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-<h2 id="headtitle">JABAWS 2.1</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> is free software which provides web services for multiple sequence alignment, prediction of protein disorder, and amino acid conservation conveniently packaged to run on your local computer, server or cluster. JABAWS v2.1 introduces protein disorder prediction services based on <a href="http://dis.embl.de/">DisEMBL</a>, <a href="http://iupred.enzim.hu">IUPred</a>, <a href="http://www.strubi.ox.ac.uk/RONN">Ronn</a>, <a href="http://globplot.embl.de/">GlobPlot</a> and protein sequence alignment conservation measures calculated by <a href="http://www.compbio.dundee.ac.uk/aacon">AACon</a>. A new multiple sequence alignment service for <a href="http://www.clustal.org/omega">Clustal Omega</a> is also provided, in addition to standard JABAWS:MSA services for <a href="http://www.clustal.org/clustal2">Clustal W</a>, <a href=\r
-"http://align.bmr.kyushu-u.ac.jp/mafft/software/">MAFFT</a>, <a href="http://www.drive5.com/muscle">MUSCLE</a>, <a href=\r
-"http://www.tcoffee.org/Projects_home_page/t_coffee_home_page.html"> TCOFFEE</a> and <a href="http://probcons.stanford.edu/">PROBCONS</a>. \r
-<span style="color:black; font-weight:normal; text-align:left;">JABA Web Services can be accessed from the <a href="http://www.jalview.org">Jalview</a> desktop application and provide multiple alignment and sequence analysis calculations limited only by your own local computing resources.<br />\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
+<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
+<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 2.1 is supported by Jalview 2.6.1 onwards, but the disorder prediction, Clustal Omega and AACon services will only be accessible in Jalview 2.8 (due for release in January 2012). In the meantime you can access all JABAWS2.1 services through the JABAWS command-line client.</p>\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
<div id="mainpagefeatures">\r
<table>\r
<tr><td>\r
- <div class="brick"> \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://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm.zip">JABAWS Virtual Appliance:</a> (520M)\r
- or <a href="man_awscloud.html">use JABAWS on Amazon Webservices Cloud</a><br/>\r
- <strong>The Client: </strong><a href="http://www.jalview.org/download.html">Jalview</a> (18M)\r
- <p>To use JABA Web Services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> the JABAWS Virtual Appliance (VA) or even easier - just start JABAWS machine on the cloud and point Jalview at it!</p>\r
+ <strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm-201.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 JABA Web Services on most operating systems, just download and <a href="manual_qs_va.html#qsc">install</a> \r
+ the JABAWS Virtual Appliance (VA) 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><strong>The Server: </strong><a href=\r
-"http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M) </p>\r
- <p>JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</p>\r
- </div>\r
- </div></td>\r
+ <div class="brick_header"><h2>For System Administrators</h2></div>\r
+ <div class="brick_content">\r
+ <p><strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)</p>\r
+ <p>JABAWS requires a Servlet 2.4 compatible servlet container like Apache-Tomcat to run. \r
+ Please check the quick start guide for <a href="manual_qs_war.html#qsc">installation instructions</a>.</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
+ <div class="brick_header"><h2>For Bioinformaticians/Developers</h2></div>\r
+ <div class="brick_content">\r
<strong>The Server: </strong><a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws.war">JABAWS Web Application aRchive</a> (55M)\r
<br/>\r
<strong>The Client: </strong>\r
- Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">binary</a> | <a href=\r
-"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.0.jar">source</a> \r
- <!-- <li><a href="http://www.jalview.org/download.html">Jalview</a> (18M)</li> -->\r
- \r
- \r
-<p>You can either use the JABAWS Virtual Appliance or the JABAWS Web Application aRchive (WAR) from your own computer or a lab server. The WAR version gives greater flexibility but requires a bit more configuration. Alternatively you can just script against our public server (see below) with the command line client or you own script. \r
+ Command Line Client <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.1.jar">binary</a> | <a href=\r
+"http://www.compbio.dundee.ac.uk/download/get?id=jaba-client-src-2.0.1.jar">source</a> \r
+\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 just 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
+ </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 JABA Web Services with our <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">command line client</a>, <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. The latest versions of Jalview are configured to use public JABAWS server by default.</p>\r
+<p> You can access our public JABA Web Services with our <a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.1.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 2.0.1.\r
+ The latest versions of Jalview are configured to use public JABAWS server by default.</p>\r
<ul>\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
-<p>These web services accept submissions of less than one thousand sequences. Should you find this to be insufficient for your needs, or if you are concerned about privacy or on an unreliable network connection, then you can <a href="http://www.compbio.dundee.ac.uk/download">download</a> and run the JABAWS Server on your own hardware.</p>\r
