Simple Modeller Public API


Jobs can be submitted programmatically via the RESTful URI at:

http://bioinf.cs.ucl.ac.uk/simple_modeller/

For automated submissions you must have the following three parameters set

  • name - a name for your incoming job
  • modeller - your valid modeller key
  • pir - Your seed alignment in PIR format
  • template - Your pdb template structure.

At the moment simple_modeller will accept only a single template structure. Data should be submitted in a multipart manner by an appropriate useragent. The script attached shows how to submit jobs in perl.

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/simple_modeller/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 successfully 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 returned URI to retrieve the results, or do something else given the return status. Submitting the URI will return an xml file called results_response.xml, here is an example:

<?xml version="1.0"?>
<bioserf_response>
<result>1</result>
<message>http://bioinf.cs.ucl.ac.uk/simple_modeller/result/6625</message>
</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. Message tag contains the URI needed to retrieve the model structure in pdb format.
  • 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 30 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 and DoSing the server.

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Kind Attachment Name Size Version Date Modified Author Change note
pl
job_submitter.pl 0.7 kB 1 02-Oct-2009 18:39 bugf
« This page (revision-1) was last changed on 16-Feb-2011 15:19 by UnknownAuthor