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-<tr><td style="width:130px;"><a href="http://www.dundee.ac.uk"><img class="logo" src="images/uod_lt.gif" alt="University of Dundee" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><h1><span class="headeru">JA</span>va <span class=\r
-"headeru">B</span>ioinformatics <span class="headeru">A</span>nalysis <span class="headeru">W</span>eb <span\r
-class="headeru">S</span>ervices</h1></td>\r
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<h2 id="headtitle">JABAWS MANUAL</h2>\r
<h2>About</h2>\r
\r
<li><a href="#wisjaba">What is JABAWS?</a></li>\r
<li><a href="#wjaba">JABAWS Benefits</a></li>\r
<li><a href="#alprog">JABA Web Services Programs </a></li>\r
- <li><a href="#whatserver">What is JABAWS Server?</a></li>\r
+ <li><a href="#jaba2.1">What is new in JABAWS 2.1?</a> </li>\r
<li><a href="#jabaclient">What is JABAWS Client</a>?</li>\r
+ <li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>\r
<li><a href="#cmdclient">Programmatic access to JABAWS</a></li>\r
- </ul>\r
+</ul>\r
+\r
\r
\r
<h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>\r
-<p>JABAWS stands for JAva Bioinformatics Analysis Web Services. It is a collection of web services for multiple sequence alignment. For simplicity we referrer to them as JABAWS. Right now, JABAWS makes it easy to access well-known multiple sequence alignment programs from JalView. However, the scope of JABAWS is not limited to multiple sequence alignment programs. Future versions of JABAWS will incorporate protein disorder prediction, BLAST, PSIBLAST and HMMER database searches and many other tools. For the list of currently supported programs see <a href="#alprog">here.</a> JABAWS consists of the two parts - the server and the client. Unlike other web services you can download and use both on your own computer! If you want a server just for yourself, then download and install JABAWS Virtual Appliance. It requires no configuration and simple to install. If you want to install JABAWS for your own lab then download JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or interested in writing your own client, the JABAWS command line client is what you need. </p>\r
+<p>\r
+ JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a \r
+ collection of web services for bioinformatics, and currently provides services that make it easy \r
+ to access well-known multiple sequence alignment and protein disorder prediction programs \r
+ (see <a href="#alprog">the list of currently supported programs</a>) from <a href="http://www.jalview.org">Jalview</a>.\r
+ Future versions of JABAWS will incorporate other tools.\r
+</p>\r
+<h4>Getting JABAWS</h4>\r
+<p>\r
+ JABAWS consists of a server and a client, but unlike most bioinformatics web service systems, you can download and \r
+ run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS \r
+ Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your \r
+ lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure \r
+ but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested \r
+ in writing your own client, the JABAWS command line client is what you need.\r
+</p>\r
+\r
+\r
+\r
<h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>\r
-<p>JABAWS can be deployed on many operating system and operate as a stand alone server or submit the jobs to the cluster. Thanks to <a href="http://www.drmaa.org/">DRMAA</a> it integrates well with a large variety of cluster job management systems. <a href="http://www.jalview.org">Jalview</a> from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder. </p>\r
+<ul>\r
+ <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>\r
+ <li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>\r
+ <li>Can operate as a stand alone server or one that submits jobs to a cluster <em>via</em> <a href="http://www.drmaa.org/">DRMAA</a>.</li>\r
+ <li>Easy to access from <a href="http://www.jalview.org">Jalview</a> using its graphical client, or using the JABAWS command line client.</li>\r
+ <li>Clients can submit jobs to any JABAWS servers that they might want to access, such as the one running on your local computer, \r
+ your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>\r
+ <li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>\r
+ <li>Wide range of configuration options to control size of jobs accepted by a server, and the command line options available for the program run by a service.</li>\r
+</ul>\r
+\r
+\r
+\r
<h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>\r
