-<?xml version="1.0" encoding="UTF-8">\r
+<?xml version="1.0" encoding="UTF-8"?>\r
<!DOCTYPE html PUBLIC "XHTML 1.0 Strict"\r
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</div>\r
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-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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\r
\r
<p class="code">http://www.compbio.ac.uk:8080/ws</p>\r
<p>JABAWS are the standard JAX-WS web services, which are WS-I basic profile compatible. </p>\r
</div><!-- content end--> \r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<div id="content">\r
<h2 id="headtitle">JABAWS 2.0.1</h2>\r
<p style="color:black; font-weight:normal; text-align:left;"><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> for multiple sequence alignment \r
-(programs available: <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
+is free software which provides <a href="http://en.wikipedia.org/wiki/Web_service">web services</a> conveniently packaged to run on your local computer, server, cluster or Amazon EC2 instance. Services for multiple sequence alignment \r
+include <a href="http://www.clustal.org/omega">Clustal Omega</a>, <a href="http://www.clustal.org/clustal2">Clustal W</a>, \r
<a href="http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, \r
-<a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">, TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>), \r
-prediction of protein disorder (programs available: <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, \r
-<a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a>, <a href="http://globplot.embl.de/">GlobPlot</a>), \r
-and amino acid conservation (program available: <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>) \r
-conveniently packaged to run on your local computer, server or cluster. \r
+<a href="http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html">TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. Analysis services allow\r
+prediction of protein disorder with <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, \r
+<a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a> and <a href="http://globplot.embl.de/">GlobPlot</a>; \r
+and calculation of amino acid alignment conservation with <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. \r
+</p><p> \r
<span style="color:black; font-weight:normal; text-align:left;">\r
-JABA Web Services can be accessed from the <a href="http://www.jalview.org">Jalview</a> desktop application and provide multiple alignment \r
-and sequence analysis calculations limited only by your own local computing resources.<br />\r
-<br />\r
-</span>Please note that JABAWS 2.0.1 is supported by Jalview 2.8 onwards. You can also access all JABAWS 2.0.1 services through the JABAWS command-line client.</p>\r
+JABA 2.0.1 Web Services installations can be accessed from the <strong><a href="http://www.jalview.org">Jalview</a> desktop application</strong> (version 2.8 onwards) and the <strong>JABAWS command-line client</strong>, and provide multiple alignment \r
+and sequence analysis calculations limited only by your own computing resources.<br />\r
+</span></p>\r
<div id="mainpagefeatures">\r
<table>\r
<tr><td>\r
or if you are concerned about privacy or on an unreliable network connection, then you can \r
<a href="http://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
<h3>Previous versions of JABAWS </h3>\r
-<p>Old JABAWS version is available here:\r
- <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a> and \r
- <a href="http://www.compbio.dundee.ac.uk/jabaws2">http://www.compbio.dundee.ac.uk/jabaws2</a></strong>. \r
- We advise you to update to the JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and \r
- contain numerous improvements. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information \r
- on versions compatibility.\r
-</p>\r
+<p>We advise you to update to JABAWS 2.0.1 as this version is fully backward compatible with JABAWS v1.0 and v2.0 and \r
+ contains <a href="man_about.html#jaba2.0.1">some important bug fixes</a>. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information \r
+ on compatibility between versions.</p><p>Should you require them, however, old versions of JABAWS are available here:</p><ul><li>\r
+ <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></ul> \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
(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 many other tools.\r
</p>\r
-\r
<h4>Getting JABAWS</h4>\r
<p>\r
JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and \r
\r
<h3><a name="wjaba" id="wjaba"></a>JABAWS Benefits</h3>\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 you 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
+<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 you 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
<h3><a name="alprog" id="alprog"/>JABA Web Services Programs </h3>\r
-<p>JABAWS currently provides access to the following programs:</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
<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
-\r
-<h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>\r
-<p>This release of JABAWS 2.0.1 is mostly bug fixing release. This is a list of bugs which have been fixed in JABAWS 2.0.1:</p>\r
+<h3><a name="jaba2.0.1"/></a>What is new in JABAWS 2.0.1? </h3>\r
+<p>JABAWS Version 2.0.1 includes several minor updates and bug fixes for <a href="#jaba2">JABAWS Version 2</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 the '>' symbols in the record identificator</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>JABAW never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties</li>\r
<li>Default web security has been incompatible with Tomcat 7.0.31 and newer</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
<h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\r
+\r
<p>\r
A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web \r
services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web \r
