help/html/webServices/index.html

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  19 <html>
  20 <head>
  21 <title>Web Services</title>
  22 </head>
  23 <body>
  24         <p>
  25                 <strong>Web services</strong>
  26         </p>
  27
  28         <p>Jalview includes clients for a variety of web services for both
  29                 bioinformatic data retrieval and analysis.
  30         <ul>
  31                 <li>The <a href="../features/seqfetch.html">Sequence Fetcher</a>
  32                         utilises web services for sequence, alignment and structure retrieval
  33                         provided by the European Bioinformatics Institute (EBI) and
  34                         Distributed Annotation System servers that are capable of serving
  35                         sequences.</li>
  36                 <li>The <a href="../features/dasfeatures.html">DAS Feature
  37                                 Fetcher</a> enables the retrieval and visualization of features from DAS
  38                         annotation sources</li>
  39                 <li>The <a href="dbreffetcher.html">Database Reference
  40                                 Fetcher</a> transfers database references from records available from
  41                         DAS or the public sequence databases.</li>
  42                 <li>The <strong>Web Services</strong> menu in each alignment
  43                         window also provides access to the following:
  44                         <ul>
  45                                 <li>Programs for <a href="msaclient.html">multiple sequence
  46                                                 alignment</a>, made available <em>via</em> <a href="JABAWS.html">Java
  47                                                 Bioinformatic Analysis Web Service (JABAWS)</a> servers.</li>
  48                                 <li>Jalview SOAP Web Services for <a href="jnet.html">secondary
  49                                                 structure prediction</a> based at the University of Dundee.</li>
  50                                 <li>Services for alignment analysis, such as <a
  51                                         href="shmr.html">Multi-Harmony</a>.
  52                         </ul>
  53                         <p>
  54                                 <strong>Web Service Dialog Box</strong>
  55                         </p> <img src="clwqueued.gif">
  56                         <p>This dialog box is displayed when a web service job is
  57                                 submitted. It gives the name of the service and any method citation
  58                                 information, and monitors the progress of the calculation. The
  59                                 cancel button will permanently cancel the job, but this is only
  60                                 possible for some services.</p> The <a href="webServicesPrefs.html">Web
  61                                 Services Preference panel</a> controls the display and appearance of the
  62                         submission and analysis services in the <strong>Web Services</strong>
  63                         menu.</li>
  64                 <li>If Jalview encounters problems accessing any services, it may
  65                         display a <a href="webServicesPrefs.html#wswarnings">warning
  66                                 dialog box</a> (this can be turned off using the web services
  67                         preferences tab).</li>
  68         </ul>
  69         </p>
  70         <p>
  71                 <strong>More about Jalview's Web Services</strong> <br> Jalview's
  72                 distributed computations utilise <a
  73                         href="http://en.wikipedia.org/wiki/SOAP">SOAP</a> and <a
  74                         href="http://en.wikipedia.org/wiki/Representational_State_Transfer">REST</a>
  75                 web services exposing sequence alignment, analysis, and secondary
  76                 structure prediction programs. Originally, Jalview 2's services were
  77                 maintained by the Barton group at the University of Dundee, and ran
  78                 programs on the Life Sciences High-performace Computing Cluster. With
  79                 the advent of <a href="http://www.compbio.dundee.ac.uk/JABAWS">JABAWS</a>,
  80                 however, it is possible for anyone to host Jalview web services.
  81         </p>
  82 </body>
  83 </html>