<!--<h4>About</h4>-->
<ul>
<li><a href="#wisjaba">What is JABAWS?</a></li>
+ <li><a href="#jabaclient">What is JABAWS Client</a>?</li>
<li><a href="#wjaba">JABAWS Benefits</a></li>
- <li><a href="#alprog">JABA Web Services Programs</a></li>
+ <li><a href="#alprog">Bioinformatics tools included in JABAWS</a></li>
<li><a href="#jaba2.2">What is new in JABAWS 2.2?</a> </li>
- <li><a href="#jabaclient">What is JABAWS Client</a>?</li>
<li><a href="#jalviewsup">JABAWS versions compatibility and Jalview support </a></li>
<li><a href="#cmdclient">Programmatic access to JABAWS</a></li>
</ul>
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>.
+ (see <a href="#alprog">the list of currently supported programs</a>).
Future versions of JABAWS will incorporate other tools.
</p>
<strong>Getting JABAWS</strong>
<p>
- JABAWS consists of a server and a 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
+ JABAWS consists of a server and a 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
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#va">JABAWS Virtual Appliance (VA)</a>.
+ It requires no configuration and is simple to install. If you want to install JABAWS for your
+ lab or institution then download the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#war">JABAWS Web Application aRchive (WAR)</a>.
+ 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.
+ in writing your own client, the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS command line (CLI) client</a> is what you need.
+ </p>
+ <p class="text-right">
+ <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
+ </p>
+ </div>
+ </div>
+ </div>
+</div>
+<div class="row" id="jabaclient">
+ <div class="col-md-12">
+ <div class="panel panel-default">
+ <div class="panel panel-heading">
+ <h1 class="panel-title">What is the JABAWS Client?</h1>
+ </div>
+ <div class="panel-body">
+ <p class="justify">A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web
+ services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web
+ services on any instance of JABAWS Server available over the web. The basic client is useful if you would like
+ to test or execute the programs provided by the JABAWS server in your own scripts, but you do not want to handle
+ any web service specific details. The client is an open source software, so you can also use the source code to
+ as an example how to manipulate with JABAWS web services in your own code.
+ <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good
+ example of a graphical JABAWS client. This client uses the same functionality as the
+ <a href="${pageContext.request.contextPath}/getting_started.jsp#client">JABAWS command line (CLI) client</a>, but
+ instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.
</p>
<p class="text-right">
<a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
</div>
<div class="panel-body">
<ul>
- <li>Can be deployed on most operating systems, as a VMware or other compatible Virtual Appliance or a Tomcat Java Web Application.</li>
+ <li>Can be deployed on most operating systems, as a VMware or compatible Virtual Appliance, as well as a Tomcat Java Web Application.</li>
<li>Comes complete with sources and binaries for all the bioinformatics programs that it runs.</li>
<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>
<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>
<div class="col-md-12">
<div class="panel panel-default">
<div class="panel panel-heading">
- <h1 class="panel-title">JABA Web Services Programs</h1>
+ <h1 class="panel-title">Bioinformatics tools included in JABAWS</h1>
</div>
<div class="panel-body">
<p>JABAWS currently provides access to the following programs:</p>
</div>
<div class="panel-body">
- <strong>JABAWS Version 2.2 (Released XX Feb 2017)</strong>
+ <strong>JABAWS Version 2.2 (Released XX March 2017)</strong>
<p >The website was improved and several service programs were update:</p>
<ul>
<li>The versions of several application programs provided by JABAWS were bumped to the latest available.
The pre-configured JABAWS Amazon Machine Image (AMI),
which allowed for JABAWS to be run
in the <a href="http://aws.amazon.com/what-is-aws">Amazon EC2 cloud</a>, is no longer provided
- due to very limited use by the scientific community.
+ due to very limited use by the scientific community peers.
</li>
</ul>
</div>
</div>
</div>
-<div class="row" id="jabaclient">
- <div class="col-md-12">
- <div class="panel panel-default">
- <div class="panel panel-heading">
- <h1 class="panel-title">What is the JABAWS Client?</h1>
- </div>
- <div class="panel-body">
- <p class="justify">A JABAWS client is a Java application that lets you run the programs for which a JABAWS server provides web
- services. The most basic JABAWS client is a command line application this is able to call any of the JABAWS web
- services on any instance of JABAWS Server available over the web. The basic client is useful if you would like
- to test or execute the programs provided by theJABAWS server in your own scripts, but you do not want to handle
- any web service specific details. The client is an open source software, so you can also use the source code to
- as an example how to manipulate with JABAWS web services in your own code.
- <a href="http://www.jalview.org/">Jalview</a>, a multiple sequence alignment and analysis application, is a good
- example of a graphical JABAWS client. This client uses the same 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>
- <p class="text-right">
- <a href="#">Back to top <i class="fa fa-arrow-up" aria-hidden="true"></i></a>
- </p>
- </div>
- </div>
- </div>
-</div>
<div class="row" id="jalviewsup">
<div class="col-md-12">
<div class="panel panel-default">
git://source.jalview.org / jabaws.git / blobdiff