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+ <meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) main page</title>\r
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<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
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<table>\r
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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 versions are 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 compatibility between versions.\r
- </p>\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
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- <meta name="Last-modified" content="Mon, 4 Apr 2011 12:00:00 GMT"/>\r
+ <meta name="Last-modified" content="Fri, 28 Jun 2013 12:00:00 GMT"/>\r
<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
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(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
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. </p>\r
+ in writing your own client, the JABAWS command line client is what you need.\r
+ </p>\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
- <h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>\r
- <p>Compared to JABAWS 1, JABAWS 2.0.1 offers a greater number and diversity of web services, Amazon EC2 integration and improved easy of use. It contains </p>\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>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
<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
</div><!-- wrapper end-->\r
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</tr>\r
<tr>\r
<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="manual_qs_amazon.html">JABAWS on the Amazon cloud </a></td>\r
+ <td><a href="manual_qs_amazon.html#qsc">JABAWS on the Amazon cloud </a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
</ol>\r
</div><!-- about end-->\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
</div><!-- wrapper end-->\r
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</tr>\r
<tr>\r
<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="manual_qs_amazon.html">JABAWS on the Amazon cloud </a></td>\r
+ <td><a href="manual_qs_amazon.html#qsc">JABAWS on the Amazon cloud </a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
</p>\r
</div><!-- about end-->\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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<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="manual_qs_amazon.html">JABAWS on the Amazon cloud </a></td>\r
+ <td><a href="manual_qs_amazon.html#qsc">JABAWS on the Amazon cloud </a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
</div>\r
</div><!-- about end-->\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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<tr>\r
<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="manual_qs_amazon.html">JABAWS on the Amazon cloud </a></td>\r
+ <td><a href="manual_qs_amazon.html#qsc">JABAWS on the Amazon cloud </a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
\r
<!-- TODO put JABAWS CMD test instructions here -->\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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<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="manual_qs_amazon.html">JABAWS on the Amazon cloud</a></td>\r
+ <td><a href="manual_qs_amazon.html#qsc">JABAWS on the Amazon cloud</a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
</tr>\r
</table>\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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