website/index.jsp

   1 <%--<?xml version="1.0" encoding="ISO-8859-1" ?>--%>
   2 <%--<%@ page language="java" contentType="text/html; charset=ISO-8859-1" pageEncoding="ISO-8859-1"%>--%>
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   8
   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 2.2 website</h1>
  19             </div>
  20             <div class="panel-body">
  21                 <div class="row">
  22                  <div class="col-md-6">
  23                         <p class="justify">
  24                             JABAWS is free software which provides web services conveniently
  25                             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 by P. Troshin and G. Barton, unpublished), and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                             The public server based on JABAWS 2.1 at the
  55                             <a href="https://www.dundee.ac.uk/">University of Dundee</a> has been in production since
  56                             October 2013 and serviced over 442,000 jobs for users worldwide.
  57                         </p>
  58                  </div>
  59                  <div class="col-md-6 ">
  60                     <img class="pull-right" src="${pageContext.request.contextPath}/static/img/aligment.png"
  61                          style="width:100%;height:100%" alt="Jalview: Sequence Alignment">
  62                  </div>
  63                </div>
  64             </div>
  65         </div>
  66     </div>
  67 </div>
  68 <div class="row">
  69     <div class="col-md-4">
  70         <div class="panel panel-default">
  71             <div class="panel panel-heading">
  72                 <h1 class="panel-title"><i class="fa fa-user" aria-hidden="true"></i>&nbsp;&nbsp;For Users</h1>
  73             </div>
  74             <div class="panel-body">
  75                 <p class="justify">
  76                     <strong>Server: </strong><a href="${pageContext.request.contextPath}/#public_server">Public JABAWS server</a> or
  77                     the <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>
  78                 </p>
  79                 <p>
  80                     <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a>
  81                 </p>
  82                 <br/>
  83                 <%--<p class="justify">--%>
  84                     <%--To use JABAWS web services on most operating systems, just download and <a href="2.1/manual_qs_va.html#qsc">install</a>--%>
  85                     <%--the JABAWS Virtual Appliance (VA). Or even easier - just start JABAWS machine on the cloud and point Jalview at it!--%>
  86                 <%--</p>--%>
  87                 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started &raquo;</a></p>
  88             </div>
  89         </div>
  90     </div>
  91     <div class="col-md-4">
  92         <div class="panel panel-default">
  93             <div class="panel panel-heading">
  94                 <h1 class="panel-title"><i class="fa fa-flask" aria-hidden="true"></i>&nbsp;&nbsp;For Bioinformaticians/Developers</h1>
  95             </div>
  96             <div class="panel-body">
  97                 <p>
  98                     <strong>Server: </strong><a href="${pageContext.request.contextPath}/#public_server">Public JABAWS server</a>,
  99                     the <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>, the
 100                 <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS Web Application aRchive (WAR)</a> or
 101                     <a href="${pageContext.request.contextPath}/docs/docker.html">Docker Containers</a>
 102                 </p>
 103                 <p>
 104                     <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a> or the
 105                     <a href="${pageContext.request.contextPath}/getting_started.jsp#client">Command Line Interface (CLI) Client</a>
 106                 </p>
 107                 <br/>
 108                 <%--<p class="justify">--%>
 109                     <%--You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server.--%>
 110                     <%--The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public--%>
 111                     <%--server (see below) with the command line client or you own script.--%>
 112                     <%--Check out the <a href="2.1/manual_qs_client.html#qsc">quick start guide</a> for further details.--%>
 113                 <%--</p>--%>
 114                 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started &raquo;</a></p>
 115             </div>
 116         </div>
 117     </div>
 118     <div class="col-md-4">
 119         <div class="panel panel-default">
 120             <div class="panel panel-heading">
 121                 <h1 class="panel-title"><i class="fa fa-server" aria-hidden="true"></i>&nbsp;&nbsp;For System Administrators</h1>
 122             </div>
 123             <div class="panel-body">
 124                 <p>
 125                     <strong>Server: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#war">
 126                     JABAWS Web Application aRchive (WAR)</a>
 127                 </p>
 128                 <p>
 129                     <strong>Client: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#client">
 130                     Command Line Interface (CLI) Client</a>
 131                 </p>
 132                 <br/>
 133                 <%--<p class="justify">--%>
 134                     <%--JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>--%>
 135                     <%--to run. Please check the <a href="2.1/manual_qs_war.html#qsc">quick start guide</a> for installation instructions.--%>
 136                 <%--</p>--%>
 137                 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started &raquo;</a></p>
 138             </div>
 139         </div>
 140     </div>
 141 </div>
 142 <div class="row" id="public_server">
 143     <div class="col-md-12">
 144         <div class="panel panel-default">
 145             <div class="panel panel-heading">
 146                 <h1 class="panel-title">Public JABAWS Server</h1>
 147             </div>
 148             <div class="panel-body">
 149
 150                 <p class="justify">
 151                     You can access our public JABAWS web services with <a href="http://www.jalview.org/">Jalview</a>,
 152                     <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS CLI</a>, or
 153                     <a href="${pageContext.request.contextPath}/docs/develop.html#accessing-jabaws-from-your-program">with your own program</a>.
 154                     The latest versions of Jalview (version 2.9 or later) are fully compatible
 155                     with JABAWS 2.2 and are configured to use the public JABAWS server by default.
 156                 </p>
 157                 <ul>
 158                     <li>The JABAWS public web services address is <strong><a href="http://www.compbio.dundee.ac.uk/jabaws">http://www.compbio.dundee.ac.uk/jabaws</a></strong> </li>
 159                     <li>A detailed description of the JABAWS web services is available from here:
 160                         <a href="${pageContext.request.contextPath}/RegistryWS?"
