-<p><strong>Troubleshooting</strong></p>\r
-<ul>\r
- <li><a href="#vmbexc"> VirtualBox fails to open the VM due to VERR_VMX_MSR_LOCKED_OR_DISABLED exception</a></li>\r
- <li><a href="#vboxinvalidstate">VirtualBox 4.0 fails to import the VM due to VBOX_E_INVALID_OBJECT_STATE exception </a></li>\r
- <li><a href="#ovfOnVmware">VMWare Player fails to open the VM with "Fail to query source for information" exception</a></li>\r
-</ul>\r
-<h3><a name="whatisvm" id="whatisvm"></a>What is JABAWS Server Virtual Appliance?</h3>\r
-<p>The JABAWS Server Virtual Appliance is an installation of JABAWS Web Application Archive (WAR) with all dependencies on TurnKey Linux within a Virtual Machine. The JABAWS <a href="http://en.wikipedia.org/wiki/Virtual_appliance">virtual appliance</a> is a way to run JABAWS server locally without the need to connect to the internet or configure JABAWS.\r
- \r
- \r
- All JABAWS clients, such as Jalview can be easily configured to use the appliance. \r
- You can run the appliance with freely available <a href="http://www.vmware.com/products/player">VMWare Player</a> or <a href="http://www.virtualbox.org/wiki/Downloads">Oracle VirtualBox</a> which you must install first. We have tested JABAWS appliance with VMware Player v 3.1.2 on Windows and Linux, and <a href="http://www.virtualbox.org/wiki/Download_Old_Builds_3_2">VirtualBox v 3.2.12</a> on Windows, Linux and Mac. \r
- However, you are not limited to these virtualization systems and can use JABAWS appliance with any commercial alternative. </p>\r
-<h3><a name="whenvm" id="whenvm"/></a>When to use the virtual appliance </h3>\r
-<p>The appliance best suits users who would like to use the JABA web services locally, without an Internet connection, want to keep their data private \r
-or uses Windows as their main OS. The appliance is a self contained unit of software and as such may be an attractive option for Linux, UNIX or Mac users too. However, they can always deploy a <a href="man_serverwar.html#instwar">JABAWS Server WAR distribution</a> instead. <br />\r
-The appliance comes pre configured to use 1 CPU and 512M of memory and the minimum amount of memory required is about 378M. If you thinking of running the JABAWS server for many users and want JABAWS to use a cluster for calculations you need a WAR version of JABAWS server instead. Virtual Appliance would not be the best option for that. </p>\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
+ 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
+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
+<h3><a name="whennotvm" id="whennotvm"/>When <em>not</em> to use the JABAWS Virtual Appliance</h3>\r
+<p>\r
+For servers that will be used heavily, we recommend that a <a href="man_serverwar.html#instwar">JABAWS Server WAR distribution</a> is deployed, rather than the Virtual Appliance version of JABAWS. \r
+This is because the JABAWS appliance is pre-configured to use only 1 CPU and 512M of memory \r
+(where the minimum amount of memory required for a JABAWS server is about 378M), which is unlikely to be sufficient for heavy computation. \r
+It is possible to reconfigure the virtual appliance so it uses more computation resources, \r
+but for most production environments, the JABAWS WAR distribution will be easier to deploy and fine tune to take advantage of the available resources.</p>\r