+<p>These web services accept submissions of less than one thousand sequences. 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://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>JABAWS 1 is available from here <strong><a href="http://www.compbio.dundee.ac.uk/jabaws1">http://www.compbio.dundee.ac.uk/jabaws1</a></strong>. We advise you to update to the JABAWS 2 as this version is fully backward compatible with JABAWS 1 and contain numerous improvements. Please consult the <a href="man_about.html#jalviewsup">manual</a> for more information on versions compatibility. </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
<h3>Reference</h3>\r
-<p><span class="hightlight"></span> Peter V. Troshin, James B. Procter and Geoffrey J. Barton - "Java Bioinformatics Analysis Web Services for Multiple Sequence Alignment - JABAWS:MSA" <span class="i">Bioinformatics</span> 2011; <a href="http://bioinformatics.oxfordjournals.org/content/early/2011/05/18/bioinformatics.btr304.abstract?keytype=ref&ijkey=gd0DwuYBzFRhe4T">doi: 10.1093/bioinformatics/btr304</a>.</p>\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
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- <a href="contacts.html">Contact Us</a>\r
- <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+</div>\r
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+</div>\r
<!-- panel end-->\r
-<div id="content">\r
\r
+\r
+<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
<h2>About</h2>\r
\r
<li><a href="#cmdclient">Programmatic access to JABAWS</a></li>\r
</ul>\r
\r
-\r
<h3><a name="wisjaba" id="wisjaba"></a>What is JABAWS?</h3>\r
-<p>JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (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.</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 many other tools.\r
+</p>\r
<h4>Getting JABAWS</h4>\r
-<p>JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the 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 are interested in writing your own client, the JABAWS command line client is what you need. </p>\r
+<p>\r
+ JABAWS consists of a server and 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. </p>\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, 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>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
<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? </h3>\r
-<p>Comparing to previous version of JABAWS JABAWS 2 offers a greater number of diverse web services, Amazon EC 2 integration and improved easy of use. It contains </p>\r
-<ul><li>updates for all multiple sequence alignment services </li>\r
+<h3><a name="jaba2"></a>What is new in JABAWS 2.0.1? </h3>\r
+<p>Comparing to previous version of JABAWS 2.0.1 offers a greater number of diverse web services, Amazon EC 2 integration and improved easy of use. 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>Clustal Omega multiple sequence alignment web service</li>\r
+ <li>amino acid conservation service</li>\r
<li>web services execution statistics visialization </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
+ <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>A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. \r
-The most basic JABAWS client is a command line Java application which can call any of the JABAWS web services methods \r
-on any instance of JABAWS Server that it can reach over the web. It is useful if you \r
-want to test, or execute the programs provided by a JABAWS server in your own scripts, and do not want to handle any web service \r
-specific details. The client is open source, so you can also use its source code to find \r
-out how to work with JABA Web Services if you would like to write your own client \r
-software. <a href="http://www.jalview.org/">Jalview</a>, which is a multiple sequence alignment and analysis application, provides a graphical JABAWS client. This client has the same \r
-functionality as the command line client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.</p>\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
+ services methods on any instance of JABAWS Server that it can reach over the web. It is useful if you want to \r
+ test, or execute the programs provided by a JABAWS server in your own scripts, and do not want to handle any web \r
+ service specific details. The client is open source, so you can also use its source code to find out how to work \r
+ with JABA Web Services if you would like to write your own client software. \r
+ <a href="http://www.jalview.org/">Jalview</a>, which is a multiple sequence alignment and analysis application, \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>JABAWS version 2 is fully backward compatible with JABAWS version 1. That means that all JABAWS 1 clients should be able to use JABAWS 2 instead. However, they will be limited to the multiple sequence alignment web services only. To benefit of new web services introduced in JABAWS 2 the clients have to be updated. <br>\r
-Jalview since version 2.6.1 integrates fully with JABAWS 1. Therefore it will be possible to use any versions of Jalview after 2.6.1 with JABAWS 1. However, the full support for JABAWS 2 is introduced in Jalview version 2.8 or later.</p>\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
+</p>\r
<h3><a name="cmdclient" id="cmdclient"></a>Programmatic access to JABAWS </h3>\r
-<p>JABA Web Services are WS-I basic profile compliant, which means they can be accessed using \r
-any programming language or system that can utilize standard SOAP web services. \r
-The WSDL for each service is published on the JABAWS home page, and you can use this to automatically generate \r
-service bindings for your program. If you use Java, however, then you may wish to use our \r
-<a href="http://www.compbio.dundee.ac.uk/download">client package</a> to access JABAWS. \r
-This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which is the Java tool for creating web service bindings; \r
-but in addition, offers some additional methods which simplify working with JABAWS. For more information please refer to the \r