-<p> JABAWS currently uses the following programs under the hood </p>\r
+<p> JABAWS currently provides access to the following programs:</p>\r
+<p>Multiple Sequence Alignement </p>\r
+<ul>\r
+ <li><a href="http://www.clustal.org/omega">Clustal Omega </a> (version 1.0.2)</li>\r
+ <li><a href="http://www.clustal.org/clustal2">ClustalW</a> (version 2.52)</li>\r
+ <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.857)</li>\r
+ <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.8.31) </li>\r
+ <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.99) </li>\r
+ <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
+ <li><a href="http://msaprobs.sourceforge.net/">MSAProbs</a> (version 0.9.7)</li>\r
+ <li><a href="http://sourceforge.net/projects/glprobs/">GLProbs</a> (version 0.9.7)</li>\r
+</ul>\r
+<p>Protein Secondary structure prediction</p>\r
+<ul>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/www-jpred">Jpred</a></span> (3.0.3) </li>\r
+</ul>\r
+\r
+<p>Protein disorder prediction</p>\r
<ul>\r
- <li><a href="http://www.clustal.org/">ClustalW</a> (version 2.0.12)</li>\r
- <li><a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">Mafft</a> (version 6.713)</li>\r
- <li><a href="http://www.drive5.com/muscle">Muscle</a> (version 3.7) </li>\r
- <li><a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">Tcoffee</a> (version 8.14) </li>\r
- <li><a href="http://probcons.stanford.edu/">Probcons</a> (version 1.12)</li>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://dis.embl.de/">DisEMBL</a></span> (1.5) </li>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://iupred.enzim.hu">IUPred</a></span> (1.0) </li>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;">Jronn - Java implementation of <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a></span> (3.1) </li>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://globplot.embl.de/">GlobPlot</a></span> (2.3) </li>\r
</ul>\r
+<p>Amino Acid conservation</p>\r
+<ul>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;"><a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a></span> (1.0) </li>\r
+</ul>\r
+<p>Secondary structure for an RNA aligment</p>\r
+<ul>\r
+ <li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>\r
+</ul>\r
+\r
+All these codes including Jronn and AAcon are available at the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
+section (registration is required).\r
+\r
+\r
+\r
+<h3><a name="jaba2.1"/>What is new in JABAWS 2.1? </h3>\r
+<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong>\r
+<p>Several new web services are available in this version of JABAWS:</p>\r
+<ul>\r
+ <li>Two multiple sequence aligners (MSAprobs and GLprobs), both services return the standard Alignment object</li>\r
+ <li>RNAalifoldWS returns RNAStructScoreManager, which is the standard ScoreManager objects with several additional methods</li>\r
+ <li>\r
+ JpredWS returns the JpredAligment object, which is the standard alignment with additional methods for extracting \r
+ Jpred predictions. These predictions are supplied as additional sequences in the aligment\r
+ </li>\r
+</ul>\r
+\r
+<p>Some bugs have been fixed and several improvements have been done:</p>\r
+<ul>\r
+ <li>WS status servlet returns version and some additional information on each web service</li>\r
+ <li>a bug with path to help in the client</li>\r
+ <li>Fix two bug with the Google Analytics library: no-stop due to running thread</li>\r
+ <li>GoogleAnalytics gets proper JABAWS version</li>\r
+</ul>\r
+\r
+\r
+<strong>JABAWS Version 2.0.1 (Released 2nd Jul 2013)</strong><p>JABAWS 2.0.1 includes several bug fixes and minor updates for <a href="#jaba2">JABAWS Version 2.0</a>. These are listed below:</p>\r
+<ul>\r
+ <li>Disembl returned swapped strings for HOTLOOPS and REM465</li>\r
+ <li>Jronn failed to process jobs with more than 3 sequences</li>\r
+ <li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
+ <li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores \r
+ in one call</li>\r
+ <li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties</li>\r
+ <li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>\r
+ <li>Documentation has been updated</li>\r
+ </ul>\r
+ <a name="jaba2"/><strong>JABAWS Version 2 (Released 16th Dec 2011)</strong><p>Compared to JABAWS 1, JABAWS 2 offers a greater number and diversity of web services, Amazon EC2 integration and improved ease of use.</p><p>It contains:</p>\r
+<ul><li>updates for all multiple sequence alignment services</li>\r
+ <li>four new protein disorder prediction services</li>\r
