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pknotsRG - WebService


This is a short introduction for the pknotsRG WebServices offered by BiBiServ. If you're not familiar with webservices in general, have a closer look at our webservice related linklist.

WSDL - methods, parameters and datatypes

In the WSDL file describing the pknotsRG webservice, there are five methods defined (request,request_orig, response, response_orig and getVersion).

Bioinformatic programs often perform computation on large data sets and therefore require much CPU time. This can cause problems like http connection timeouts (usually after 5 minutes) during online usage. To avoid such problems when using pknotsRG WebService we use a technique called Request and Reply with polling based on BiBiWS. First the client side (e.g. your program) requests a pknotsRG job submitting the necessary data (parameter and data) and gets an id after the job is started. Afterwards, the client can request the result by calling the corresponding response method with the id returned earlier. If the pknotsRG job is not finished, the user gets a status code with an enhanced description of current status back (see HOBIT status codes for more information).
Currently the pknotsRG WebService support two different pairs of request/response methods, request/response using sequenceML as Input and RNAStructML as output format. Both formats are supported by BioDOM. The request_orig/response_orig pair deals with the original data formats (Fasta as Input and a DotBracket Notation as Output).

request/request_orig
The request method get two parameters as input - a parameter array with key/value pairs as described in the following table and a valid sequenceML document (request) or one or more sequences in FASTA format (request_orig) - and returns either a unique id or in case of an error a fault message.

key value description
strategy m,f,l strategy used by pknotsRG
s show suboptimals
c 0.0 ≤ 3.0 set energy range for suboptimals (%)
n positive double value set npp-value
k positive integer value set maximal pknot-length
p positive integer value set pkinit-value
note:
  • all parameters are optional
  • defaults are in bold style

response/response_orig
The response/response_orig methods gets the id returned by the request method as input parameter and returns the calculated result as RNAStructML or in DotBracket notation (Vienna format).

Example clients

We offer two slightly different clients written in Java. pknotsrgCOrig.java uses request_orig/response_orig functions of pknotsRG WebService. pknotsrgC.java works with sequenceML as input and RNAStructML as output and is using request/response. The Java programs needs additional libraries to run/compile:
project download url tested release
Apache AXIS download 1.3
JavaBeans Activation Framework (JAF) download 1.0.2
JavaMail download 1.3.2
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Fri May 3 14:45:58 2013