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23 <title>VAMSAS Interoperation</title>
27 <strong>VAMSAS Interoperation</strong>
30 Jalview can interact with other applications using "the <strong>VAMSAS
31 Interoperation framework</strong>" which is an experimental model for
32 interoperation between bioinformatics applications (<strong>V</strong>isualization
33 and <strong>A</strong>nalysis of <strong>Molecular</strong> <strong>S</strong>equences,
34 <strong>Alignements</strong> and <strong>S</strong>tructures).
35 Currently, the only other VAMSAS enabled application is <a
36 href="http://www.topali.org"
37 >TOPALi</a> - a user friendly program for phylogenetics and
38 evolutionary analysis.
40 VAMSAS enabled applications access a shared bioinformatics dataset
41 containing sequences, alignments, annotation and trees, which can be
42 represented by an XML document analogous to a <a
43 href="../features/jalarchive.html"
44 >Jalview Project Archive</a>.
47 <strong>Connecting to a VAMSAS session</strong>
48 <br> The VAMSAS functionality in Jalview is accessed through the
50 <strong>Vamsas</strong> menu. The options available in this menu
51 depend on whether the application is currently interacting with a
53 <strong>VAMSAS session</strong>. When the application is not connected
54 to a session is active, the menu options are as follows:
57 <li><em>Connect to an existing session</em><br> If
58 visible, this submenu contains a list of existing sessions that
59 the VAMSAS framework has discovered on your computer. <br>
60 Choose one to connect to it.</li>
61 <li><em>New VAMSAS Session</em><br> This option will
62 create a new session on your computer.</li>
63 <li><em>Load VAMSAS Session...</em><br> This option will
64 open a file browser window allowing you to select a VAMSAS session
65 archive from which a new session will be created.<br /> <em>New
66 in 2.5:</em>Sessions created from an imported document inherit the
67 file or URL for the document.</li>
71 <strong>VAMSAS and Firewalls</strong>: VAMSAS uses sockets to
72 communicate between different programs. This means that after starting
73 a session, your firewall software may ask you whether to allow the
74 java executable access to the internet (port 53782). If you do not
75 allow this, messages will not be exchanged with other VAMSAS
78 <br> Once you have successfully connected to a VAMSAS session,
79 any data made available by other VAMSAS applications will be
80 automatically imported into Jalview. However, in order to share the
81 data in Jalview with other VAMSAS applications, you must manually
83 <strong>Vamsas→"Session Update"</strong> entry that is
84 visible when a session is active. Selecting this option will update
85 the VAMSAS session document, with the data loaded into Jalview. Any
86 new alignments, trees and annotation will be written to the session,
87 in addition to any edits you have made to data originally stored in
90 <strong>Saving the current session</strong>
91 <br> You can save the current session as a VAMSAS Session archive
93 <strong>Vamsas→"Session Update"</strong>. The file
94 contains a snapshot of the current VAMSAS session, including data from
95 any other applications connected to the session.
96 <strong>Leaving a VAMSAS session</strong>
97 <br> A session can be disconnected from at any time using the
98 <strong>Vamsas→"Stop Session"</strong> option.
99 Selecting this option will only disconnect Jalview from the session -
100 any other applications will remain connected to the session. If
101 Jalview is the only application connected to the session and you have
102 not yet saved the VAMSAS session then you will be prompted with an
103 optional 'Save VAMSAS session...' dialog box, allowing the session to
104 be saved and returned to at a later date.
106 <strong>VAMSAS Session Persistence</strong>
107 <br> VAMSAS sessions are persistent - this means that they exist
108 independently of any VAMSAS applications that are connected to them.
109 This means that if something goes wrong with a VAMSAS application and
110 it crashes or otherwise fails, the VAMSAS session it is connected to
111 will (hopefully) be unaffected. For instance, if Jalview is killed or
112 crashes whilst it is still connected to a session, that session can be
113 recovered in a new Jalview instance using the
114 <strong>Vamsas→"Existing session"</strong> sub menu.
117 <strong>A quick Demo</strong> <br> Jalview can talk to itself
118 through VAMSAS. Simply start two copies of the application, create a
119 new vamsas session in one, and connect to the new session in the
120 other. Then load your data into one of the applications, and use the
121 <strong>Vamsas→"Session Update"</strong> menu entry
122 to try to propagate the data to the other application. <br>
125 <td>Data Sharing Capability</td>
126 <td>Jalview Version</td>
129 <td>Alignments, sequences and annotation, trees, database
130 references, cDNA/protein mappings.</td>
134 <td>Mouseover location across linked DNA, protein and
135 structure positions.</td>
139 <td>Jalview project settings (Multiple views, groups, tree
140 partitions, colouring, window positions)</td>
144 <td>Sequence region and column selections</td>
150 Version 0.2 of the VAMSAS client library is used in <em>Jalview
151 2.5</em>. For further details about the VAMSAS framework, please check
152 the <a href="http://www.vamsas.ac.uk">VAMSAS website</a>. The VAMSAS
153 framework is implemented as a Java 1.4 Library and depends on a
154 number of other open source projects. Its source is released under
155 the LGPL license.