-<a href="dm_javadoc/index.html">data model javadoc</a>.\r
+<p>\r
+JABA 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, however, \r
+then you may wish to use our <a href="http://www.compbio.dundee.ac.uk/download">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; 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
</div> \r
<!-- about end-->\r
<!-- content end--> \r
-<div id="copyright">Last update: 16 September 2011<br/>\r
-Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
\r
+\r
+<div id="copyright">Last update: 16 September 2011<br /> Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
+Dundee, UK</div>\r
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</div>\r
-\r
<!-- panel end-->\r
+\r
+\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<h2>JABAWS Server in the Amazon Cloud</h2>\r
<ul>\r
- <li><a href="#jabawsOnCloud">JABAWS on the Cloud</a></li>\r
- <li><a href="man_awscloud_ec2.html">How to use JABAWS on the Amazon EC2 cloud</a></li>\r
- <li><a href="man_awscloud_bs.html">How to use JABAWS WAR on Amazon Elastic Beanstalk</a> </li>\r
+ <li><a href="man_awscloud_ec2.html">How to use JABAWS on the Amazon EC2 cloud</a></li>\r
+ <li><a href="man_awscloud_bs.html">How to use JABAWS WAR on Amazon Elastic Beanstalk</a> </li>\r
</ul>\r
<div id="jabaws_on_cloud">\r
<h3><a name="jabawsOnCloud" id="jabawsOnCloud"></a>JABAWS on the Cloud</h3>\r
</ul>\r
<p>If you know what to do than JABAWS AMI ID is <strong>ami-d1d5e9a5</strong>, manifest <strong>846107356395/JABAWS 2</strong> to get you started, if not please refer to <a href="man_awscloud_ec2.html">How to use JABAWS on the Amazon EC2 cloud</a> pages. </p>\r
<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
-</div> \r
-<!-- end of jabaws_on_cloud div -->\r
-</div>\r
-<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
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-\r
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+ <a class="selected" href="man_awscloud.html" title="JABAWS Server in the Amazon EC2 Cloud">Server in the Cloud</a>\r
+ <a href="man_serverwar.html" title="JABAWS Server as Web Application aRchive">Server WAR</a>\r
+ <a href="man_configuration.html" >Server Configuration</a>\r
+ <a href="man_client.html" title="JABAWS Command Line Client">CMD Client</a>\r
+ <a href="man_stats.html" title="JABAWS Usage Statistics">Usage Statistics</a>\r
+ <a href="man_dev.html" title="Accessing JABAWS from your program">Accessing JABAWS</a>\r
+ <a href="man_server_dev.html" >JABAWS Development</a>\r
+ </div>\r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+ <a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+ <a 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 href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
</div>\r
-\r
<!-- panel end-->\r
+\r
+\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
-<h2>How to use JABAWS on Amazon Elastic Beanstalk</h2>\r
+<h2>How to use JABAWS on Amazon Elastic Beanstalk</h2>\r
<div id="jabaws_on_cloud">\r
<ol>\r
<li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
<li>Give a name to your JABAWS instance. This name will be a part of the access URL for your JABAWS. </li>\r
<img src="images/aws_bs_launch2.gif" alt="Elastic Beanstalk launch JABAWS war step 3" width="530" height="492">\r
\r
-<li>Choose the type of hardware you want to run JABAWS on. </li>\r
+<li>Choose the type of hardware you want to run JABAWS on.</li>\r
<img src="images/aws_bs_launch3.gif" alt="Elastic Beanstalk launch JABAWS war step 4"/> \r
<li>If everything goes well you should be able to access your JABAWS on http://jabaws.elasticbeanstalk.com</li>\r
<img src="images/aws_bs_done.gif" alt="Elastic Beanstalk launch JABAWS war " width="682" height="422"> \r
</ol>\r
<p> </p>\r
-</div> <!-- end of jabaws_on_cloud div -->\r
-</div>\r
-<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
-\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
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</div>\r
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<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<h2><a name="jabawsOnCloudHow" id="jabawsOnCloudHow"/></a>How to use JABAWS on the Amazon EC2 cloud </h2>\r
<div id="jabaws_on_cloud">\r
<ol>\r
- <li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
+ <li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
<li><a href="https://console.aws.amazon.com/ec2/home?region=eu-west-1#selectInstance=&launchAmi=&s=Home">Log in into the Amazon Web Services (AWS) console.</a> Make sure you are in the EU West (Ireland) region. JABAWS image is not available in other regions as yet. See marker 1. </li>\r
<li>Click on "Launch Instance" button marker 2. </li>\r
\r
\r
<img src="images/aws_launch_instance3.gif" width="872" height="592">\r
<li>Create a new security group with a single HTTP (80) port as shown below. You may want to add SSH (22) port if you are planning to manage your instance via SSH. For starting/stopping your JABAWS instance SSH is not necessary, you can do this from the Amazon Webservices Console (AWS). </li>\r
-\r
<img src="images/aws_launch_instance_sec_group.gif" alt="ese" width="856" height="588">\r
<li>Review the configuration and launch the instance, then click "view your instances on the Instances page". </li>\r
<img src="images/aws_launch_instance5.gif" width="870" height="430">\r
</div> <!-- end of jabaws_on_cloud div -->\r
</div>\r
<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
+<div id="copyright">Last update: 16 September 2011<br />Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
Dundee, UK</div>\r
</div>\r
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+ <td class="bg"><img src="images/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.01" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
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</div>\r
