X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Fman_about.html;h=057b0c956b07fdd38e283ce08728add204bc60d4;hb=6256f785b5baf779b46ac1d9a5d3d9bec7a2b96c;hp=ac1c6867015f142d5775341492320805c853430a;hpb=b0423691d9a44eae86799ad242c4fea58f9acd8d;p=jabaws.git diff --git a/website/man_about.html b/website/man_about.html index ac1c686..057b0c9 100644 --- a/website/man_about.html +++ b/website/man_about.html @@ -13,9 +13,9 @@
@@ -27,16 +27,22 @@ - Download + Download + Usage Statistics + Services Status Contact Us - Barton Group
+ Barton Group +
@@ -47,19 +53,21 @@
  • What is JABAWS?
  • JABAWS Benefits
  • JABA Web Services Programs
    • +
  • What is new in JABAWS 2?
  • What is JABAWS Client?
    • +
  • JABAWS versions compatibility and Jalview support
  • Programmatic access to JABAWS

    • What is JABAWS?

    -

    JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment programs (see the list of currently supported programs) from Jalview. - However, the scope of JABAWS is not limited to multiple sequence alignment programs. Future versions of JABAWS will incorporate protein disorder prediction, BLAST, PSIBLAST and HMMER database searches and many other tools.

    +

    JABAWS stands for JAva Bioinformatics Analysis Web Services. As the name suggests, JABAWS is a collection of web services for bioinformatics, and currently provides services that make it easy to access well-known multiple sequence alignment and protein disorder prediction programs (see the list of currently supported programs) from Jalview. + Future versions of JABAWS will incorporate many other tools.

    Getting JABAWS

    JABAWS consists of a server and client, but unlike most bioinformatics web service systems, you can download and run both parts on your own computer! If you want a server just for yourself, then download and install the JABAWS Virtual Appliance. It requires no configuration and is simple to install. If you want to install JABAWS for your lab or institution then download the JABAWS Web Application aRchive. It is slightly more complicated to configure but is very straightforward too. Finally, if you want to script against any version of JABAWS or are interested in writing your own client, the JABAWS command line client is what you need.

    JABAWS Benefits

    JABA Web Services Programs

    JABAWS currently provides access to the following programs:

    +

    Multiple Sequence Alignement

    -

    What is JABAWS client?

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    Protein disorder prediction

    + +

    Amino Acid conservation

    + +

    What is new in JABAWS 2?

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    Comparing to previous version of JABAWS JABAWS 2 offers a greater number of diverse web services, Amazon EC 2 integration and improved easy of use. It contains

    + + +

    What is JABAWS client?

    +

    A JABAWS client is a program that lets you run the bioinformatics methods for which a JABAWS server provides web services. The most basic JABAWS client is a command line Java application which can call any of the JABAWS web services methods on any instance of JABAWS Server that it can reach over the web. It is useful if you @@ -86,12 +123,15 @@ specific details. The client is open source, so you can also use its source code out how to work with JABA Web Services if you would like to write your own client software. Jalview, which is a multiple sequence alignment and analysis application, provides a graphical JABAWS client. This client has the same functionality as the command line client, but instead allows JABAWS services to be accessed in a more user-friendly manner, through a graphical user interface.

    +

    JABAWS versions compatibility and Jalview support

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    JABAWS version 2 is fully backward compatible with JABAWS version 1. That means that all JABAWS 1 clients should be able to use JABAWS 2 instead. However, they will be limited to the multiple sequence alignment web services only. To benefit of new web services introduced in JABAWS 2 the clients have to be updated.
    +Jalview since version 2.6.1 integrates fully with JABAWS 1. Therefore it will be possible to use any versions of Jalview after 2.6.1 with JABAWS 1. However, the full support for JABAWS 2 is introduced in Jalview version 2.8 or later.

    Programmatic access to JABAWS

    JABA Web Services are WS-I basic profile compliant, which means they can be accessed using any programming language or system that can utilize standard SOAP web services. The WSDL for each service is published on the JABAWS home page, and you can use this to automatically generate service bindings for your program. If you use Java, however, then you may wish to use our -client package to access JABAWS. +client package to access JABAWS. This package is based on the autogenerated source code produced by wsimport, which is the Java tool for creating web service bindings; but in addition, offers some additional methods which simplify working with JABAWS. For more information please refer to the data model javadoc. @@ -99,7 +139,7 @@ but in addition, offers some additional methods which simplify working with JABA

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