X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=fd2584a3282c8b3cac46334d87458f4f48f509c8;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=19fcd8fec63ca0bd8909785fbd98d91f92a3b002;hpb=8ee7a0f79f6da26d5011c60a80226d6994733cab;p=jalview.git
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-
-Web Services
-
-Web services
-Originally Jalview used SRS server to retrieve sequence features for a given
- alignment. In addition certain remote alignment programs could be called from
- the Jalview interface and the results displayed in a new alignment panel.
-Jalview's web based computations are now being developed further,
- using SOAP based services to expose protein sequence alignment and
- secondary structure prediction programs. These services actually run
- on the cluster based in Dundee, and maintained by the Barton group.
-
In the future, Jalview will be able to discover services
- dynamically, and the repertoire will include methods for repeat
- analysis, sequence identification and remote homology
- detection. The web service methodology will also allow potentially
- expensive Jalview analysis functions like PCA to be distributed, if
- necessary, when the user is dealing with very large numbers of sequences.
-
-
+
+
+
+Web Services
+
+
+
+ Web services
+
+
+ Jalview includes clients for a variety of web services for both
+ bioinformatic data retrieval and analysis.
+
+ - The Sequence
+ Fetcher utilises web services for sequence, alignment and
+ structure retrieval provided by the European Bioinformatics
+ Institute (EBI) and Distributed Annotation System servers that are
+ capable of serving sequences.
+
+ - The DAS Feature
+ Fetcher enables the retrieval and visualization of features from
+ DAS annotation sources
+
+ - The Database Reference
+ Fetcher transfers database references from records available
+ from DAS or the public sequence databases.
+
+ - The Web Services menu in each alignment
+ window also provides access to the following:
+
+
+ Web Service Dialog Box
+
+ This dialog box is displayed when a web service job is
+ submitted. It gives the name of the service and any method
+ citation information, and monitors the progress of the
+ calculation. The cancel button will permanently cancel the job,
+ but this is only possible for some services.
The Web Services Preference panel controls the display and appearance
+ of the submission and analysis services in the Web
+ Services menu.
+
+ - If Jalview encounters problems accessing any services, it
+ may display a warning
+ dialog box (this can be turned off using the web services
+ preferences tab).
+
+
+
+
+ More about Jalview's Web Services
+ Jalview's distributed computations utilise SOAP and REST web services exposing sequence alignment, analysis, and
+ secondary structure prediction programs. Originally, Jalview 2's
+ services were maintained by the Barton group at the University of
+ Dundee, and ran programs on the Life Sciences High-performace
+ Computing Cluster. With the advent of JABAWS, however, it is possible for anyone to host Jalview web
+ services.
+
+
+