-\r
<!-- panel end-->\r
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+\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\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
<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>\r
-\r
-<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
-\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
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+ <div id="submenu">\r
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+ </div>\r
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-\r
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+\r
+\r
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<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<li><a href="#locEngConf">Local Engine Configuration</a></li>\r
<li><a href="#clustEngConf">Cluster Engine Configuration</a></li>\r
<li><a href="#exec">Executable Configuration</a></li>\r
- <li><a href="#setexecenv">Defining Environment Variables for\r
- Executables</a></li>\r
- <li><a href="#mafftconf">Configure JABAWS to Work\r
-with Mafft</a></li>\r
+ <li><a href="#setexecenv">Defining Environment Variables for Executables</a></li>\r
+ <li><a href="#mafftconf">Configure JABAWS to Work with Mafft</a></li>\r
<li><a href="#settinglimit">Limiting the size of the job accepted by JABAWS Server </a></li>\r
<li><a href="#diffbin">Using a different version of the alignment program with JABAWS</a></li>\r
<li><a href="#mixuse">Load balancing </a></li>\r
</ol>\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>\r
-<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
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</div>\r
-\r
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<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<h3><a name="buildart" id="buildart"></a>Building web services artifacts</h3>\r
<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>\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><!-- wrapper end-->\r
+</div><!-- page end-->\r
\r
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-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
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-\r
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</div>\r
<!-- panel end-->\r
-<div id="content">\r
\r
+<div id="content">\r
<h2 id="headtitle">For JABAWS Developers</h2>\r
<h2>The JABAWS project </h2>\r
<p>This page is for anyone who wants to add a new webservice into the JABAWS framework. </p>\r
<li> Test on the cluster.</li>\r
</ol>\r
<p> </p>\r
-</div>\r
-<!-- content end--> \r
-<div id="copyright">Last update: 16 September 2011<br/>\r
- Peter Troshin, The Barton Group, University of Dundee, UK</div>\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
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+ </div>\r
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+ <a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+ <a 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
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</div>\r
-\r
<!-- panel end-->\r
+\r
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<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<h2>JABAWS Server Virtual Appliance</h2>\r
<ul>\r
- <li><a href="#whatisvm">What is JABAWS Virtual Appliance?</a></li>\r
- <li><a href="#whenvm">When to use virtual appliance</a> </li>\r
- <li><a href="#howtoinstallvm">How to install VMware Player </a></li>\r
- <li><a href="#vmplayer">VMware Player appliance configuration </a></li>\r
- <li><a href="#jabawsAppliance">JABAWS Appliance details </a></li>\r
- <li><a href="#jalviewWithJaba">Configuring Jalview to work with your JABAWS VM</a></li>\r
- <li><a href="#vmiaccess">VM Network Settings </a></li>\r
- </ul>\r
+ <li><a href="#whatisvm">What is JABAWS Virtual Appliance?</a></li>\r
+ <li><a href="#whenvm">When to use virtual appliance</a> </li>\r
+ <li><a href="#howtoinstallvm">How to install VMware Player </a></li>\r
+ <li><a href="#vmplayer">VMware Player appliance configuration </a></li>\r
+ <li><a href="#jabawsAppliance">JABAWS Appliance details </a></li>\r
+ <li><a href="#jalviewWithJaba">Configuring Jalview to work with your JABAWS VM</a></li>\r
+ <li><a href="#vmiaccess">VM Network Settings </a></li>\r
+</ul>\r
\r
<p> </p>\r
<h3><a name="whatisvm" id="whatisvm"></a>What is the JABAWS Server Virtual Appliance?</h3>\r
<p>The JABAWS <a href="http://en.wikipedia.org/wiki/Virtual_appliance">Virtual Appliance</a> is a \r
way to run JABAWS server locally without the need to connect to the internet or configure JABAWS. \r
-What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), running an installation of the JABAWS \r
-Web Application Archive (WAR) on TurnKey Linux. Once this has started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS client (such as Jalview or the JABAWS command line client) to connect to it.<br/>\r
-You can run the appliance with freely available program such as <a href="http://www.vmware.com/products/player">VMware Player</a>, but you will need to install it first. We have tested the JABAWS appliance \r
-with VMware Player v 3.1.2 on Windows and Linux, and VMware Fusion on Mac. \r
+What the appliance provides is a 'virtual server machine' (or more simply - virtual machine or VM), \r
+running an installation of the JABAWS Web Application Archive (WAR) on TurnKey Linux. Once this has \r
+started up, it displays a message indicating the IP address of the JABAWS server, allowing any JABAWS \r
+client (such as Jalview or the JABAWS command line client) to connect to it.<br/>\r
+You can run the appliance with freely available program such as \r
+<a href="http://www.vmware.com/products/player">VMware Player</a>, but you will need to install it \r
+first. We have tested the JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and \r
+VMware Fusion on Mac. \r
