JWS-109 Updated the Documentation pages. Fixed the links and fixed chuncks of text...

[jabaws.git] / website / man_about.jsp

diff --git a/website/man_about.jsp b/website/man_about.jsp
index a4444e9..62edca5 100644 (file)
--- a/website/man_about.jsp
+++ b/website/man_about.jsp
@@ -26,10 +26,10 @@
                 <!--<h4>About</h4>-->
                 <ul>
                     <li><a href="#wisjaba">What is JABAWS?</a></li>
                 <!--<h4>About</h4>-->
                 <ul>
                     <li><a href="#wisjaba">What is JABAWS?</a></li>

+                    <li><a href="#jabaclient">What is JABAWS Client</a>?</li>

                     <li><a href="#wjaba">JABAWS Benefits</a></li>
                     <li><a href="#wjaba">JABAWS Benefits</a></li>

-                    <li><a href="#alprog">JABA Web Services Programs</a></li>
+                    <li><a href="#alprog">Bioinformatics tools included in JABAWS</a></li>

                     <li><a href="#jaba2.2">What is new in JABAWS 2.2?</a> </li>
                     <li><a href="#jaba2.2">What is new in JABAWS 2.2?</a> </li>

-                    <li><a href="#jabaclient">What is JABAWS Client</a>?</li>

                     <li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
                     <li><a href="#cmdclient">Programmatic access to JABAWS</a></li>
                 </ul>
                     <li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
                     <li><a href="#cmdclient">Programmatic access to JABAWS</a></li>
                 </ul>

@@ -51,17 +51,46 @@
                     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
                     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>.
+                    (see <a href="#alprog">the list of currently supported programs</a>).

                     Future versions of JABAWS will incorporate other tools.
                 </p>
                 <strong>Getting JABAWS</strong>
                 <p>
                     Future versions of JABAWS will incorporate other tools.
                 </p>
                 <strong>Getting JABAWS</strong>
                 <p>

-                    JABAWS consists of a server and a 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
+                    JABAWS consists of a server and a 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
+                    <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>.
+                    It requires no configuration and is simple to install. If you want to install JABAWS for your
+                    lab or institution then download the
+                    <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS Web Application aRchive (WAR)</a>.
+                    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
                     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.
+                    in writing your own client, the
+                    <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS command line (CLI) client</a> is what you need.
+                </p>
+                <p class="text-right">
+                    <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
+                </p>
+            </div>
+        </div>
+    </div>
+</div>
+<div class="row" id="jabaclient">
+    <div class="col-md-12">
+        <div class="panel panel-default">
+            <div class="panel panel-heading">
+                <h1 class="panel-title">What is the JABAWS Client?</h1>
+            </div>
+            <div class="panel-body">
+                <p class="justify">A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web
+                    services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web
+                    services on any instance of JABAWS Server available over the web. The basic client is useful if you would like
+                    to test or execute the programs provided by the JABAWS server in your own scripts, but you do not want to handle
+                    any web service specific details. The client is an open source software, so you can also use the source code to
+                    as an example how to manipulate with JABAWS web services in your own code.
+                    <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good
+                    example of a graphical JABAWS client. This client uses the same functionality as the
+                    <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS command line (CLI) client</a>, but
+                    instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.

                 </p>
                 <p class="text-right">
                     <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
                 </p>
                 <p class="text-right">
                     <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>

@@ -78,7 +107,7 @@
             </div>
             <div class="panel-body">
                 <ul>
             </div>
             <div class="panel-body">
                 <ul>

-                    <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>
+                    <li>Can be deployed on most operating systems, as a VMware or compatible Virtual Appliance, as well as a Tomcat Java Web Application.</li>

                     <li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>
                     <li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>
                     <li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>
                     <li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>
                     <li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>
                     <li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>

@@ -98,7 +127,7 @@
     <div class="col-md-12">
         <div class="panel panel-default">
             <div class="panel panel-heading">
     <div class="col-md-12">
         <div class="panel panel-default">
             <div class="panel panel-heading">

-                <h1 class="panel-title">JABA Web Services Programs</h1>
+                <h1 class="panel-title">Bioinformatics tools included in JABAWS</h1>

             </div>
             <div class="panel-body">
                 <p>JABAWS currently provides access to the following programs:</p>
             </div>
             <div class="panel-body">
                 <p>JABAWS currently provides access to the following programs:</p>

@@ -155,7 +184,7 @@
             </div>
             <div class="panel-body">
 
             </div>
             <div class="panel-body">
 

-                <strong>JABAWS Version 2.2 (Released XX Feb 2017)</strong>
+                <strong>JABAWS Version 2.2 (Released XX March 2017)</strong>

                 <p >The website was improved and several service programs were update:</p>
                 <ul>
                     <li>The versions of several application programs provided by JABAWS were bumped to the latest available.
                 <p >The website was improved and several service programs were update:</p>
                 <ul>
                     <li>The versions of several application programs provided by JABAWS were bumped to the latest available.

@@ -170,7 +199,7 @@
                         The pre-configured JABAWS Amazon Machine Image (AMI),
                         which allowed for JABAWS to be run
                         in the <a href="http://aws.amazon.com/what-is-aws">Amazon EC2 cloud</a>, is no longer provided
                         The pre-configured JABAWS Amazon Machine Image (AMI),
                         which allowed for JABAWS to be run
                         in the <a href="http://aws.amazon.com/what-is-aws">Amazon EC2 cloud</a>, is no longer provided

-                        due to very limited use by the scientific community.
+                        due to very limited use by the scientific community peers.

                     </li>
                 </ul>
 
                     </li>
                 </ul>
 

@@ -227,30 +256,6 @@
         </div>
     </div>
 </div>
         </div>
     </div>
 </div>

-<div class="row" id="jabaclient">
-    <div class="col-md-12">
-        <div class="panel panel-default">
-            <div class="panel panel-heading">
-                <h1 class="panel-title">What is the JABAWS Client?</h1>
-            </div>
-            <div class="panel-body">
-                <p class="justify">A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web
-                    services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web
-                    services on any instance of JABAWS Server available over the web. The basic client is useful if you would like
-                    to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle
-                    any web service specific details. The client is an open source software, so you can also use the source code to
-                    as an example how to manipulate with JABAWS web services in your own code.
-                    <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good
-                    example of a graphical JABAWS client. This client uses the same functionality as the command line client, but
-                    instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.
-                </p>
-                <p class="text-right">
-                    <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
-                </p>
-            </div>
-        </div>
-    </div>
-</div>

 <div class="row" id="jalviewsup">
     <div class="col-md-12">
         <div class="panel panel-default">
 <div class="row" id="jalviewsup">
     <div class="col-md-12">
         <div class="panel panel-default">