Web Services

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=fd2584a3282c8b3cac46334d87458f4f48f509c8;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=2b24bfe4531938e0542a6992e0afc9e352b4cc62;hpb=1693646e78fb0dddebcd94f8bef7e2acd3bdaae0;p=jalview.git diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 2b24bfe..fd2584a 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -1,15 +1,98 @@ - - - -

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.

The main emphasis of the current development of the Jalview Project is to implement - various sequence alignment programs, tree analysis, PCA algorithms on a large - cluster based witihin the Barton Group. Jalview will be able to call these remote - procedures without the user having to install any new software.
- The main advantage of using these remote web services is that the computing - power available is much greater than that of the users work station.

- - + + + +Web Services + + +

+ Web services +

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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: +
- Programs for multiple + sequence alignment, made available via Java Bioinformatic Analysis Web Service (JABAWS) servers. +
- Jalview SOAP Web Services for secondary + structure prediction based at the University of Dundee. +
- Services for alignment analysis, such as Multi-Harmony. +
+
+ Web Service Dialog Box +
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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. +

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