However, you are not limited to these virtualization systems and can use the JABAWS appliance with any other virtualization platform. You can use <a href="http://communities.vmware.com/community/vmtn/server/vsphere/automationtools/ovf">VMware OVF tool</a> to prepare JABAWS image for a different virtualization platform e.g. <a href="http://www.virtualbox.org/">VirtualBox</a>.</p>\r
<h3><a name="whenvm" id="whenvm"/></a>When to use the JABAWS Virtual Appliance</h3>\r
<p>The appliance best suits users who would like to use the JABA web services locally. This might be because they do not want to access \r
<p>If you need to configure a static IP address the configuration console will help you with this. Shutting down the VM is best from the configuration console as well.</p>\r
<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>\r
-\r
-<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\r
-</div>\r
-\r
-<!-- wrapper end-->\r
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+</div>\r
<!-- panel end-->\r
+\r
+\r
<div id="content">\r
<h2 id="headtitle">JABAWS MANUAL</h2>\r
\r
<li><a href="#instwar">Installing the JABAWS WAR file</a></li>\r
<li><a href="#prepexec">Preparing executables for use with JABAWS</a></li>\r
<li><a href="#useprebin">Using the pre-compiled i386 binaries on Linux</a></li>\r
- <li><a href="#recompbinaries">Recompiling the bundled\r
- programs for your system</a></li>\r
- <li><a href="#haveexec">Reuse the binaries that are\r
- already in your system</a></li>\r
+ <li><a href="#recompbinaries">Recompiling the bundled programs for your system</a></li>\r
+ <li><a href="#haveexec">Reuse the binaries that are already in your system</a></li>\r
<li><a href="#obtainexec">Obtaining command line binaries </a><a href="#obtainexec">for your operating system</a></li>\r
<li><a href="#usingWsTester">Testing JABAWS Server</a></li>\r
<li><a href="#diffcontexts">Running many JABAWS instances on the same server</a> </li>\r
<li><a href="#clustsubsys">JABAWS supported cluster batch management systems </a></li>\r
<li><a href="#tomstopundeploy">Manually deploying JABAWS application on Apache-Tomcat </a></li>\r
</ul>\r
+\r
<p><strong>Troubleshooting</strong></p>\r
<ul>\r
<li><a href="#tomdeploy">Apache-Tomcat fails to deploy the jabaws.war file</a></li>\r
<li>Restart the Tomcat, sometimes it will not since that the new war file is added without restart</li>\r
<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>\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><!-- wrapper end-->\r
+</div><!-- page end-->\r
\r
-<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
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-<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
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+<table>\r
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+ <td style="width:158px;"><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/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.01" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
+ <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
+ </tr>\r
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+ <div id="submenu">\r
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+ <a href="man_configuration.html" >Server Configuration</a>\r
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+ <a href="man_server_dev.html" >JABAWS Development</a>\r
+ </div>\r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+ <a href="PublicAnnualStat" title="JABAWS usage statistics">Usage Statistics</a>\r
+ <a 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
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</div>\r
-\r
<!-- panel end-->\r
+\r
+\r
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</p>\r
</div>\r
-\r
<!-- content end-->\r
-<div id="copyright">Last update: 16 September 2011<br />\r
- Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of\r
-Dundee, UK</div>\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>\r
-\r
<!-- wrapper end-->\r
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+<title>Java Bioinformatics Analyses Web Services (JABAWS) manual - getting started</title>\r
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+<table>\r
+ <tr>\r
+ <td style="width:158px;"><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/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.01" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
+ <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
+ </tr>\r
+</table>\r
+</div>\r
+<!-- banner end-->\r
+\r
+\r
+<div id="wrapper">\r
+<div id="panel">\r
+<a href="index.html">Home</a>\r
+ <a class="selected" href="quick_start.html">Getting Started</a> \r
+ <a href="man_about.html">Manual</a> \r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a 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 href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+<!-- panel end-->\r
+\r
+\r
+<div id="content">\r
+<h2 id="headtitle">Getting Started</h2>\r
+<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
+<table id="choicematrix">\r
+<tr>\r
+ <th>I want to use JABAWS for...</th>\r
+ <th>Quick Guide</th>\r
+</tr>\r
+<tr>\r
+ <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
+ <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
+</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
+</tr>\r
+<tr>\r
+ <td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
+ <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
+</tr>\r
+<tr>\r
+ <td>Accessing a JABAWS server from my own code</td>\r
+ <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
+</tr>\r
+</table>\r
+\r
+\r
+<a name="qsc"/>\r
+<h3>Running JABAWS in the Amazon Cloud</h3>\r
+<ol>\r
