Web Services

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=help%2Fhtml%2FwebServices%2Findex.html;h=b41e643fc087df3fd313737a4f17c2c85ebe86f4;hb=a16c37a5983e3c581dc3d3030e1439e8fb3239f1;hp=5d4025a6eb28e16b0ad3e0adba8b60c73b215941;hpb=3396e9f33cf3a16a7f38f5163cd057df4b859e7e;p=jalview.git diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 5d4025a..b41e643 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -1,15 +1,97 @@ - -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.

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 +

+ +

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. +
- Services for submitting IDs and sequences to external + bioinformatics services such as Envision2 (see below).
+
+ 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). +

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