BioSerf Public API


Jobs can be submitted via the RESTful URI as follows:

http://bioinf.cs.ucl.ac.uk/bio_serf/public_submission?name=<YOUR NAME HERE>&sequence=<YOUR SEQUENCE HERE>&xml=1&modeller=<YOUR MODELLER KEY HERE>

For automated submissions you must have the following three parameters set

  • name - a name for your incoming job
  • sequence - the sequence you are submitting (must be longer than 20 residues)
  • xml - must be set to 1 to indicate that you require an xml based response. You will get an html response otherwise.
  • modeller - You must provide valid modeller licence key

assuming all goes to plan you will be returned an xml file called submission_respnose.xml. Here is an example:

<?xml version="1.0"?>
<bioserf_response>
<submitted>1</submitted>
<message>http://bioinf.cs.ucl.ac.uk/bio_serf/public_result/116.xml</message>
</bioserf_response>

The submitted tag gives the state that the server returned for your job submission, there are 3 possible states. The message tag returns the appropriate message paired to the appropriate submission state

  • 1 - job was succesful submitted. Message tag will contain the URI for the results
  • 0 - job submission failed. Message tag contains a human readable descriptor.
  • 2 - Modeller licence key invalid

You can then use the given URI to retrieve the results or poll the job state. Submitting that URI will return an xml file called results_response.xml, here is an example:

<?xml version="1.0"?>
<bioserf_response>
<result>1</result>
<message>Your bioserf job compelted succesfully</message>
<results>
<pdbfile>http://bioinf.cs.ucl.ac.uk/bio_serf/getresultattached/6625</pdbfile>
<blasttemplates>http://bioinf.cs.ucl.ac.uk/bio_serf/getresultattached/6610</blasttemplates>
<pgentemplates>http://bioinf.cs.ucl.ac.uk/bio_serf/getresultattached/6615</pgentemplates>
<selectedtemplates>http://bioinf.cs.ucl.ac.uk/bio_serf/getresultattached/6620</selectedtemplates>
</results>
</bioserf_response>

The result tag gives you the result state the job is in and the message tag gives you the appropriate message associated to that results state. There are 3 result states

  • 0 - job has stopped in an error state, Message tag contains a human readable message
  • 1 - job has completed. Results tag will contain the URIs needed to retrieve the model structure, the putative psiblast templates, the putative pGenTHREADER templates and the final selected templates.
  • 2 - job is still being processed. Message tag contains a human readable message
  • 3 - No job with that ID is available. Message tag contains a human readable message

In an automated system you can now use this URI to poll the server until your job completes or enters an error state. Run time for modeller is typically below 5 seconds but large jobs can take some time, we recommend that you only poll the server a maximum of once every 5 minutes. If you are running many, many jobs please try and stagger your polling attempts, rather than hitting the server with many, many progress requests at once.

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« This page (revision-1) was last changed on 02-Nov-2011 17:06 by UnknownAuthor