X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=b41e643fc087df3fd313737a4f17c2c85ebe86f4;hb=a16c37a5983e3c581dc3d3030e1439e8fb3239f1;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.
+
+
+ Envision2 Services
+
+
+
+ Since version 2.5, Jalview has included a client to enable the user to
+ submit one or more sequences or sequence IDs to analysis workflows
+ provided by the EnVision2
+ web application. This allows Jalview users to easily access the
+ EnCore network of databases and analysis services developed by ENFIN (www.enfin.org).
+
+
+