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- <h2><span class="headeru">JA</span>va <span class="headeru">B</span>ioinformatics <span class="headeru">A</span>nalyses <span class="headeru">W</span>eb <span class="headeru">S</span>ervices</h2>\r
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+ <td style="width:150px;height:80px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" width="158" height="90" alt="University of Dundee" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
+ <td class="bg"><img src="images/jabaws21.png" width="256" height="67" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
+ <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
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- <a class="selected" href="index.html">Home</a>\r
- <a href="manual.html">Manual</a>\r
- <a href="howto.html">How To</a>\r
- <a href="download.html">Download</a>\r
- <a href="http://www.jalview.org">Jalview</a>\r
+ <a class="newpressed" href="index.html">Home</a> \r
+ <a class="newa" href="quick_start.html">Getting Started</a> \r
+ <a class="newa" href="man_about.html">Manual</a> \r
+ <a class="newa" href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+ <a class="newa" href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a class="newa" href="ServiceStatus" title="JABAWS webservices status. Click to test all web services. Please be patient while the services are being checked">Services Status</a>\r
+ <a class="newa" href="contacts.html">Contact Us</a>\r
+ <a class="newa" href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
+ <a class="newa" href="jabaws_funding.html">Funding</a>\r
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+<div id="wrapper">\r
<div id="content">\r
+<h2 id="headtitle">JABAWS 2.1</h2>\r
+<p style="color:black; font-weight:normal; text-align:left;">\r
+<span style="border-bottom:dotted 1px #666" title="JAva Bioinformatics Analysis Web Services">JABAWS</span> \r
+is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently \r
+packaged to run on your local computer, server, cluster or Amazon EC2 instance.\r
+</p>\r
+\r
+<p> Services for multiple sequence alignment include \r
+<a href="http://www.clustal.org/omega">Clustal Omega</a>, \r
+<a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
+<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, \r
+<a href="http://www.drive5.com/muscle">MUSCLE</a>, \r
+<a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">T-Coffee</a>, \r
+<a href="http://probcons.stanford.edu/">ProbCons</a>,\r
+<a href="http://msaprobs.sourceforge.net/">MSAProbs</a>, and\r
+<a href="http://sourceforge.net/projects/glprobs/">GLProbs</a>. \r
+Analysis services allow prediction of the protein secondary structure with \r
+<a href="http://www.compbio.dundee.ac.uk/www-jpred/">Jpred</a> and protein disorder with \r
+<a href="http://dis.embl.de/">DisEMBL</a>, \r
+<a href="http://iupred.enzim.hu">IUPred</a>, \r
+Jronn (a Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> by P. Troshin and G. Barton, unpublished), and \r
+<a href="http://globplot.embl.de/">GlobPlot</a>; and calculation of amino acid alignment conservation \r
+with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. \r
+The secondary structure for an RNA aligment can be predicted with the RNAalifold program from the \r
+<a href="http://www.tbi.univie.ac.at/RNA">Vienna RNA package</a>.\r
+</p>\r
+\r
+<p><span style="color:black; font-weight:normal; text-align:left;">\r
+JABAWS 2.1 installation can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop \r
+application</strong> (version 2.8 onwards) and the <a href="man_client.html">JABAWS command-line client</a>. <br/>\r
+JABAWS 2.1 is able to provide multiple alignment and sequence analysis calculations limited only by your own \r
+computing resources.<br />\r
+</span></p>\r
+\r
+<div id="mainpagefeatures">\r
+<table>\r
+<tr><td>\r
+ <div class="brick">\r
+ <div class="brick_header"><h2>For Users</h2></div>\r
+ <div class="brick_content">\r
+ <strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=JABAWS201.pack.tar.gz">JABAWS Virtual Appliance:</a> (440M)\r
+ or <a href="man_awscloud.html">JABAWS on Amazon Webservices Cloud</a><br/>\r
+ <strong>The Main Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)\r
+ <p>To use JABAWS web services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> \r
+ the JABAWS Virtual Appliance (VA). <br/>\r
+ Or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\r
+ </div>\r
+ </div>\r
+ </td>\r
