-% The Envision 2 services presented in the webservice menu provides are the first
-% example of one-way services where multiple sequences or sequence IDs can be
-% sent. The {\sl Web service $\Rightarrow$ Envision 2 Services} menu entry
-% provides two sub-menus that enable you to submit the sequences or IDs
-% associated with the alignment or just the currently selected sequences to one
-% of the Envision2 workflows. Selecting any one will open a new browser window on
-% the Envision2 web application. The menu entries and their tooltips provide
-% details of the Envision2 workflow and the dataset set that will be submitted
-% ({\sl i.e.} the database reference type, or associated sequence subset). Please
-% note, due to technical limitations, Jalview can currently only submit small
-% numbers of sequences to the workflows - if no sequence or ID submissions are
-% presented in the submenus, then try to select a smaller number of sequences to
-% submit.
-
-\subsection{Remote Analysis Web Services}
-Remote analysis services enable Jalview to use external computational
-facilities. There are curently three types of service - multiple sequence
-alignment, protein secondary structure prediction, and alignment analysis.
-Many of these are provided by JABA servers, which are described at the end of
-this section. In all cases, Jalview will construct a job based on the alignment
-or currently selected sequences, ask the remote server to run the job, monitor
-status of the job and, finally, retrieve the results of the job and display
-them. The Jalview user is kept informed of the progress of the job through a
-status window.
-
-Currently, web service jobs and their status windows are not stored in Jalview
-Project Files\footnote{This may be rectified in future versions.}, so it is
-important that you do not close Jalview whilst a job is running. It is also
-essential that you have a continuous network connection in order to
-successfully use web services from Jalview, since it periodically checks the
-progress of running jobs.
-
-
-\subsection{JABA Web Services for Sequence Alignment and Analysis}
-\label{jabaservices}
-JABA stands for ``JAva Bioinformatics Analysis'', which is a system developed
-by Peter Troshin and Geoff Barton at the University of Dundee for running
-computationally intensive bioinformatics analysis programs. A JABA installation
-typically provides a range of JABA web services (JABAWS) for use by other
-programs, such as Jalview.
-
-Exercises in the remainder of this section will demonstrate the simplest way of
-installing JABA on your computer, and configuring Jalview so it can access the JABA services. If you
-need any further help or more information about the services, please go to the
-\href{http://www.compbio.dundee.ac.uk/jabaws}{JABAWS home page}.
-%% \subsubsection{Aims}
-%% \begin{list}{$\bullet$}{}
-%% \item Gain experience using the different alignment services provided by
-% JABA
-%%\item Learn about the way that Jalview stores user presets for JABA services
-%%\item Learn how to install JABA services and configure Jalview to access them
-%%\end{list}
-
-\subsection{Changing the Web Services Menu Layout}
-\label{changewsmenulayout}
-If you are working with a lot of different JABA services, you may wish to change
-the way Jalview lays out the web services menu. You can do this from the Web
-Services tab of the {\sl Preferences} dialog box.
-
-\exercise{Changing the Layout of the Web Services Menu}{
-\label{changewsmenulayoutex}
-\exstep{Make sure you have loaded an alignment into Jalview, and examine the
-current layout of the alignment window's {\sl Web Service} menu.}
-\exstep{Open the preferences dialog box and select the web services tab.}
-\exstep{Ensure the {\sl Enable JABAWS services} checkbox is selected, and unselect
-the {\sl Enable Enfin Services} checkboxes.}
-\exstep{Hit {\sl Refresh Services} to update the web services menu -- once the
-progress bar has completed, open the {\sl Web Service} menu to view the changes.}
-\exstep{Select the {\sl Index by host} checkbox and refresh the services once again.
-
-{\sl Observe the way the layout of the JABAWS Alignment submenu changes.}
-}
-\exstep{Do the same with the {\sl Index by type} checkbox.}
-}
-
-Jalview provides these options for configuring the layout of the {\sl Web Service}
-menu because different Jalview users may have access to a different number of
-JABA services, and each will have their own preference regarding the layout of
-the menu.
-
-\begin{figure}[htbc]
-\begin{center}
-\includegraphics[width=3in]{images/jvjabawsconfig.pdf}
-\caption{{\bf The Jalview Web Services preferences panel.} Options are provided
-for configuring the list of JABA servers that Jalview will use, enabling and
-disabling Enfin services, and configuring the layout of the web services
-menu.}
-\label{jvjabawsconfig}
-\end{center}
-\end{figure}
-
-
-\subsubsection{Testing JABA services}
-The JABAWS configuration dialog shown in Figure \ref{jvjabawsconfig} has colour
-codes to indicate whether the Desktop can access the server, and whether all
-services advertised by the server are functional. The colour codes are:
-
-\begin{list}{$\bullet$}{}
- \item Red - Server cannot be contacted or reports a connection error.
