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
+ Future versions of JABAWS will incorporate other tools.\r
</p>\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
+ JABAWS consists of a server and a client, but unlike most bioinformatics web service systems, you can download and \r
run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS \r
Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your \r
lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure \r
<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
+ <li>Clients can submit jobs to any JABAWS servers that they might want to access, such as the one running on your local computer, \r
your lab's server, or the publicly available services at the <a href="http://www.compbio.dundee.ac.uk/">University of Dundee</a>.</li>\r
<li>Local or intranet installation eliminates any security concerns you might have about sending sensitive data over the internet.</li>\r
- <li>Wide range of configuration options to control size of jobs accepted by a server and the command line options available for the program run by a service.</li>\r
+ <li>Wide range of configuration options to control size of jobs accepted by a server, and the command line options available for the program run by a service.</li>\r
</ul>\r
\r
\r
<li><span style="color:black; font-weight:normal; text-align:left;">RNAalifold from <a href="http://www.tbi.univie.ac.at/RNA">ViennaRNA</a></span> (2.0) </li>\r
</ul>\r
\r
-All these codes including Jronn and AAcon are available at the <a href="http://www.compbio.dundee.ac.uk/download">Download</a> \r
+All these codes including Jronn and AAcon are available at the <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/download">Download</a> \r
section (registration is required).\r
\r
\r
<strong>JABAWS Version 2.1 (Released 1st Oct 2013)</strong>\r
<p>Several new web services are available in this version of JABAWS:</p>\r
<ul>\r
- <li>Two multiple sequence aligners: MSAprobs and GLprobs. Both services return the standard Alignment object</li>\r
- <li>RNAalifoldWS returns RNAStructScoreManager which is the standard ScoreManager objects with several additional methods.</li>\r
+ <li>Two multiple sequence aligners (MSAprobs and GLprobs), both services return the standard Alignment object</li>\r
+ <li>RNAalifoldWS returns RNAStructScoreManager, which is the standard ScoreManager objects with several additional methods</li>\r
<li>\r
- JpredWS returns the JpredAligment object which is the standard Alignment with additional methods for extracting \r
- Jpred predictions. These predictions are supplied as additional sequences in the aligment.\r
+ JpredWS returns the JpredAligment object, which is the standard alignment with additional methods for extracting \r
+ Jpred predictions. These predictions are supplied as additional sequences in the aligment\r
</li>\r
</ul>\r
\r
<li>JABAWS could not deal with FASTA records with '>' symbols in the record identificator</li>\r
<li>Change of parameter description for AAcon: parameters have been replaced with options for calculation methods. This allows a user to get several AAcon's conservation scores \r
in one call</li>\r
- <li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer then a period defined in Engine.properties</li>\r
+ <li>JABAWS never cleaned up job directories. Now JABAWS deletes the job directory if it exist longer than a period defined in Engine.properties</li>\r
<li>Default web security has been incompatible with Tomcat 7.0.31 and newer</li>\r
<li>Documentation has been updated</li>\r
</ul>\r
\r
<h3><a name="jabaclient" id="jabaclient"></a>What is JABAWS client?</h3>\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
+ A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web \r
+ services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web \r
+ services on any instance of JABAWS Server available over the web. The basic client is useful if you would like \r
+ to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle \r
+ any web service specific details. The client is an open source software, so you can also use the source code to \r
+ as an example how to manipulate with JABAWS web services in your own code. \r
+ <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good \r
+ example of a graphical JABAWS client. This client uses the same functionality as the command line client, but \r
+ instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.\r
</p>\r
\r
\r
\r
<h3><a name="jalviewsup"></a>JABAWS versions compatibility and Jalview support </h3>\r
<p>\r
- JABAWS version 2.1 is fully backward compatible with JABAWS v1.0 and v2.0. That means that all JABAWS v1.0 and \r
- v2.0 clients should also be able to use JABAWS 2.1 services. To access the analysis web services introduced in\r
- JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.\r
+ JABAWS version 2.1 is fully backward compatible with JABAWS v1.0 and v2.0. This means all JABAWS 1.0 and 2.0 and \r
+ 2.0.1 clients should also be able to use JABAWS 2.1 services. To access the analysis web services introduced in \r
+ JABAWS 2.0, however, clients that were designed for JABAWS v1.0 must be updated.\r
</p>\r
\r
\r
\r
<h3><a name="cmdclient" id="cmdclient"></a>Programmatic access to JABAWS </h3>\r
<p>\r
- JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language \r
+ JABAWS web services are WS-I basic profile compliant, which means they can be accessed using any programming language \r
or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home \r
- page, and you can use this to automatically generate service bindings for your program. If you use Java, 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
+ page, and you can use this to automatically generate service bindings for your program. If you use Java \r
+ you may wish to use our <a href="http://gjb-www-4.cluster.lifesci.dundee.ac.uk:8091/jabaws-dev">client package</a> to access JABAWS. \r
This package is based on the autogenerated source code produced by <span class="hightlight">wsimport</span>, which \r
- is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify \r
+ is the Java tool for creating web service bindings. In addition, this offers some additional methods that simplify \r
working with JABAWS. For more information please refer to the <a href="dm_javadoc/index.html">data model javadoc</a>.\r
</p>\r
</div><!-- content end-->\r
-<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
+<div id="copyright">Last update: 30 April 2014<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
</div><!-- wrapper end-->\r
</div><!-- page end-->\r
\r
git://source.jalview.org / jabaws.git / blobdiff