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10 <c:import url="template_header.jsp" >
11 <c:param name="title">Main Page</c:param>
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>
20 <div class="panel-body">
22 <div class="col-md-6">
24 JABAWS is free software which provides web services conveniently
25 packaged to run on your local computer, server or cluster.
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 by P. Troshin and G. Barton, unpublished), and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>.
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.
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.
59 <div class="col-md-6 ">
60 <img class="pull-right" src="${pageContext.request.contextPath}/static/img/aligment.png"
61 style="width:100%;height:100%" alt="Jalview: Sequence Alignment">
69 <div class="col-md-4">
70 <div class="panel panel-default">
71 <div class="panel panel-heading">
72 <h1 class="panel-title"><i class="fa fa-user" aria-hidden="true"></i> For Users</h1>
74 <div class="panel-body">
76 <strong>Server: </strong><a href="${pageContext.request.contextPath}/#public_server">Public JABAWS server</a> or
77 the <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>
80 <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a>
83 <%--<p class="justify">--%>
84 <%--To use JABAWS web services on most operating systems, just download and <a href="2.1/manual_qs_va.html#qsc">install</a>--%>
85 <%--the JABAWS Virtual Appliance (VA). Or even easier - just start JABAWS machine on the cloud and point Jalview at it!--%>
87 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started »</a></p>
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> For Bioinformaticians/Developers</h1>
96 <div class="panel-body">
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> or the
100 <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS Web Application aRchive (WAR)</a>
103 <strong>Client: </strong><a href="http://www.jalview.org/">Jalview</a> or the
104 <a href="${pageContext.request.contextPath}/getting_started.jsp#client">Command Line Interface (CLI) Client</a>
107 <%--<p class="justify">--%>
108 <%--You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server.--%>
109 <%--The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public--%>
110 <%--server (see below) with the command line client or you own script.--%>
111 <%--Check out the <a href="2.1/manual_qs_client.html#qsc">quick start guide</a> for further details.--%>
113 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started »</a></p>
117 <div class="col-md-4">
118 <div class="panel panel-default">
119 <div class="panel panel-heading">
120 <h1 class="panel-title"><i class="fa fa-server" aria-hidden="true"></i> For System Administrators</h1>
122 <div class="panel-body">
124 <strong>Server: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#war">
125 JABAWS Web Application aRchive (WAR)</a>
128 <strong>Client: </strong><a href="${pageContext.request.contextPath}/getting_started.jsp#client">
129 Command Line Interface (CLI) Client</a>
132 <%--<p class="justify">--%>
133 <%--JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>--%>
134 <%--to run. Please check the <a href="2.1/manual_qs_war.html#qsc">quick start guide</a> for installation instructions.--%>
136 <p><a class="btn btn-default" href="${pageContext.request.contextPath}/getting_started.jsp" role="button">Getting Started »</a></p>
141 <div class="row" id="public_server">
142 <div class="col-md-12">
143 <div class="panel panel-default">
144 <div class="panel panel-heading">
145 <h1 class="panel-title">Public JABAWS Server</h1>
147 <div class="panel-body">
150 You can access our public JABAWS web services with <a href="http://www.jalview.org/">Jalview</a>,
151 <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS CLI</a>, or
152 <a href="${pageContext.request.contextPath}/docs/develop.html#accessing-jabaws-from-your-program">with your own program</a>.
153 The latest versions of Jalview (version 2.9 or later) are fully compatible
154 with JABAWS 2.2 and are configured to use the public JABAWS server by default.
157 <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>
158 <li>A detailed description of the JABAWS web services is available from here:
159 <a href="${pageContext.request.contextPath}/RegistryWS?"
160 title="${pageContext.request.contextPath}/RegistryWS?" rel=nofollow">WSDL List</a></li>
163 These web services accept submissions of <strong>less than one thousand sequences</strong>.
164 Should you find this to be insufficient for your needs, or if you are concerned about privacy,
165 then you can download and
166 run the <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS WAR</a> on your own hardware.
173 <div class="col-md-12">
174 <div class="panel panel-default">
175 <div class="panel panel-heading">
176 <h1 class="panel-title">New in JABAWS 2.2</h1>
178 <div class="panel-body">
180 The current JABAWS version is 2.2 released on 19 May 2017. Among the new developments in JABAWS 2.2 are:
183 <li>Several programs included in JABAWS, including Clustal Omega, ClustalW, Mafft and T-coffee, were updated.
184 <li><a href="http://www.compbio.dundee.ac.uk/aacon/">AACon</a>
185 was also updated to the latest release, version 1.1.</li>
186 <li><a href="${pageContext.request.contextPath}/ServiceStatus" >Service Status</a> and
187 <a href="${pageContext.request.contextPath}/PublicAnnualStat" >Usage Statistics</a>
188 are now cached and refreshed asynchronously for improved Website loading times.</li>
189 <li>The website looks were updated to use the Twitter <a href="http://getbootstrap.com/">Bootstrap</a> CSS framework,
190 and documentation pages are now generated with <a href="http://www.sphinx-doc.org/en/stable/">Sphinx</a>.
194 More information about the changes introduced in the latest release can be found in the
195 <a href="${pageContext.request.contextPath}/docs/changelog.html">changelog</a> pages.
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204 <div class="panel panel-default">
205 <div class="panel panel-heading">
206 <h1 class="panel-title">Reference</h1>
208 <div class="panel-body">
210 Peter V. Troshin, James B. Procter and Geoffrey J. Barton (2011)
211 Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MS
212 <em>Bioinformatics</em> 27 (14): 2001-2002. doi: <a href="https://doi.org/10.1093/bioinformatics/btr304">
213 10.1093/bioinformatics/btr304</a>.
216 Peter V. Troshin, Alexander Sherstnev, James B. Procter, Daniel L. Barton, Fábio Madeira and Geoffrey J. Barton (2017)
217 JABAWS 2.2 Distributed Web Services for Bioinformatics: Protein Disorder, Conservation and RNA Secondary Structure.
218 <em>Paper in preparation</em>.
226 <div class="col-md-12">
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229 <h1 class="panel-title">ELIXIR-UK</h1>
231 <div class="panel-body">
234 <div class="col-md-3">
235 <span class="align-middle"><a href="https://www.elixir-europe.org/">
236 <img src="static/img/elixir_uk.png" style="width:80%;height:80%" alt="ELIXIR UK"
237 title="UK BBSRC"/></a>
240 <div class="col-md-9">
242 We are pleased that alongside with
243 <a href="http://www.jalview.org/">Jalview</a> and
244 <a href="http://www.compbio.dundee.ac.uk/jpred/index.html">Jpred</a>, JABAWS is a proud member of
245 <a href="https://www.elixir-europe.org/">ELIXIR</a> -
246 the European-wide project providing high quality and sustainable infrastructure for biological information.
247 Following a strict selection procedure, JABAWS has been identified as a "Tier 1"
248 resource by ELIXIR-UK, as part of the Dundee Resources.
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>
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>
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"
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