help/html/webServices/index.html

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