+ <li><a href="https://www.amazon.com/ap/signin/175-8261537-7969810?_encoding=UTF8&openid.assoc_handle=aws&openid.return_to=https%3A//aws-portal.amazon.com/gp/aws/developer/registration/index.html/175-8261537-7969810&openid.mode=checkid_setup&openid.ns=http%3A//specs.openid.net/auth/2.0&openid.claimed_id=http%3A//specs.openid.net/auth/2.0/identifier_select&openid.pape.max_auth_age=600&siteState=awsMode%3A%3Aregistration%3A%3AheaderMessage%3A%3AAmazon Web Services Sign Up%3A%3A&pageId=aws.ssop&openid.pape.preferred_auth_policies=http%3A//schemas.openid.net/pape/policies/2007/06/multi-factor-physical&marketplaceId=ATVPDKIKX0DER&accountStatusPolicy=P1&openid.ns.pape=http%3A//specs.openid.net/extensions/pape/1.0&openid.identity=http%3A//specs.openid.net/auth/2.0/identifier_select&authCookies=1">Create Amazon Web Services account</a>. </li>\r
+ <li>Configure JABAWS either on the <a href="man_awscloud_ec2.html">Amazon EC2 cloud</a> or on <a href="man_awscloud_bs.html">Amazon Elastic Beanstalk</a></li>\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><!-- wrapper end-->\r
+</div> <!-- page end-->\r
+\r
+\r
+\r
+<!-- Google analitics -->\r
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+\r
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-<table> \r
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws21.png" 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
-</tr>\r
+<table>\r
+ <tr>\r
+ <td style="width:158px;"><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/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.01" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
+ <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
+ </tr>\r
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- <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
- <a 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 href="contacts.html">Contact Us</a>\r
- <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
-\r
-<!-- panel end--> \r
+ <a class="selected" href="quick_start.html">Getting Started</a> \r
+ <a href="man_about.html">Manual</a> \r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a 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 href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+<!-- panel end-->\r
\r
<div id="content">\r
-\r
<h2 id="headtitle">Getting Started</h2>\r
-\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
-\r
<table id="choicematrix">\r
<tr>\r
<th>I want to use JABAWS for...</th>\r
<th>Quick Guide</th>\r
</tr>\r
<tr>\r
- <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
- <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
+ <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
+ <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="man_awscloud.html">JABAWS on the Amazon cloud </a></td>\r
+ <td><a href="manual_qs_amazon.html">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
- <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
+ <td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
+ <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
</tr>\r
<tr>\r
- <td>Accessing a JABAWS server from my own code</td>\r
- <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
+ <td>Accessing a JABAWS server from my own code</td>\r
+ <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
</tr>\r
</table>\r
\r
\r
-\r
-\r
<a name="qsc"/>\r
<h3><a name="client"/>The JABAWS command line client</h3>\r
-<ul><li><a href=\r
-"http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">Download the Client Jar</a> (80 K)</li>\r
-</ul>\r
-<p>This is a single java archive which contains the JABAWS command line client. \r
-It requires Java version 1.6 to run, and allows anyone who wants to connect \r
-to and to use JABAWS from their own software. \r
-You can read more about how to use command line client <a href="man_client.html">in the CMD Client</a> section of the manual. \r
-You can also get command line help by changing to the directory where you downloaded the client jar, and typing:\r
-<ul>\r
- <li><span class="hightlight">java -jar jaba-client.jar</span></li>\r
+<ul><li><a href="http://www.compbio.dundee.ac.uk/download/get?id=min-jaba-client-2.0.jar">Download the Client Jar</a> (80 K)</li>\r
</ul>\r
-<p>A JABAWS server's Web Services are WS-I compliant. This means that you can access them from any \r
-language that has libraries or functions for consuming interoperable SOAP web services.\r
-<!-- PETER TODO Provide list of libraries for different languages --></p>\r
-</div> \r
+<p>\r
+ This is a single java archive which contains the JABAWS command line client. It requires Java \r
+ version 1.6 to run, and allows anyone who wants to connect to and to use JABAWS from their own \r
+ software. You can read more about how to use command line client <a href="man_client.html">in \r
+ the CMD Client</a> section of the manual. You can also get command line help by changing to \r
+ the directory where you downloaded the client jar, and typing:\r
+ <ul>\r
+ <li><span class="hightlight">java -jar jaba-client.jar</span></li>\r
+ </ul>\r
+\r
+<p>\r
+ A JABA Web Services are WS-I compliant. This means that you can access them from any \r
+ language that has libraries or functions for consuming interoperable SOAP web services.\r
+ <!-- TODO Provide list of libraries for different languages -->\r
+</p>\r
+</div>\r
<!-- about end-->\r
</div>\r
<!-- content end--> \r
-<div id="copyright">Last update: 16 September 2011<br/>\r
-Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+\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><!-- wrapper end-->\r
</div> <!-- page end-->\r
\r
<!DOCTYPE html PUBLIC "XHTML 1.0 Strict" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
<head>\r
-<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) manual - getting started</title>\r
<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
<link rel="stylesheet" type="text/css" media="print" href="print.css"/>\r
-\r
<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
</head>\r
+\r
<body>\r
<div id="page">\r
<div id="banner">\r
-<table> \r
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws21.png" 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
-</tr>\r