- \item Amber - Jalview can connect, but one or more services are non-functional.
- \item Green - Server is functioning normally.
-\end{list}
- %TODO green and a tick, red and a cros, amber and a value indicating whether its all going
-
-Test results from JABAWS are reported on Jalview's console output (opened from
-the Tools menu). Tests are re-run every time Jalview starts, and when the
-[Refresh Services] button is pressed on the Jalview JABAWS configuration panel.
-
-\subsubsection{Resetting the JABA Services Setting to their Defaults}
-Once you have configured a JABAWS server and selected the OK button of the
-preferences menu, the settings will be stored in your Jalview preferences file,
-along with any preferences regarding the layout of the web services menu. If
-you should ever need to reset the JABAWS server list to its defaults, use the
-`Reset Services' button on the Web Services preferences panel.
-
-\subsection{Running your own JABA Server}
-You can download and run JABA on your own machine using the `VMWare' or
-VirtualBox virtual machine environments. If you would like to learn how to do
-this, there are full instructions at the
-\href{http://www.compbio.dundee.ac.uk/jabaws/}{JABA web site}.
-
-\exercise{Installing a JABA Virtual Machine on your Computer}{
-\label{jabawsvmex}{\sl This tutorial will demonstrate the simplest way of
-installing JABA on your computer, and configuring Jalview so it can access the JABA services.
-
-{\bf Prerequisites}
-
-You will need a copy of VMWare Player/Workstation/Fusion on your machine.
-}
-
-\exstep{If you do not have VMWare player installed, download it from
-www.vmware.com (this takes a few minutes -- you will need to register and wait
-for an email with a download link).}
-\exstep{Download the JABA virtual appliance archive called `jaba-vm.zip' from
-\textsf{http://www.compbio.dundee.ac.uk/jabaws/archive/jabaws-vm.zip}
-
-WARNING: This is large (about 300MB) and will take some time to download.
-}
-\exstep{Unpack the archive's contents to a place on your machine with at least
-2GB of free space.
-
-(On Windows, right click on the archive, and use the 'Extract archive..' option).
-}
-\exstep{Open the newly extracted directory and double click the VMWare virtual
-machine configuration file (jabaws.vcf). This will launch the VMWare player.
-}
-\exstep{Once VMWare player has started up, it may ask the question ``Did you move or copy
-this virtual appliance?'' -- select `Copy'.}
-\exstep{You may be prompted to download the VMWare linux tools. These are not
-necessary, so close the window or click on `Later'.}
-\exstep{You may also be prompted to install support for one or more devices (USB
-or otherwise). Say `No' to these options.}
-\exstep{Once the machine has loaded, it will display a series of IP addresses
-for the different services provided by the VM. Make a note of the JABAWS URL --
-this will begin with `http:' and end with `/jabaws''.}
-}
-
-\exercise{Configuring Jalview to Access your new JABAWS Virtual Appliance}{
-\label{confnewjabawsappl}
-\exstep{Start Jalview (If you have not done so already).}
-\exstep{Enable the Jalview Java Console by selecting its option from the Tools
-menu.
+% \exercise{Creating and using user defined presets}{\label{createandusepreseex}
+% \exstep{Import the file at
+% \textsf{http://www.jalview.org/tutorial/fdx\_unaligned.fa} into jalview.}
+% \exstep{Use the `{\slDiscover Database Ids}' function to recover the PDB cross
+% references for the sequences.}
+% \exstep{Align the sequences using the default ClustalW parameters.}
+% \exstep{Use the `{\sl Edit and run..}'
+% option to open the ClustalW parameters dialog box, and create a new preset using
+% the following settings:
+% \begin{list}{$\bullet$}{}
+% \item BLOSUM matrix (unchanged)
+% \item Gap Opening and End Gap penalties = 0.05
+% \item Gap Extension and Separation penalties = 0.05
+% \end{list}
+%
+% As you edit the parameters, buttons will appear on the dialog box
+% allowing you revert your changes or save your settings as a new parameter
+% set.
+%
+% Before you save your settings, remeber to give them a meaningful name by editing
+% the text box at the top of the dialog box.
+% }
+% \exstep{Repeat the alignment using your new parameter set by selecting it from
+% the {\sl ClustalW Presets menu}.}
+% \exstep{These sequences have PDB structures associated with them, so it is
+% possible to compare the quality of the alignments.
+%
+% Use the {\sl View all {\bf N}
+% structures} option to calculate the superposition of 1fdn on 1fxd for both
+% alignments (refer to section \ref{superposestructs} for instructions). Which
+% alignment gives the best RMSD ? }
+% \exstep{Apply the same alignment parameter settings to the example alignment
+% (available from \textsf{http://www.jalview.org/examples/uniref50.fa}).
+%
+% Are there differences ? If not, why not ?
+% }
+% }