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-<title>Java Bioinformatics Analyses Web Services (JABAWS) Server Virtual Appliance Manual</title>\r
+<title>Java Bioinformatics Analyses Web Services (JABAWS): Manual</title>\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/jabaws25.png" width="263" height="60" alt="JABAWS-2.1" title="Java Bioinformatics Analysis Web Services version 2.1"/></td>\r
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<h2 id="headtitle">JABAWS MANUAL</h2>\r
\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
+<h3><a name="whenvm" id="whenvm"/>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
systems over an internet, or just want to keep their data private. It is also \r
the recommended option for users who want to install JABAWS on Windows, which does not support all the bioinformatics programs that JABAWS can run.</p>\r
<em>Access:</em> root@VM_IP</li>\r
</ul>\r
<p>Where VM_IP is the VM IP address. Under VMware Player host only networking, the first VM may have 192.168.227.128 IP address. </p>\r
-<h3><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</a> </h3>\r
-<p>After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview <a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>. </p>\r
+\r
+\r
+<h3><a name="jalviewWithJaba" id="jalviewWithJaba"/>Configuring Jalview to work with your JABAWS VM</h3>\r
+<p>\r
+After booting the JABAWS VM, you should see similar screen, however, the IP address of your VM may be different. \r
+To enable Jalview to work with your JABAWS appliance you need to go to Jalview->Tools->Preferences->Web Services -> \r
+New Service URL, and add JABAWS URL into the box provided. For more information please refer to Jalview \r
+<a href="http://www.jalview.org/help/html/webServices/JABAWS.html">help pages</a>.\r
+</p>\r
<p><img src="images/vm_welcome_screen.png" alt="JABAWS welcome screen" width="734" height="461" /></p>\r
<p>If you click on Advanced Menu, you will see the configuration console, similar to the one below. </p>\r
<p><img src="images/VMware_booted.png" alt="JABAWS welcome screen" width="735" height="461" /></p>\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
+<h3><a name="vmiaccess" id="vmiaccess"/>VM Network Settings </h3>\r
+<p>\r
+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, \r
+but no other machines can. Similarly, the VM cannot communicate with any other computers apart from the host. If you want to connect \r
+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 \r
+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 \r
+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 \r
+server to do that)</p>\r
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<div id="copyright">Last update: 28 June 2013<br/>Sasha Sherstnev, Peter Troshin, Jim Procter and Geoff Barton, The Barton Group, University of Dundee, UK</div>\r
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