X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=website%2Findex.html;h=47a9c37537782d2ca4d8bd3f855b98477c9c24e3;hb=6648d48e760ddfd676aaadd10a0bc15fb60f71b0;hp=b83b96f8426172e752b7e6341b19592ee4f60cfd;hpb=cfbceac612220d0a877942f7fb6658a5848d1ccf;p=jabaws.git diff --git a/website/index.html b/website/index.html index b83b96f..47a9c37 100644 --- a/website/index.html +++ b/website/index.html @@ -5,6 +5,7 @@ + Java Bioinformatics Analyses Web Services (JABAWS) main page
Home Manual How To Download Jalview +href="manual.html">Manual How To +Javadoc +Download Barton Group
@@ -51,11 +52,9 @@ collection of SOAP web services for bioinformatics.
JABAWS is designed to make it easy to access bioinformatics -analysis programs over the web, by providing web services, which -make it easy to access programs and databases from anywhere, at -anytime. The flavour of web services that JABAWS provides are SOAP -web services, which are designed for use by other programs, rather -than people.
+analysis programs and databases over the web from anywhere, at +anytime. Unlike other web services, JABAWS can be easily installed on different platforms and work straight out of the box with minimum configuration. JABA Web Services are designed for use by other programs rather +than people. The current version of JABAWS is compatible with version 2.6 of Jalview, and provides five web services for multiple sequence alignment:

@@ -77,86 +76,13 @@ TCOFFEE

Why JABAWS?

-

JABA Web Services has a number of distinct features that are not -found in other bioinformatics web services systems. In particular, -JABAWS:

- -
    -
  1. Provides uniform remote access to a number of command line -tools This allows you to access a number of -programs anywhere, at any time. For instance, all multiple sequence -alignment services can be accessed with a single command line -interface, simplifying their invocation. However, most of the -command line options for each program are supported, so you have -nearly the same level of control as if you were running them on the -command line yourself.
    2. - -
  2. Enables web based or stand-alone applications, like Jalview, to -access a variety of bioinformatics analysis methods The java web service client library makes it very easy to -connect to one or more instances of JABAWS, so if one server is off -line, all you need to know is the URL of another server that will -do the job for you.
    -JABAWS provides WS-I basic -profile v. 1.1 compatible services, which means that clients -can be created for them in almost any programming -language.
    3. - -
  3. Can be easily deployed as a server on a variety of platforms, -with command line tools run on the same machine or on a -cluster.JABAWS -integrates with a number of cluster job management systems (e.g. -GridEngine, PBS, LSF, Condor). It also intelligently manages -task scheduling depending on their size, eliminatng the scalability -issues and let you focus on your research.
    4. -
- -

Here are just some of the problems that JABAWS can solve:

- - - -

Public JABAWS Server

- +

JABAWS can be deployed on nearly any operation system, it can operate on a stand alone server as well as submit the jobs to the cluster. Thanks to DRMAA it integrates well with a large variety of cluster job management systems. Jalview from version 2.6 integrates with JABAWS and can be configured to submit jobs to different versions of JABAWS, for example to your local, lab version, or publicly available version elsewhere. As JABAWS can be installed in your lab, or indeed on your personal computer, it eliminates the need to send your private information to the outside, to one of the publicly accessible servers. JABAWS can run programs with additional parameters defined by you, so you are no longer limited to defaults. JABAWS is safe to install for public access as it could limit the size of the tasks which it accepts and denies access to resources within web application folder. Please look in the how to for more information on JABAWS benefits.

+

Public JABAWS Server

- - + + @@ -168,8 +94,7 @@ cluster, which is straightforward.

-
FeatureDescriptionFeatureDescription
Execution limitsLocal execution limit is 40 sequnces with no more than 500 -letters average length. Larger tasks are send to the College of +JABAWS installation is backed up by the College of Life Sciences HPC cluster. Tasks exceeding 1000×1000 (sequences per letters) will not be accepted for alignment. If you would like to work with bigger alignments consider installing @@ -185,8 +110,8 @@ title="http://www.compbio.dundee.ac.uk/jabaws/ClustalWS?" rel=
+For programmatic access to JABAWS please refer to the How To section using JABAWS in your program.

Authors

-

Peter Troshin and Geoff Barton are the authors of the JABA Web Services. Jim Procter helped with the JABAWS design process and web pages, and developed the interface and management components in @@ -194,7 +119,7 @@ Jalview to access JABAWS servers.

-