tracker">Bug tracker email list</a><br> @@ -353,6 +388,7 @@ + <a href="https://sourceforge.net/svn/?group_id=76834">Phenote source code (obo sourceforge svn)</a><br> @@ -365,6 +401,7 @@ + <a href="https://lists.sourceforge.net/lists/listinfo/obo-svn-commit">Phenote svn commit email list</a><br> @@ -377,6 +414,7 @@ + <a href="http://wiki.dictybase.org/dictywiki/index.php/Phenotype_Curation_Tool_Documentation#Usage">Dicty webby phenote wiki developer docs</a><br> @@ -389,6 +427,7 @@ + <a href="http://www.bioontology.org/wiki-internal/index.php/Phenotype_Annotation_Tool">Phenote ncbo internal wiki (ncbo folk only)</a><br> @@ -396,10 +435,12 @@ + <a href="developer-docs/dataadapter.html">Phenote dataadapter developer doc</a><br> + <a href="developer-docs/developer-docs.html">More developer docs</a><br> @@ -411,6 +452,7 @@ + <br> @@ -422,6 +464,7 @@ + <br> @@ -433,6 +476,7 @@ + If the Phenote webstart link fails to do anything, then there are probably problems with webstart and/or java(has to be jdk 1.5). Take a look at the <a href="webstart-troubleshooting.html">webstart troubleshooting</a><br> @@ -446,6 +490,7 @@ + page.<br> @@ -457,6 +502,7 @@ + <br> @@ -468,6 +514,7 @@ + Click here for <a href="phenote-java-requirements.html">phenote java requirements</a><br> @@ -480,6 +527,7 @@ + <br> @@ -491,6 +539,7 @@ + <br> @@ -502,6 +551,7 @@ + <br> @@ -513,6 +563,7 @@ + Old releases: <br> @@ -524,11 +575,15 @@ + <a href="1.3-beta1/phenote.jnlp">Phenote 1.3-beta1</a><br> + <a href="1.2/phenote.jnlp">Phenote 1.2</a><br> + <a href="1.1/phenote.jnlp">Phenote 1.1</a><br> + <a href="1.0/phenote-flybase.jnlp">Phenote 1.0 for fly</a><br> @@ -540,6 +595,7 @@ + <a href="1.0/phenote-zfin.jnlp">Phenote 1.0 for zfin</a><br> @@ -550,6 +606,7 @@ + <a href="1.0/phenote-human.jnlp">Phenote 1.0 for human</a><br> @@ -558,6 +615,7 @@ + <br> @@ -569,6 +627,7 @@ + <a href="0.9/phenote-flybase.jnlp">Phenote 0.9 for fly</a><br> @@ -580,6 +639,7 @@ + <a href="0.9/phenote-zfin.jnlp">Phenote (standalone) 0.9 for zfin</a><br> @@ -590,6 +650,7 @@ + <br> @@ -600,6 +661,7 @@ + <a href="0.8/phenote-flybase.jnlp">Phenote 0.8 for fly.</a><br> @@ -611,6 +673,7 @@ + <a href="0.8/phenote-zfin.jnlp">Phenote (standalone) 0.8 for zfin</a><br> @@ -622,6 +685,7 @@ + <br> @@ -633,6 +697,7 @@ + <a href="0.7/phenote-flybase.jnlp">Phenote 0.7 for fly.</a><br> @@ -644,6 +709,7 @@ + <a href="0.7/phenote-zfin.jnlp">Phenote (standalone) 0.7 for zfin</a><br> @@ -655,6 +721,7 @@ + <br> @@ -666,6 +733,7 @@ + <a href="0.6/phenote-flybase.jnlp">Phenote 0.6 with fly anatomy</a><br> @@ -677,6 +745,7 @@ + <br> @@ -688,6 +757,7 @@ + <a href="0.6/phenote-zfin.jnlp">Phenote 0.6 with zebrafish anatomy</a><br> @@ -699,6 +769,7 @@ + <br> @@ -710,6 +781,7 @@ + <a href="0.5/phenote-flybase.jnlp">Phenote 0.5 webstart for FlyBase</a><br> @@ -721,6 +793,7 @@ + <br> @@ -732,6 +805,7 @@ + <a href="0.5/phenote-zfin.jnlp">Phenote 0.5 webstart for ZFIN</a><br> @@ -743,6 +817,7 @@ + <br> @@ -754,6 +829,7 @@ + <a href="0.4/phenote-flybase.jnlp">Phenote 0.4 webstart for FlyBase</a><br> @@ -765,6 +841,7 @@ + <br> @@ -776,6 +853,7 @@ + <a href="0.4/phenote-zfin.jnlp">Phenote 0.4 webstart for ZFIN</a><br> @@ -787,6 +865,7 @@ + <br> @@ -798,6 +877,7 @@ + <a href="0.3.1/phenote-webstart.jnlp">Phenote for CToL group (0.3.1)</a> (a special release for the CToL group that uses fish taxonomy)<br> @@ -811,6 +891,7 @@ + <br> @@ -822,6 +903,7 @@ + <a href="0.3/phenote-webstart.jnlp">Phenote 0.3</a><br> @@ -833,6 +915,7 @@ + <br> @@ -844,6 +927,7 @@ + <a href="0.2/phenote-webstart.jnlp">Phenote 0.2</a><br> @@ -855,6 +939,7 @@ + <br> @@ -866,6 +951,7 @@ + <a href="0.1/phenote-webstart.jnlp">Phenote 0.1</a><br> @@ -877,6 +963,7 @@ + <br> @@ -888,6 +975,7 @@ + <br> @@ -899,5 +987,6 @@ + </body> </html> Modified: phenote/trunk/doc/phenote-website/phenote.jnlp =================================================================== --- phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 16:53:44 UTC (rev 733) +++ phenote/trunk/doc/phenote-website/phenote.jnlp 2007-07-18 18:16:56 UTC (rev 734) @@ -36,6 +36,7 @@ <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" /> </resources> <!-- no cmd line param will ask user for config at initialization --> <application-desc main-class="phenote.main.Phenote"> This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |