Web Services

X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=help%2Fhtml%2FwebServices%2Findex.html;h=29c74a9a3f01d84d5e3ee1d2f060b65bc20f6955;hb=6d69275a18e2773d73d84b9fe4291e7313abfda4;hp=5b507bee10a7525529a521c613a2ae42a89748b3;hpb=72f4770815185305bd18aeeb74f829b1f9ed55c8;p=jalview.git diff --git a/help/html/webServices/index.html b/help/html/webServices/index.html index 5b507be..29c74a9 100755 --- a/help/html/webServices/index.html +++ b/help/html/webServices/index.html @@ -1,44 +1,85 @@ - - 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: +
- 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 +
+
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. +

+ +