new web site design and updates to the web pages

[jabaws.git] / website / man_about.html

diff --git a/website/man_about.html b/website/man_about.html
index ac1c686..3758bfe 100644 (file)
--- a/website/man_about.html
+++ b/website/man_about.html
@@ -13,9 +13,9 @@
 <div id="page">\r
 <div id="banner">\r
 <table> \r
-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt.gif"  alt="University of Dundee" class="logo"  title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws.png" title="JABAWS:MSA" alt="JABAWS:MSA"/></td>\r
-<td class="bg"><img src="images/align.png"/></td>\r
+<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif"  alt="University of Dundee" width="158" height="90" class="logo"  title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+<td class="bg"><img src="images/jabaws2.png" alt="JABAWS-2.0:Disorder" width="353" height="67" title="JABAWS-2.0:Disorder"/></td>\r
+<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
 </tr>\r
 </table>\r
 </div><!-- banner end-->\r
@@ -31,12 +31,15 @@
                <a href="man_configuration.html" >Server<br/>\r
                Configuration</a>\r
                <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
+               <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
                <a href="man_dev.html" title="Accessing JABAWS from your program">Accessing<br/>\r
                JABAWS</a>      \r
        </div>\r
        <a href="download.html">Download</a>\r
        <a href="contacts.html">Contact Us</a>\r
-       <a href="http://www.compbio.dundee.ac.uk">Barton Group</a></div>\r
+       <a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+    <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+\r
 <!-- panel end-->\r
 <div id="content">\r
 \r
@@ -53,8 +56,8 @@
 \r
 \r
 <h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>\r
-<p>JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment programs (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.\r
- However, the scope of JABAWS is not limited to multiple sequence alignment programs. Future versions of JABAWS will incorporate protein disorder prediction, BLAST, PSIBLAST and HMMER database searches and many other tools.</p>\r
+<p>JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.\r
+  Future versions of JABAWS will incorporate many other tools.</p>\r
 <h4>Getting JABAWS</h4>\r
 <p>JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the JABAWS command line client is what you need. </p>\r
 <h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>\r
@@ -69,14 +72,26 @@
 </ul>\r
 <h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>\r
 <p> JABAWS currently provides access to the following programs:</p>\r
+<p>Multiple Sequence Alignement </p>\r
 <ul>\r
   <li><a href="http://www.clustal.org/">ClustalW</a> (version 2.0.12)</li>\r
-  <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.713)</li>\r
-  <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.7) </li>\r
-  <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.14) </li>\r
+  <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
+  <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
+  <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
   <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
   </ul>\r
 \r
+<p>Protein disorder prediction</p>\r
+<ul>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://iupred.enzim.hu">IUPred</a></span> (1.0) </li>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>\r
+  </ul>\r
+<p>Amino Acid conservation </p>\r
+<ul>\r
+  <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>\r
+</ul>\r
 <h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\r
 <p>A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. \r
 The most basic JABAWS client is a command line Java application which can call any of the JABAWS web services methods \r