Keio Bioinformatics Web Services (server side) (version 1.0.1)

All rights reserved. Copyright © 2012 by OSHITA Kazuki

License

This Service is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either or version 2 of the License. See also GNU General Public License Version 2.

About

Keio Bioinformatics Web Service (KBWS) is an EMBASSY (EMBOSS associated software) package for accessing popular bioinformatics web services. As an EMBOSS package, KBWS can be accessed from a number of graphical user interfaces, including EMBOSS Explorer, JEMBOSS, and wEMBOSS.

SOAP interface provides language-independent access to 42 bioinformatics analysis programs. The WSDL file contains descriptions for all available programs in a single file, and can be readily loaded in Taverna 2 workbench to integrate with other services to construct workflows. Example workflows are available at the myExperiment website.

REST interface provides RESTful URL-based access to all analysis programs of KBWS. Here all anallysis resource can be accessed through HTTP GET/POST request.

Project page

http://www.g-language.org/kbws/

WSDL file (SOAP)

• RPC/Encoded : http://soap.g-language.org/kbws.wsdl
• Document/Literal : http://soap.g-language.org/kbws_dl.wsdl

Endpoint (REST)

• http://soap.g-language.org/kbws/rest/

List of available processes

• BioCatalogue web site
• Project page
  • available services, categories, documents, original services, references and quick starts (link to EMBOSS Explorer)

Publication

"KBWS: an EMBOSS associated package for accessing bioinformatics web services", Oshita K, Arakawa K, Tomita M, Source Code Biol. Med., 2011 , 6, 8 (PubMed).

Requirements

• System

  • perl
    • version 5.8.8 or later
  • centroidfold

• Perl module

  • SOAP::Lite
    • version 0.712 or later
  • LWP::UserAgent
  • LWP::Simple
  • HTML::Form
  • JSON
  • MIME::Base64 (for Document/Literal access)
  • BioPerl (for BLAST service)
    • Bio::Tools::Run::RemoteBlast
    • Bio::SearchIO

Usage

In this service, all methods require fasta format sequence data named as 'in0'.

SOAP interface

Users are able to connect to this service via SOAP 1.1 (RPC/Encoded and Document/Literal).

Sample scripts

• Sample codes for accessing via SOAP interface (Perl, Ruby, Python, Java)
  • RPC/Encoded
  • Document/Literal

Taverna workflow

Sample workflow for Taverna 2 is available from here.

REST interface

User are able to access to REST interface through HTTP GET/POST methods.

Available method list is here.

Sample script (Perl)

#!/usr/bin/env perl
use LWP::Simple;
use LWP::UserAgent;

my $ua= LWP::UserAgent->new();
my %param= (in0 => $seq);

my $response= $ua->post('http://soap.g-language.org/kbws/rest/weblogo', \%param);

my $jobid= $response->content();

if ($jobid) {
    print "My Jobid is ",$jobid,"\n";
} else {
    die "Failed calling ".$param{query}.". Server returns undefined jobid ($jobid)\n";
}

my $pollstar= 0;
while (get('http://soap.g-language.org/kbws/rest/checkStatus/'.$jobid) == 0) {
    print '*';
    sleep 3;
}
print "\n" if $pollstar;

print get('http://soap.g-language.org/kbws/rest/getResult/'.$jobid);

Contact

Kazuki Oshita cory@g-language.org
Institute for Advanced Biosciences, Keio University.