<div class="panel-body">
<p class="justify">
<p style="color:black; font-weight:normal; text-align:left;">
- <span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span>
- is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently
- packaged to run on your local computer, server or cluster.
+ <span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services (JABAWS)">
+ JAva Bioinformatics Analysis Web Services (JABAWS)</span>
+ is free software which provides web services conveniently packaged to run on your local computer, server or cluster.
</p>
<p class="justify">
Services for multiple sequence alignment include
<a href="http://probcons.stanford.edu/">ProbCons</a>,
<a href="http://msaprobs.sourceforge.net/">MSAProbs</a>, and
<a href="http://sourceforge.net/projects/glprobs/">GLProbs</a>.
- Analysis services allow prediction of the protein disorder with
+ Analysis services allow prediction of protein disorder with
<a href="http://dis.embl.de/">DisEMBL</a>,
<a href="http://iupred.enzim.hu">IUPred</a>,
Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), and
<a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.
</p>
<p class="justify">
- <span style="color:black; font-weight:normal; text-align:left;">
- JABAWS 2.2 installation can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop
- application</strong> (version 2.8 onwards) and the <a href="man_client.jsp">JABAWS command-line client</a>.
- JABAWS is able to provide multiple alignment and sequence analysis calculations limited only by your own
- computing resources.<br/>
- </span>
+ JABAWS web-services can be accessed through the <a href="http://www.jalview.org">Jalview</a> desktop
+ graphical user interface (GUI) (version 2.8 onwards) or the command line interface (CLI) client.
+ In this way you can perform computations on your sequences using the publicly available servers
+ running at the University of Dundee. Alternatively, JABAWS installation allows you to perform analysis
+ limited only by your own computing resources, by running it in your local computer, server or cluster.
+ </p>
+ <p class="justify">
+
</p>
</div>
</div>
<div class="col-md-4">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">For Users</h1>
+ <h1 class="panel-title"><i class="fa fa-user" aria-hidden="true"></i> For Users</h1>
</div>
<div class="panel-body">
<p class="justify">
- <strong>The Server: </strong><a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=JABAWS201.pack.tar.gz">JABAWS Virtual Appliance:</a> (440M)
- or <a href="2.1/man_awscloud.html">JABAWS on Amazon Webservices Cloud</a><br/>
- <strong>The Main Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)
+ <strong>Server: </strong><a href="${pageContext.request.contextPath}/#public_server">Public JABAWS server</a> or
+ the <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>
</p>
- <p class="justify">
- To use JABAWS web services on most operating systems, just download and <a href="2.1/manual_qs_va.html#qsc">install</a>
- the JABAWS Virtual Appliance (VA). Or even easier - just start JABAWS machine on the cloud and point Jalview at it!
+ <p>
+ <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a>
</p>
+ <br/>
+ <%--<p class="justify">--%>
+ <%--To use JABAWS web services on most operating systems, just download and <a href="2.1/manual_qs_va.html#qsc">install</a>--%>
+ <%--the JABAWS Virtual Appliance (VA). Or even easier - just start JABAWS machine on the cloud and point Jalview at it!--%>
+ <%--</p>--%>
+ <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started »</a></p>
</div>
</div>
</div>
<div class="col-md-4">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">For System Administrators</h1>
+ <h1 class="panel-title"><i class="fa fa-flask" aria-hidden="true"></i> For Bioinformaticians/Developers</h1>
</div>
<div class="panel-body">
- <p class="justify">
- <strong>The Server: </strong><a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=jabaws.war">JABAWS Web
- Application aRchive</a> (55M)
+ <p>
+ <strong>Server: </strong><a href="${pageContext.request.contextPath}/#public_server">Public JABAWS server</a>,
+ the <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a> or the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS Web Application aRchive (WAR)</a>
</p>
- <p class="justify">
- JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>
- to run. Please check the <a href="2.1/manual_qs_war.html#qsc">quick start guide</a> for installation instructions.
+ <p>
+ <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a> or the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#client">Command Line Interface (CLI) Client</a>
</p>
+ <br/>
+ <%--<p class="justify">--%>
+ <%--You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server.--%>
+ <%--The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public--%>
+ <%--server (see below) with the command line client or you own script.--%>
+ <%--Check out the <a href="2.1/manual_qs_client.html#qsc">quick start guide</a> for further details.--%>
+ <%--</p>--%>
+ <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started »</a></p>
</div>
</div>
</div>
<div class="col-md-4">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">For Bioinformaticians/Developers</h1>
+ <h1 class="panel-title"><i class="fa fa-server" aria-hidden="true"></i> For System Administrators</h1>
</div>
<div class="panel-body">
- <strong>The Server: </strong><a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)
- <br/>
- <strong>The Client: </strong>
- Command Line Client <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=min-jaba-client-2.1.jar">binary</a> |
- <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=jaba-client-src-2.1.jar">source</a>
- <p class="justify">
- You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server.