+ </tr>\r
+ <tr>\r
+ <td><div class="brick">\r
+ <div class="brick_header"><h2>For System Administrators</h2></div>\r
+ <div class="brick_content">\r
+ <p>\r
+ <strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jabaws.war">JABAWS Web \r
+ Application aRchive</a> (55M)\r
+ </p>\r
+ <p>JABAWS requires a Servlet 2.4 compatible servlet container like <a href="http://tomcat.apache.org">Apache Tomcat</a>\r
+ to run. Please check the <a href="manual_qs_war.html#qsc">quick start guide</a> for installation instructions.\r
+ </p>\r
+ </div>\r
+ </div></td>\r
+ </tr>\r
+ <tr>\r
+ <td><div class="brick">\r
+ <div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
+ <div class="brick_content">\r
+<strong>The Server: </strong><a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)\r
+ <br/>\r
+ <strong>The Client: </strong>\r
+ Command Line Client <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=min-jaba-client-2.1.jar">binary</a> | <a href=\r
+"http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=jaba-client-src-2.1.jar">source</a> \r
\r
-<h4>What is JABAWS?</h4>\r
-<p><span class="u">JA</span>va <span class="u">B</span>ioinformatics <span class="u">A</span>nalysis <span class="u">W</span>eb <span class="u">S</span>ervices (JABAWS) is a collection of <a href="http://www.w3schools.com/SOAP/soap_intro.asp">SOAP</a> web services for bioinformatics. Web services make it easy to access well-known tools from anywhere anytime. SOAP Web Services are designed for use by other programmes, rather than people. Current version of JABA web services integrates with <a href="http://www.jalview.org">Jalview</a> and provides five web services for multiple sequence alignment. They are: </p>\r
+<p>\r
+You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. \r
+The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can script against our public \r
+server (see below) with the command line client or you own script. \r
+Check out the <a href="manual_qs_client.html#qsc">quick start guide</a> for further details.</p>\r
+\r
+ </div>\r
+</div></td>\r
+ </tr>\r
+</table>\r
+</div>\r
+\r
+<h3 style="margin:0;">Public JABAWS Server</h3>\r
+<p> You can access our public JABAWS web services with our <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev/get?id=min-jaba-client-2.1.jar">command line client</a>, \r
+ <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.\r
+ The latest versions of Jalview are configured to use public JABAWS server by default.</p>\r
<ul>\r
- <li><a href="http://www.clustal.org/">ClustalW</a></li>\r
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a></li>\r
- <li><a href="http://www.drive5.com/muscle">Muscle</a></li>\r
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a></li>\r
- <li><a href="http://probcons.stanford.edu/">Probcons</a></li>\r
+ <li>The JABAWS public web services address is <strong>http://www.compbio.dundee.ac.uk/jabaws</strong> </li>\r
+ <li>A detailed web services description is available from here: <a href="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?"\r
+title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=\r
+"nofollow">WSDL List</a></li>\r
</ul>\r
-<h4>Why JABAWS?</h4>\r
-<p> JABA Web Services have a number of distinct features not found elsewhere. \r
-<p>In particular JABAWS\r
-<ol>\r
- <li>gives uniform remote access for a number of command line tools <span class="box"> This allows you to access a number of programmes anywhere anytime. All multiple sequence alignment services comply with a single interface, simplifying command invocation. Most of the command line programmes' options are supported, so you have the same level of control as with the command line. </span></li>\r
- <li>enables Jalview to perform variety of analysis (more to come in the future) on the alignments <span class="box">It is very easy to connect the different instances of JABAWS. So if one is off line, another one will do the job for you. If you use it in your software it is only the matter of a server name change, no other magic is required. </span> </li>\r
- <li>can be easily deployed on a large variety of platforms and run on a single server or on the cluster. <span class="box"><a href="howto.html#clustsubsys">JABAWS integrates with a large number of cluster job management systems.</a>This eliminates the scalability issues and let you focus on your research, JABAWS will take care of the task management. </span></li>\r
