website/index.jsp

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   9
  10 <c:import url="template_header.jsp" >
  11     <c:param name="title">Main Page</c:param>
  12 </c:import>
  13
  14 <div class="row">
  15     <div class="col-md-12">
  16         <div class="panel panel-default">
  17             <div class="panel panel-heading">
  18                 <h1 class="panel-title">Welcome to the JABAWS website</h1>
  19             </div>
  20             <div class="panel-body">
  21                 <p class="justify">
  22                 <p style="color:black; font-weight:normal; text-align:left;">
  23                 <span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services (JABAWS)">
  24                     JAva Bioinformatics Analysis Web Services (JABAWS)</span>
  25                     is free software which provides web services conveniently packaged to run on your local computer, server or cluster.
  26                 </p>
  27                 <p class="justify">
  28                     Services for multiple sequence alignment include
  29                     <a href="http://www.clustal.org/omega">Clustal Omega</a>,
  30                     <a href="http://www.clustal.org/clustal2">Clustal W</a>,
  31                     <a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>,
  32                     <a href="http://www.drive5.com/muscle">MUSCLE</a>,
  33                     <a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-Coffee</a>,
  34                     <a href="http://probcons.stanford.edu/">ProbCons</a>,
  35                     <a href="http://msaprobs.sourceforge.net/">MSAProbs</a>, and
  36                     <a href="http://sourceforge.net/projects/glprobs/">GLProbs</a>.
  37                     Analysis services allow prediction of protein disorder with
  38                     <a href="http://dis.embl.de/">DisEMBL</a>,
  39                     <a href="http://iupred.enzim.hu">IUPred</a>,
  40                     Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), and
  41                     <a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation
  42                     with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>.
  43                     The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the
  44                     <a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.
  45                 </p>
  46                 <p class="justify">
  47                     JABAWS web-services can be accessed through the <a href="http://www.jalview.org">Jalview</a> desktop
  48                     graphical user interface (GUI) (version 2.8 onwards) or the JABAWS Command Line Interface (CLI) client.
  49                     In this way you can perform computations on your sequences using the publicly available servers
  50                     running at the University of Dundee. Alternatively, JABAWS installation allows you to perform analysis
  51                     limited only by your own computing resources, by running it in your local computer, server or cluster.
  52                 </p>
  53                 <p class="justify">
  54
  55                 </p>
  56             </div>
  57         </div>
  58     </div>
  59 </div>
  60 <div class="row">
  61     <div class="col-md-4">
  62         <div class="panel panel-default">
  63             <div class="panel panel-heading">
  64                 <h1 class="panel-title"><i class="fa fa-user" aria-hidden="true"></i>&nbsp;&nbsp;For Users</h1>
  65             </div>
  66             <div class="panel-body">
  67                 <p class="justify">
  68                     <strong>Server: </strong><a href="${pageContext.request.contextPath}/#public_server">Public JABAWS server</a> or
  69                     the <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>
  70                 </p>
  71                 <p>
  72                     <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a>
  73                 </p>
  74                 <br/>
  75                 <%--<p class="justify">--%>
  76                     <%--To use JABAWS web services on most operating systems, just download and <a href="2.1/manual_qs_va.html#qsc">install</a>--%>
  77                     <%--the JABAWS Virtual Appliance (VA). Or even easier - just start JABAWS machine on the cloud and point Jalview at it!--%>
  78                 <%--</p>--%>
  79                 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started &raquo;</a></p>
  80             </div>
  81         </div>
  82     </div>
  83     <div class="col-md-4">
  84         <div class="panel panel-default">
  85             <div class="panel panel-heading">
  86                 <h1 class="panel-title"><i class="fa fa-flask" aria-hidden="true"></i>&nbsp;&nbsp;For Bioinformaticians/Developers</h1>
  87             </div>
  88             <div class="panel-body">
  89                 <p>
  90                     <strong>Server: </strong><a href="${pageContext.request.contextPath}/#public_server">Public JABAWS server</a>,
  91                     the <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a> or the
  92                 <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS Web Application aRchive (WAR)</a>
  93                 </p>
  94                 <p>
  95                     <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a> or the
  96                     <a href="${pageContext.request.contextPath}/getting_started.jsp#client">Command Line Interface (CLI) Client</a>
  97                 </p>
  98                 <br/>
  99                 <%--<p class="justify">--%>
 100                     <%--You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server.--%>
 101                     <%--The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public--%>
 102                     <%--server (see below) with the command line client or you own script.--%>
