X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=04ccd8f847adc5ec31324e000ad72550e5595902;hb=99d5f1d805e530f23a53dad4484d44ecd0fbfdf3;hp=5b507bee10a7525529a521c613a2ae42a89748b3;hpb=72f4770815185305bd18aeeb74f829b1f9ed55c8;p=jalview.git
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-
- Web Services
-
- Web services
- A variety of web services are available from the Alignment window's
- Calculations→Web Service→ menu.
-
- Jalview's distributed computations are SOAP based services exposing
- protein sequence alignment and secondary structure prediction programs. These services actually run
- on the cluster based in the School of Life Sciences, University of
- Dundee, and are maintained by the Barton group.
-
- Web Service Dialog Box
-![]()
-
- This dialog box is displayed when a web service job is submitted.
-
- Current services:
-
- - ClustalW Multiple Alignment
- The clustal W service remains one of the more popular Jalview features.
-
- - Muscle Multiple Alignment
- High Quality and High Throughput multiple alignments of proteins. This
- method can sometimes be more accurate than ClustalW when dealing with
- diverse sets of sequences.
-
- - JNet Secondary Structure Prediction
- This is a front end to the existing JNet www server.
-
-
-
- Watch this space! These are some of the services
- planned to be released soon:
- - Repeat analysis
-
- - Remote Homology Detection
-
-
- In the future, Jalview will also be able to new discover services
- dynamically, and distribute expensive analysis functions like PCA to the Dundee machines.
-
-
+
+
+
+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.
+
+
+