- The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public
- server (see below) with the command line client or you own script.
- Check out the <a href="2.1/manual_qs_client.html#qsc">quick start guide</a> for further details.
+ <p>
+ <strong>Server: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#war">
+ JABAWS Web Application aRchive (WAR)</a>
+ </p>
+ <p>
+ <strong>Client: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#client">
+ Command Line Interface (CLI) Client</a>
</p>
+ <br/>
+ <%--<p class="justify">--%>
+ <%--JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>--%>
+ <%--to run. Please check the <a href="2.1/manual_qs_war.html#qsc">quick start guide</a> for installation instructions.--%>
+ <%--</p>--%>
+ <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started »</a></p>
</div>
</div>
</div>
</div>
-<div class="row">
+<div class="row" id="public_server">
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
<div class="panel-body">
<p class="justify">
- You can access our public JABAWS web services with our
- <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/jabaws-dev/get?id=min-jaba-client-2.1.jar">command line client</a>,
- <a href="http://www.jalview.org/download.html">Jalview</a>,
- or with your own program. Jalview version 2.8 or later is fully compatible with JABAWS 2.1.
- The latest versions of Jalview are configured to use public JABAWS server by default.</p>
+ You can access our public JABAWS web services with the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#client">command line client</a>,
+ <a href="http://www.jalview.org/">Jalview</a>,
+ or with your own program. The latest versions of Jalview (version 2.9 or later) are fully compatible
+ with JABAWS 2.2 and are configured to use the public JABAWS server by default.
+ </p>
<ul>
- <li>The JABAWS public web services address is <strong>http://www.compbio.dundee.ac.uk/jabaws</strong> </li>
+ <li>The JABAWS public web services address is <strong><a href="http://www.compbio.dundee.ac.uk/jabaws">http://www.compbio.dundee.ac.uk/jabaws</a></strong> </li>
<li>A detailed web services description is available from here:
- <a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?"
- title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=nofollow">WSDL List</a></li>
+ <a href="${pageContext.request.contextPath}/RegistryWS?"
+ title="${pageContext.request.contextPath}/RegistryWS?" rel=nofollow">WSDL List</a></li>
</ul>
<p class="justify">
These web services accept submissions of <strong>less than one thousand sequences</strong>.
Should you find this to be insufficient for your needs, or if you are concerned about privacy
or on an unreliable network connection, then you can
- <a href="http://gjb-www-1.cluster.lifesci.dundee.ac.uk:8086/download">download</a> and
+ <a href="${pageContext.request.contextPath}/download.jsp">download</a> and
run the JABAWS Server on your own hardware.
</p>
</div>
</div>
</div>
</div>
-<div class="row">
- <div class="col-md-12">
- <div class="panel panel-default">
- <div class="panel panel-heading">
- <h1 class="panel-title">Previous versions of JABAWS</h1>
- </div>
- <div class="panel-body">
- <p class="justify">
- We advise you to update to JABAWS 2.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and contains
- <a href="man_about.jsp#jaba2.2">some important bug fixes</a>. Please consult the <a href="man_about.jsp#jalviewsup">manual</a>
- for more information on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p>
- <ul>
- <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li>
- <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li>
- <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws201">http://www.compbio.dundee.ac.uk/jabaws201</a></strong></li>
- </ul>
- </div>
- </div>
- </div>
-</div>
+<%--<div class="row">--%>
+ <%--<div class="col-md-12">--%>
+ <%--<div class="panel panel-default">--%>
+ <%--<div class="panel panel-heading">--%>
+ <%--<h1 class="panel-title">JABAWS version 2.2</h1>--%>
+ <%--</div>--%>
+ <%--<div class="panel-body">--%>
+ <%--<p class="justify">--%>
+ <%--The current JABAWS version is 2.2.0 released on XX March 2017. We advise you to update to JABAWS 2.2 as this version is fully backward compatible with JABAWS v1.0, v2.0 and v2.1.--%>
+ <%--Please consult the <a href="${pageContext.request.contextPath}/man_about.jsp#jaba2.2">documentation pages</a>--%>
+ <%--for the changelog and more information on compatibility between versions.</p>--%>
+ <%--<%–<p>Should you require them, however, old versions of JABAWS are available here:</p>–%>--%>
+ <%--<%–<ul>–%>--%>
+ <%--<%–<li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li>–%>--%>
+ <%--<%–<li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li>–%>--%>
+ <%--<%–<li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws201">http://www.compbio.dundee.ac.uk/jabaws201</a></strong></li>–%>--%>
+ <%--<%–</ul>–%>--%>
+ <%--</div>--%>
+ <%--</div>--%>
+ <%--</div>--%>
+<%--</div>--%>
<div class="row">
<div class="col-md-12">
<div class="panel panel-default">
git://source.jalview.org / jabaws.git / commitdiff