 103                     <%--Check out the <a href="2.1/manual_qs_client.html#qsc">quick start guide</a> for further details.--%>
 104                 <%--</p>--%>
 105                 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started &raquo;</a></p>
 106             </div>
 107         </div>
 108     </div>
 109     <div class="col-md-4">
 110         <div class="panel panel-default">
 111             <div class="panel panel-heading">
 112                 <h1 class="panel-title"><i class="fa fa-server" aria-hidden="true"></i>&nbsp;&nbsp;For System Administrators</h1>
 113             </div>
 114             <div class="panel-body">
 115                 <p>
 116                     <strong>Server: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#war">
 117                     JABAWS Web Application aRchive (WAR)</a>
 118                 </p>
 119                 <p>
 120                     <strong>Client: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#client">
 121                     Command Line Interface (CLI) Client</a>
 122                 </p>
 123                 <br/>
 124                 <%--<p class="justify">--%>
 125                     <%--JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>--%>
 126                     <%--to run. Please check the <a href="2.1/manual_qs_war.html#qsc">quick start guide</a> for installation instructions.--%>
 127                 <%--</p>--%>
 128                 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started &raquo;</a></p>
 129             </div>
 130         </div>
 131     </div>
 132 </div>
 133 <div class="row" id="public_server">
 134     <div class="col-md-12">
 135         <div class="panel panel-default">
 136             <div class="panel panel-heading">
 137                 <h1 class="panel-title">Public JABAWS Server</h1>
 138             </div>
 139             <div class="panel-body">
 140
 141                 <p class="justify">
 142                     You can access our public JABAWS web services with <a href="http://www.jalview.org/">Jalview</a>,
 143                     <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS CLI</a>, or
 144                     <a href="${pageContext.request.contextPath}/docs/develop.html#accessing-jabaws-from-your-program">with your own program</a>.
 145                     The latest versions of Jalview (version 2.9 or later) are fully compatible
 146                     with JABAWS 2.2 and are configured to use the public JABAWS server by default.
 147                 </p>
 148                 <ul>
 149                     <li>The JABAWS public web services address is <strong><a href="http://www.compbio.dundee.ac.uk/jabaws">http://www.compbio.dundee.ac.uk/jabaws</a></strong> </li>
 150                     <li>A detailed description of the JABAWS web services is available from here:
 151                         <a href="${pageContext.request.contextPath}/RegistryWS?"
 152                            title="${pageContext.request.contextPath}/RegistryWS?" rel=nofollow">WSDL List</a></li>
 153                 </ul>
 154                 <p class="justify">
 155                     These web services accept submissions of <strong>less than one thousand sequences</strong>.
 156                     Should you find this to be insufficient for your needs, or if you are concerned about privacy
 157                     or you are on an unreliable network connection, then you can
 158                     download and
 159                     run the <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS WAR</a> on your own hardware.
 160                 </p>
 161             </div>
 162         </div>
 163     </div>
 164 </div>
 165 <%--<div class="row">--%>
 166     <%--<div class="col-md-12">--%>
 167         <%--<div class="panel panel-default">--%>
 168             <%--<div class="panel panel-heading">--%>
 169                 <%--<h1 class="panel-title">JABAWS version 2.2</h1>--%>
 170             <%--</div>--%>
 171             <%--<div class="panel-body">--%>
 172                 <%--<p class="justify">--%>
 173                     <%--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.--%>
 174                     <%--Please consult the <a href="${pageContext.request.contextPath}/man_about.jsp#jaba2.2">documentation pages</a>--%>
 175                     <%--for the changelog and more information on compatibility between versions.</p>--%>
 176                 <%--&lt;%&ndash;<p>Should you require them, however, old versions of JABAWS are available here:</p>&ndash;%&gt;--%>
 177                 <%--&lt;%&ndash;<ul>&ndash;%&gt;--%>
 178                     <%--&lt;%&ndash;<li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li>&ndash;%&gt;--%>
 179                     <%--&lt;%&ndash;<li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li>&ndash;%&gt;--%>
 180                     <%--&lt;%&ndash;<li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws201">http://www.compbio.dundee.ac.uk/jabaws201</a></strong></li>&ndash;%&gt;--%>
 181                 <%--&lt;%&ndash;</ul>&ndash;%&gt;--%>
 182             <%--</div>--%>
 183         <%--</div>--%>
 184     <%--</div>--%>
 185 <%--</div>--%>
 186 <div class="row">
 187     <div class="col-md-12">
 188         <div class="panel panel-default">
 189             <div class="panel panel-heading">
 190                 <h1 class="panel-title">Reference</h1>
 191             </div>
 192             <div class="panel-body">
 193                 <p class="justify">
 194                     Peter V. Troshin, James B. Procter and Geoffrey J. Barton -
 195                     Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS
 196                     <em>Bioinformatics</em> 2011. 27 (14): 2001-2002. doi: <a href="https://doi.org/10.1093/bioinformatics/btr304">
 197                     10.1093/bioinformatics/btr304</a>.
 198                 </p>
 199             </div>
 200         </div>
 201     </div>
 202 </div>
 203
 204
 205 <jsp:include page="template_footer.jsp" />