- <li> services are <a href="http://www.ws-i.org/">WS-I basic profile</a> v. 1.1 compatible<span class="box">This means that programmes or other web services written in almost any programming languages should have no difficulties using JABA web services.</span></li>\r
- </ol>\r
-<p>Below are the examples of things that you can do with JABAWS</p>\r
+<p>These web services accept submissions of <strong>less than one thousand sequences</strong>. Should you find this to be insufficient for your needs, \r
+ or if you are concerned about privacy or on an unreliable network connection, then you can \r
+ <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
+\r
+\r
+\r
+<h3>Previous versions of JABAWS </h3>\r
+<p>\r
+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 \r
+<a href="man_about.html#jaba2.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> \r
+for more information on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p>\r
<ul>\r
- <li>\r
- <p><strong>Unhappy with the defaults settings? </strong><br /> \r
- Want to use PAM200 substitution matrix, set the number of iterations, or sequence clustering method? No problems, JABAWS can do that. Any additional parameters or combinations of where of can be defined. You are no longer limited to defaults!</p>\r
- </li>\r
- <li>\r
- <p><strong>JABAWS in Dundee is not available? </strong>No problem, choose a different service provider and off you go. We hope that other major service providers like EBI will soon be housing JABAWS. </p>\r
- </li>\r
- <li>\r
- <p><strong>Worried about sending your data to the internet?</strong> Install JABAWS in your lab. Point your Jalview client to the services in your lab, and no data will leave you lab any longer.</p>\r
- </li>\r
- <li>\r
- <p><strong>Want to install JABAWS but are not sure what is required? </strong>JABA Web Services will work happily on a single server as well as on the cluster. For large number of request of cause it is better to use a cluster. Little configuration is involved. </p>\r
- </li>\r
- </ul>\r
-<h3> Public JABAWS Server</a></h3>\r
- <table>\r
- <tbody>\r
- <tr>\r
- <th> Feature </th>\r
- <th> Description </th>\r
- </tr>\r
- <tr>\r
- <td><acronym title="Uniform Resource Locator">URL</acronym> </td>\r
- <td><a href="http://www.compbio.dundee.ac.uk/jaba" title="http://www.compbio.dundee.ac.uk/jaba" rel="nofollow">http://www.compbio.dundee.ac.uk/jaba</a> </td>\r
- </tr>\r
- <tr>\r
- <td> Execution limits </td>\r
- <td> Local execution limit is 40 sequnces with no more than 500 letters average length. Larger tasks are send to the cluster. Tasks exceeding 1000×1000 (sequences per letters) will not be accepted for alignment. If you would like to work with bigger alignments consider installing JABAWS in your lab. </td>\r
- </tr>\r
- <tr>\r
- <td> Web Services Description </td>\r
- <td><a href="http://www.compbio.dundee.ac.uk/jaba/ClustalWS?" title="http://www.compbio.dundee.ac.uk/jaba/ClustalWS?" rel="nofollow">WSDL List</a> </td>\r
- </tr>\r
- </tbody>\r
- </table>\r
-\r
-<h4>Authors</h4>\r
-<p>Conceptually, Java Bioinformatics Analysis Web Services are the successor of the Jalview Web Services. At the code level, however, JABA Web Services do not contain any code from Jalview Web Services because of the complete change of technologies in time of coding. Jim Procter and Geoff Barton are the authors of Jalview Web Services. Peter Troshin and Geoff Barton are the authors of the JABA Web Services. Jim Procter has contributed to JABAWS development by making useful suggestions, integrating JABAWS with Jalview, and correcting some of its configuration files.</p>\r
-</div><!-- content end--> \r
-<div id="copyright">Last update: 9 July 2010<br/>\r
-Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong></li> \r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong></li>\r
+ <li><strong><a href="http://www.compbio.dundee.ac.uk/jabaws201">http://www.compbio.dundee.ac.uk/jabaws201</a></strong></li>\r
+</ul> \r
+\r
+\r
+\r
+<h3>Reference</h3>\r
+<p><span class="hightlight">\r
+</span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for \r
+Multiple Sequence Alignment - JABAWS:MSA" <span class="i">Bioinformatics</span> 2011; \r
+<a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr304.abstract?keytype=ref&ijkey=gd0DwuYBzFRhe4T">\r
+doi: 10.1093/bioinformatics/btr304</a>.</p>\r
+</div><!-- content end-->\r
+<div id="copyright">Last update: 30 April 2014<br /> This site is best viewed in Firefox 3.6, Google Chrome 10, Internet Explorer 8 or above </div>\r
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