+<table>\r
+ <tr>\r
+ <td style="width:158px;"><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/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.01" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
+ <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
+ </tr>\r
</table>\r
-</div><!-- banner end-->\r
+</div>\r
+<!-- banner end-->\r
+\r
<div id="wrapper">\r
<div id="panel">\r
<a href="index.html">Home</a>\r
- <a class="selected" href="quick_start.html">Getting Started</a> \r
- <a href="man_about.html">Manual</a> \r
- <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
- <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
- <a 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 href="contacts.html">Contact Us</a>\r
- <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+ <a class="selected" href="quick_start.html">Getting Started</a> \r
+ <a href="man_about.html">Manual</a> \r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a 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 href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
<!-- panel end-->\r
-<div id="content">\r
\r
-<h2 id="headtitle">Getting Started</h2>\r
\r
+<div id="content">\r
+<h2 id="headtitle">Getting Started</h2>\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
-\r
<table id="choicematrix">\r
<tr>\r
<th>I want to use JABAWS for...</th>\r
<th>Quick Guide</th>\r
</tr>\r
<tr>\r
- <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
- <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
+ <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
+ <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="man_awscloud.html">JABAWS on the Amazon cloud </a></td>\r
+ <td><a href="manual_qs_amazon.html">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
- <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
+ <td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
+ <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
</tr>\r
<tr>\r
- <td>Accessing a JABAWS server from my own code</td>\r
- <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
+ <td>Accessing a JABAWS server from my own code</td>\r
+ <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
</tr>\r
</table>\r
\r
+\r
<a name="qsc"/>\r
<h3>Running JABAWS on your local machine</h3>\r
-<ul> <li>Download <a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm.zip">JABAWS Virtual Appliance</a> (520M) </li>\r
+<ul><li>Download <a href="http://www.compbio.dundee.ac.uk/download/get?id=jabaws-vm.zip">JABAWS Virtual Appliance</a> (520M) </li>\r
</ul>\r
-<p>The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a virtual machine on your laptop or desktop computer. A <a href="man_servervm.html#whenvm">complete guide to the JABAWS VA</a> is given in the manual, but for the impatient, a brief instructions are given below:\r
+<p>\r
+ The Virtual Appliance (VA) package allows you to run a JABAWS server installed on TurnKey Linux as a \r
+ virtual machine on your laptop or desktop computer. A <a href="man_servervm.html#whenvm">complete guide \r
+ to the JABAWS VA</a> is given in the manual, but for the impatient, a brief instructions are given below:\r
\r
<p>If you work on Windows, Linux or Unix </p>\r
<ol>\r
<li>Open the Jalview desktop's preferences panel (from the Tools->Preferences menu option), select the <span class="hightlight">Webservices</span> panel and press the <span class="hightlight">New Service URL</span> button.</li>\r
<li>Enter the JABAWS URL for your new server. This is shown once the appliance is booted up.</li>\r
</ol>\r
-</div> \r
</div>\r
-<!-- about end-->\r
-</div>\r
-<!-- content end--> \r
-<div id="copyright">Last update: 16 September 2011<br/>\r
-Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</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><!-- wrapper end-->\r
</div> <!-- page end-->\r
\r
+\r
+\r
<!-- Google analitics -->\r
<script type="text/javascript">\r
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
<!DOCTYPE html PUBLIC "XHTML 1.0 Strict" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
<head>\r
-<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) manual - getting started</title>\r
<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
<link rel="stylesheet" type="text/css" media="print" href="print.css"/>\r
-\r
<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
</head>\r
+\r
<body>\r
<div id="page">\r
<div id="banner">\r
-<table> \r
-<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws21.png" 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
-</tr>\r
+<table>\r
+ <tr>\r
+ <td style="width:158px;"><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/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.1" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
+ <td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
+ </tr>\r
</table>\r
-</div><!-- banner end-->\r
+</div>\r
+<!-- banner end-->\r
\r
<div id="wrapper">\r
<div id="panel">\r
<a href="index.html">Home</a>\r
- <a class="selected" href="quick_start.html">Getting Started</a> \r
- <a href="man_about.html">Manual</a> \r
- <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
- <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
- <a 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 href="contacts.html">Contact Us</a>\r
- <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a>\r
-\r
-</div><!-- panel end-->\r
+ <a class="selected" href="quick_start.html">Getting Started</a> \r
+ <a href="man_about.html">Manual</a> \r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a 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 href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
+<!-- panel end-->\r
\r
<div id="content">\r
-\r
<h2 id="headtitle">Getting Started</h2>\r
-\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
-\r
<table id="choicematrix">\r
<tr>\r
<th>I want to use JABAWS for...</th>\r
<th>Quick Guide</th>\r