+ <li>Clustal Omega multiple sequence alignment web service</li>\r
+ <li>amino acid conservation service</li>\r
+ <li>web services execution statistics visualization </li>\r
+ <li>web services status check from a web page</li>\r
+ <li>VirtualBox support was dropped in favour of VMware</li>\r
+ <li>new WAR package for Mac users</li>\r
+ <li>Amazon Machine Image (AMI) distributive to enable users to use JABAWS on the EC2 cloud</li>\r
+ <li>Improved web services client API</li>\r
+ <li>Simplified WAR package installation</li>\r
+</ul>\r
+\r
+\r
\r
-<h3><a name="whatserver" id="whatserver"></a>What is JABAWS Server? </h3>\r
-<p>JABAWS Server is a Web Application which exposes a number of widely used Bioinformatics programs as SOAP web services. Currently it supports 5 multiple<a href="#alprog"> sequence alignment programs</a>. You can download and install JABAWS on your own computer. JABAWS can be configured to execute programs on computer it is installed or submit them to the cluster. JABAWS provides the uniform API for each web service if supports. </p>\r
<h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\r
-<p>JABAWS client is a command line Java application which can call all JABAWS methods on any instance of JABAWS Server, no matter local or remote. It is useful if you want to script against a JABAWS server and do not want to handle any web service specific details. We also offer a source code of the client so that you can find out how to work with JABA Web Services if you would like to write your own client software. JABAWS command line client offers the same functionality as Jalview when connected to JABAWS. </p>\r
+<p>\r
+ A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web \r
+ services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web \r
+ services on any instance of JABAWS Server available over the web. The basic client is useful if you would like \r
+ to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle \r
+ any web service specific details. The client is an open source software, so you can also use the source code to \r
+ as an example how to manipulate with JABAWS web services in your own code. \r
+ <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good \r
+ example of a graphical JABAWS client. This client uses the same functionality as the command line client, but \r
+ instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.\r
+</p>\r
+\r
+\r
+\r
+<h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>\r
+<p>\r
+ JABAWS version 2.1 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0 and 2.0 and \r
+ 2.0.1 clients should also be able to use JABAWS 2.1 services. To access the analysis web services introduced in \r
+ JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.\r
+</p>\r
+\r
+\r
+\r
<h3><a name="cmdclient" id="cmdclient"></a>Programmatic access to JABAWS </h3>\r
-<p>JABA Web Services are WS-I basic profile compliant, they can be accessed in a standard way as any other web service. The WSDL for each service is published on the JABAWS home page. If you use Java, then you can use our <a href="download.html#minclient">client package</a> to access JABAWS. This package contains value objects which you could alternatively generate with <span class="hightlight">wsimport</span> in Java, or similar tool in other language. On top of that it offers some additional methods which further simplify working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>. </p>\r
-</div> \r
-<!-- about end-->\r
-</div>\r
-<!-- content end--> \r
-<div id="copyright">Last update: 7 January 2011<br/>\r
-Peter Troshin and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<p>\r
+ JABAWS web services are WS-I basic profile compliant, which means they can be accessed using any programming language \r
+ or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home \r
+ page, and you can use this to automatically generate service bindings for your program. If you use Java \r
+ you may wish to use our <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev">client package</a> to access JABAWS. \r
+ This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which \r
+ is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify \r
+ working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.\r
+</p>\r
+</div><!-- content end-->\r
+<div id="copyright">Last update: 30 April 2014<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
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+</div><!-- page end-->\r
+\r
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