 161                            title="${pageContext.request.contextPath}/RegistryWS?" rel=nofollow">WSDL List</a></li>
 162                 </ul>
 163                 <p class="justify">
 164                     These web services accept submissions of <strong>less than one thousand sequences</strong>.
 165                     Should you find this to be insufficient for your needs, or if you are concerned about privacy,
 166                     then you can download and
 167                     run the <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS WAR</a> on your own hardware.
 168                 </p>
 169             </div>
 170         </div>
 171     </div>
 172 </div>
 173 <div class="row">
 174     <div class="col-md-12">
 175         <div class="panel panel-default">
 176             <div class="panel panel-heading">
 177                 <h1 class="panel-title">New in JABAWS 2.2</h1>
 178             </div>
 179             <div class="panel-body">
 180                 <p class="justify">
 181                     The current JABAWS version is 2.2 released on 18 August 2017. Among the new developments in JABAWS 2.2 are:
 182                                 </p>
 183                     <ul>
 184                         <li>Several programs included in JABAWS, including Clustal Omega, ClustalW, Mafft and T-coffee, were updated.
 185                         <li><a href="http://www.compbio.dundee.ac.uk/aacon/">AACon</a>
 186                             was also updated to the latest release, version 1.1.</li>
 187                         <li><a href="${pageContext.request.contextPath}/ServiceStatus" >Service Status</a> and
 188                             <a href="${pageContext.request.contextPath}/PublicAnnualStat" >Usage Statistics</a>
 189                             are now cached and refreshed asynchronously for improved Website loading times.</li>
 190                         <li>We now provide a <a href="https://www.docker.com/" >Docker</a> image which allows for JABAWS to be run in Docker containers. </li>
 191                         <li>The website looks were updated to use the Twitter <a href="http://getbootstrap.com/">Bootstrap</a> CSS framework,
 192                             and documentation pages are now generated with <a href="http://www.sphinx-doc.org/en/stable/">Sphinx</a>.
 193                         </li>
 194                     </ul>
 195                 <p class="justify">
 196                     More information about the changes introduced in the latest release can be found in the
 197                     <a href="${pageContext.request.contextPath}/docs/changelog.html">changelog</a> pages.
 198                 </p>
 199             </div>
 200         </div>
 201     </div>
 202 </div>
 203
 204 <div class="row">
 205     <div class="col-md-12">
 206         <div class="panel panel-default">
 207             <div class="panel panel-heading">
 208                 <h1 class="panel-title">Reference</h1>
 209             </div>
 210             <div class="panel-body">
 211                 <p class="justify">
 212                     Peter V Troshin,  James B Procter,  Alexander Sherstnev,  Daniel L Barton,  F&aacute;bio Madeira and Geoffrey J. Barton (2018)
 213                     <strong>JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure</strong>
 214                     <em>Bioinformatics</em> bty045. doi: <a href="https://doi.org/10.1093/bioinformatics/bty045">
 215                     10.1093/bioinformatics/bty045</a>.
 216                 </p>
 217                 <p class="justify">
 218                     Peter V. Troshin, James B. Procter and Geoffrey J. Barton (2011)
 219                     <strong>Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS</strong>
 220                     <em>Bioinformatics</em> 27 (14): 2001-2002. doi: <a href="https://doi.org/10.1093/bioinformatics/btr304">
 221                     10.1093/bioinformatics/btr304</a>.
 222                 </p>
 223             </div>
 224         </div>
 225     </div>
 226 </div>
 227 <%--</div>--%>
 228 <div class="row">
 229     <div class="col-md-12">
 230         <div class="panel panel-default">
 231             <div class="panel panel-heading">
 232                 <h1 class="panel-title">ELIXIR-UK</h1>
 233             </div>
 234             <div class="panel-body">
 235
 236                 <div class="row">
 237                     <div class="col-md-3">
 238                         <span class="align-middle"><a href="https://www.elixir-europe.org/">
 239                             <img src="static/img/elixir_uk.png" style="width:80%;height:80%" alt="ELIXIR UK"
 240                                  title="UK BBSRC"/></a>
 241                         </span>
 242                     </div>
 243                     <div class="col-md-9">
 244                         <p class="justify">
 245                             <a href="http://www.compbio.dundee.ac.uk/jabaws/">JABAWS</a> and
 246                             <a href="http://www.compbio.dundee.ac.uk/aacon/">AACon</a> are part of the
 247                             "Dundee Resource for Protein Sequence analysis and structure prediction", which is an
 248                             <a href="http://www.elixir-uk.org/">ELIXIR-UK</a> resource.
 249                         </p>
 250                         <div class="row">
 251                             <div class="col-md-4">
 252                                 <span class="align-left"><a href="http://www.bbsrc.ac.uk/">
 253                                     <img src="static/img/bbsrc_flat.jpg" style="width:110%;height:110%" alt="UK BBSRC"
 254                                          title="UK BBSRC"/></a>
 255                                 </span>
 256                             </div>
 257                             <div class="col-md-4">
 258                                 <span class="align-right"><a href="http://www.jalview.org/">
 259                                     <img src="static/img/jalview.svg" style="width:100%;height:100%" alt="JALVIEW"
 260                                          title="JALVIEW"/></a>
 261                                 </span>
 262                             </div>
 263                             <div class="col-md-4">
 264                                 <span class="align-right"><a href="http://www.compbio.dundee.ac.uk/jpred/index.html">
 265                                     <img src="static/img/jpred4.svg" style="width:100%;height:100%" alt="JPRED"
 266                                          title="JPRED"/></a>
 267                                 </span>
 268                             </div>
 269                         </div>
 270                     </div>
 271                 </div>
 272             </div>
 273         </div>
 274     </div>
 275 </div>
 276
 277 <jsp:include page="template_footer.jsp" />