</tr>\r
<tr>\r
- <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
- <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
+ <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
+ <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
</tr>\r
<tr>\r
- <td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="man_awscloud.html">JABAWS on the Amazon cloud </a></td>\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
</tr>\r
<tr>\r
- <td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
- <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
+ <td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
+ <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
</tr>\r
<tr>\r
- <td>Accessing a JABAWS server from my own code</td>\r
- <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
+ <td>Accessing a JABAWS server from my own code</td>\r
+ <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
</tr>\r
</table>\r
\r
-<a name="qsc"/>\r
\r
+<a name="qsc"/>\r
<h3>Installing A JABAWS Server Web Application Archive (WAR) package</h3>\r
-\r
-<p>This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable their local JABA server to use the cluster or perform very large tasks.</p>\r
+<p>\r
+ This is for anyone who wants to run JABAWS for their group, lab or organization, or wants to enable \r
+ their local JABA server to use the cluster or perform very large tasks.\r
+</p>\r
\r
<ol>\r
<li>Download the <a href="http://www.compbio.dundee.ac.uk/download">JABAWS WAR for your platform </a></li>\r
<!-- TODO put JABAWS CMD test instructions here -->\r
</div> <!-- content end-->\r
<!-- about end-->\r
-<div id="copyright">Last update: 16 September 2011<br/>\r
-Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
-\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><!-- wrapper end -->\r
\r
+\r
+\r
<!-- Google analitics -->\r
<script type="text/javascript">\r
var gaJsHost = (("https:" == document.location.protocol) ? "https://ssl." : "http://www.");\r
<!DOCTYPE html PUBLIC "XHTML 1.0 Strict" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">\r
<html xmlns="http://www.w3.org/1999/xhtml">\r
<head>\r
-<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) manual - getting started</title>\r
<link href="ws.css" rel="stylesheet" type="text/css" media="screen, projection, handheld, tv" />\r
<link rel="stylesheet" type="text/css" media="print" href="print.css"/>\r
-\r
<script type="text/javascript" src="prototype-1.6.0.3.js"></script>\r
</head>\r
+\r
<body>\r
<div id="page">\r
<div id="banner">\r
-<table> \r
+<table>\r
<tr><td style="width:158px;"><a href="http://www.dundee.ac.uk"><img src="images/uod_lt_long.gif" alt="University of Dundee" width="158" height="90" class="logo" title="University of Dundee" longdesc="http://www.dundee.ac.uk"/></a></td>\r
-<td class="bg"><img src="images/jabaws21.png" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
+<td class="bg"><img src="images/jabaws201-2.png" width="263" height="60" alt="JABAWS-2.0.1" title="Java Bioinformatics Analysis Web Services version 2.0.1"/></td>\r
<td class="bg"><img src="images/banner_right.png" alt="Disorder" width="200" height="80"/></td>\r
</tr>\r
</table>\r
</div><!-- banner end-->\r
+\r
<div id="wrapper">\r
<div id="panel">\r
- <a href="index.html">Home</a>\r
- <a class="selected" href="quick_start.html">Getting Started</a> \r
- <a href="man_about.html">Manual</a> \r
- <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
- <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
- <a 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 href="contacts.html">Contact Us</a>\r
- <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
-\r
+ <a href="index.html">Home</a>\r
+ <a class="selected" href="quick_start.html">Getting Started</a> \r
+ <a href="man_about.html">Manual</a> \r
+ <a href="http://www.compbio.dundee.ac.uk/download">Download</a>\r
+ <a href="PublicAnnualStat" title="JABAWS server usage statistics">Usage Statistics</a>\r
+ <a 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 href="contacts.html">Contact Us</a>\r
+ <a href="http://www.compbio.dundee.ac.uk" title="University of Dundee, The Barton Group" >Barton Group</a></div>\r
<!-- panel end-->\r
-<div id="content">\r
\r
-<h2 id="headtitle">Getting Started</h2>\r
\r
+<div id="content">\r
+<h2 id="headtitle">Getting Started</h2>\r
<h3><a name="whichjaba" id="whichjaba"></a>Choose a JABAWS distribution</h3>\r
-\r
<table id="choicematrix">\r
<tr>\r
<th>I want to use JABAWS for...</th>\r
<th>Quick Guide</th>\r
</tr>\r
<tr>\r
- <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
- <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
+ <td>Running Muptiple Sequence Alignments through Jalview on my <strong>own</strong> computer</td>\r
+ <td><a href="manual_qs_va.html#qsc">JABAWS Virtual Appliance (VA)</a></td>\r
</tr>\r
<tr>\r
<td>Running JABAWS on the <strong>cloud</strong>, for one or many users</td>\r
- <td><a href="man_awscloud.html">JABAWS on the Amazon cloud</a></td>\r
+ <td><a href="manual_qs_amazon.html">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
- <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
+ <td>Running JABAWS for my group, lab, or organization on the <strong>local</strong> infrastructure </td>\r
+ <td><a href="manual_qs_war.html#qsc">JABAWS Web Application aRchive (WAR)</a></td>\r
</tr>\r
<tr>\r
- <td>Accessing a JABAWS server from my own code</td>\r
- <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
+ <td>Accessing a JABAWS server from my own code</td>\r
+ <td><a href="manual_qs_client.html#qsc">JABAWS Java Client</a></td>\r
</tr>\r
</table>\r
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<!-- about end-->\r
</div>\r
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-<div id="copyright">Last update: 16 September 2011<br/>\r
-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/>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