Events News Research CBS CBS Publications Bioinformatics
Staff Contact About Internal CBS CBS Other

NetGlycate 1.0.ws0

Template service

NOTE: a newer version of this service (NetGlycate 1.0.ws1) is available.

WSDL NetGlycate/NetGlycate_1_0_ws0.wsdl
Schema definitions ../common/ws_common_1_0b.xsd
ws_netglycate_1_0_ws0.xsd

We recommend that the first time users should load the WSDL file above to SoapUI and investigate the Web Service operations in that environment. SoapUI is a desktop application for inspecting, invoking, developing and functional/load/compliance testing of Web Services over HTTP. It can be downloaded free of charge from http://www.soapui.org/.

Other versions and implementations

Ver.Last updated
1.0.ws1  2012-04-20(most recent)
1.0.ws0  2009-07-07(this version)
1.0  2006-09-26

Examples of client side scripts using the service

FilenameTypeCompatibilityAuthorDescription
netglycate.pl (3.8 KB) Perl 1.0 ws0 Edita Bartaseviciute
This script runs the NetGlycate 1.0.ws0 Web Service. It reads a FASTA file from STDIN and produces predictions in a simple table.
netglycate_soap_analysis (8.3 KB) 1.0 ws1 Karunakar Bayyapu
Detailed analysis of SOAP and WSDL versions with supported clients
netglycate_perl2 (5.5 KB) Perl 1.0 ws1 Karunakar Bayyapu
Client script in Perl (XML::Compile) running the NetGlycate Web Service
netglycate_perl1 (5.6 KB) Perl 1.0 ws1 Karunakar Bayyapu
Client script in Perl (SOAP::Lite) running the NetGlycate Web Service
test_netglycate.pl (4.4 KB) Perl 1.0 ws0 Edita Bartaseviciute
This script runs the NetGlycate 1.0.ws0 Web Service. It requires no input; to be used for testing in the EMBRACE WS Registry.
netglycate_python (4.9 KB) Python 1.0 ws1 Karunakar Bayyapu
Client script in Python (suds) running the NetGlycate Web Service
example.fsa (1.3 KB)
netglycate_java (6.5 KB) Java 1.0 ws1 Karunakar Bayyapu
Client script in Java (apache) running the NetGlycate Web Service
xml-compile.pl (1.9 KB) Perl NA Peter Fischer Hallin
Helper scripts used to initiate XML::Compile's proxys (WSDL+XSD)
netglycate_php (4.6 KB) PHP 1.0 ws1 Karunakar Bayyapu
Client script in PHP running the NetGlycate Web Service
netglycate_csharp (5.5 KB) C# 1.0 ws1 Karunakar Bayyapu
Client script in C# (mono) running the NetGlycate Web Service

Usage

# download the required scripts
wget http://www.cbs.dtu.dk/ws/NetGlycate/examples/xml-compile.pl
wget http://www.cbs.dtu.dk/ws/NetGlycate/examples/netglycate.pl

perl netglycate.pl [-g] < example.fsa 

Documentation

      INTRODUCTION

      This Web Service implements NetGlycate v. 1.0.ws0. It predicts glycation of
      Epsilon amino groups of lysines in mammalian proteins. The method
      is described in detail in the following article:

      Analysis and prediction of mammalian protein glycation.
      Morten Bo Johansen, Lars Kiemer and Soren Brunak
      Glycobiology, 16:844-853, 2006.

      Alongside this Web Service the NetGlycate method is also implemented as
      a traditional paste-and-click WWW server at:

          http://www.cbs.dtu.dk/services/NetGlycate/
          
      The traditional server offers extended functionality and comprehensive 
      documentation. It is suitable for close investigation of few proteins; 
      this service is recommended for high throughput projects.

      WEB SERVICE OPERATION

      This Web Service is fully asynchronous; the usage is split into the
      following three operations:

      1. runService    

         Input:  The following parameters and data
         
                 *  'graph'            Generate  graphics,  plotting  the  score reported 
                                       for each lysine residue against the sequence
                                       position of that residue (no value, just presence/absence).
                                       One GIF file is generated for each sequence;


                
                 *  'sequencedata'       mulitple elements of type 'sequence':
                       * 'sequence'         answers to one sequence:
                          * 'id'              unique identifier for the sequence;
                          * 'comment'         optional comment;
                          * 'seq'             protein sequence. The sequence must be written 
                                              using the one letter amino acid code:
                                              `acdefghiklmnpqrstvwy' or `ACDEFGHIKLMNPQRSTVWY'.
                                              Other letters will be converted to `X' and treated
                                              as unknown amino acids. Other symbols, 
                                              such as whitespace and numbers, will be ignored.

   
         Output: Unique job identifier

      2. pollQueue

         Input:  Unique job identifier

         Output: 'jobstatus' - the status of the job
                 Possible values are QUEUED, ACTIVE, FINISHED, WAITING,
                 REJECTED, UNKNOWN JOBID or QUEUE DOWN

      3. fetchResult

         Input:  Unique job identifier of a FINISHED job

         Output:  *  'anndata'
                       'annsource'
                         'method'              name of the method, here always 'NetGlycate';
                         'version'             version of the method: here always '1.0 ws0';

                       'ann'                 annotations - one element per input sequence;
                         'sequence'            standard sequence object;
                           'id'                  sequence identifier;
                         'annrecords/annrecord'
                           'feature'             feature name, here always 'glycate';
                           'pos'                 always present, indicates sequence residue;                       
                           'score'
                             'key'                 score key name, here always 'main', indicating the main prediction score;
                             'value'               prediction score value, if above 0 the residue
                                                   is a predicted glycation site, the higher
                                                   the score the more secure the prediction;                  
                           'comment'             appears only when the score is above 0, contains the word 'YES'.  
                     
                    *  'image'
                         'comment'             name of the image;
                         'encoding'            encoding of the binary content of the image (base64);
                         'MIMEtype'            file type (image/gif);
                         'content'             encoded binary content;            
    
      CONTACT

      Questions concerning the scientific aspects of the NetGlycate method
      should go to Morten Bo Johansen, mbj@cbs.dtu.dk; technical questions
      concerning the Web Service should go to Edita Bartaseviciute,
      edita@cbs.dtu.dk or Kristoffer Rapacki, rapacki@cbs.dtu.dk.