provides a graphical JABAWS client. This client has 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
<h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>\r
<p>\r
JABAWS version 2.0.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and \r
- v2.0 clients should be able to use JABAWS 2.0.1 instead. To benefit of new web services introduced in JABAWS 2.0 \r
- the clients compitible with JABAWS v1.0 have to be updated.\r
+ v2.0 clients should also be able to use JABAWS 2.0.1 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
<h3><a name="cmdclient" id="cmdclient"></a>Programmatic access to JABAWS </h3>\r
<p>\r
JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language \r
is the Java tool for creating web service bindings; but in addition, offers some additional methods which 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
-\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<p>Alternatively you can use JABAWS on the <a href="http://docs.amazonwebservices.com/elasticbeanstalk/latest/dg/index.html?GettingStarted.html">Amazon Elastic BeanStalk</a>. You may want to use this option to deploy JABAWS in the cluster configuration.</p>\r
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-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<p> </p>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<p> </p>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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\r
--fastaparttree<br />\r
--retree=10<br />\r
--op=2.2</span></p>\r
-<p>The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but the setting controlling output are not. This is due to the fact the output have to be handled by JABAWS, so must remain within its control. For a list of parameters supported by a web service see the next example. In <span class="hightlight">prm.in</span> parameters are separated by the new line, and name of the parameter is separated from its value with an equal sign. This format is constant no matter which JABAWS web service is used. <br />\r
+<p>The format of the file is the same for all JABAWS web services. Parameters are specified in exactly the same way as for native executables - alignment programs like Mafft etc. So parameters which you can use with command line version of an alignment program can be used with JABAWS. Most of the settings controlling alignment process are supported, but because any output has to be handled by JABAWS, settings controlling output are not allowed to be changed. For a list of parameters supported by a web service see the next example. In <span class="hightlight">prm.in</span> parameters are separated by the new line, and name of the parameter is separated from its value with an equals sign. This format is constant no matter which JABAWS web service is used. <br />\r
<span class="code"> java -jar jabaws-min-client.jar -h=http://myhost.compbio.ac.uk:8080/jabaws -s=MafftWS -parameters</span></p>\r
<p>The same client can be used to access JABAWS on different hosts. Just point the client to the host you want to use by changing the value of -h key. For example you used <span class="hightlight">-h=http://myhost.compbio.ac.uk:8080/jabaws</span> server, now you want to use another server to <span class="hightlight">-h=http://mylabserver.myuni.edu.</span> This comes handy if your favorite server is off and you need to do the job yesterday. </p>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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\r
<p> Google Analytics can be disabled or adjusted by removing/editing <span class="hightlight">conf/GA.properties</span> Google Analytics (GA) settings file. We would appreciate it greatly if you could leave it on!</p>\r
<p>All calls to GA are very lightweight, completed asynchronously, create very little overhead and do not influence the server response time or performance.</p>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<p>JABAWS are the standard <a href="http://jax-ws.java.net/">JAX-WS</a> SOAP web services, which are <a href="http://www.ws-i.org/">WS-I</a> basic profile compatible. This means that you could use whatever tool your language has to work with web services. Below is how you can generate portable artifacts to work with JABAWS from Java. However, if programming in Java we recommend using our client library as it provides a handful of useful methods in addition to plain data types. </p>\r
<p class="code">wsimport -keep http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?wsdl</p>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<p> </p>\r
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-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<h3><a name="vmiaccess" id="vmiaccess"/></a></a>VM Network Settings </h3>\r
<p>By default the JABAWS VM is configured to use host-only networking. This means that the host can communicate with the VM via a network, but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect to the Internet from the VM, configure your VM to use NAT network. However, you will not be able to connect to the VM from the host in such case. If you want to be able to connect to your VM and let VM connect to the internet at the same time you would have to use a Bridged network. In such a case you would have to configure the VM IP address manually (unless of course your network has a DHCP server to do that)</a></p>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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<li>If Tomcat still refuses to unpack the war file, unpack it manually into web application folder (the war file is just a zip archive). Restart the Tomcat.</li>\r
</ul>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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</p>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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+<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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git://source.jalview.org / jabaws.git / commitdiff