HIVpred XMPP service

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This is an XMPP service that predicts the susceptibility of an HIV protease sequence for seven drugs based on the proteochemometric model described in:

Lapins M, Eklund M, Spjuth O, Prusis P, Wikberg JE. Proteochemometric modeling of HIV protease susceptibility, BMC Bioinformatics. 2008 Apr 10;9:181. .

Prerequisites

You need a Jabber ID to use XMPP services. This can be done with any Jabber client, I use PSI.

Use the hivpred service with the client plugin installed

  • Check out the feature from SVN: se.uu.farmbio.hivpred-feature along with the net.bioclipse.xws4j-feature.
  • Check out the plugins: se.uu.farmbio.hivpred.model and se.uu.farmbio.hivpred.client
  • Run the bioclipse.product with the features (together with net.bioclipse-feature of course)
  • Go to preferences and add your credentials in the XMPP section:
Server=ws1.bmc.uu.se
Jabber ID = your_jabber_id (e.g. user123456@jabber.org)
password = your_registered_password
Resource: Bioclipse
port=5222

Now, in the console, run the commands:

var seq="AAAALWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF";

and then

hivpred.predict(seq)

This should produce the following output:

js> hivpred.predict(seq)
Result: 
	amprenavir: -9.344846031197962
	atazanavir: -8.081778845481008
	indinavir: -8.306376101045098
	lopinavir: -8.789871555954795
	nelfinavir: -7.661361493579009
	ritonavir: -8.108639981136413
	saquinanvir: -8.702355550536716

Mutations not in dataset: P1A, 
Mutations outside model boundaries: Q2A, I3A,

Use the hivpred service with generated binding

The following script is a demonstration how to use the service as a general XMPP service with generated bindings:

The script is available at: http://gist.github.com/47421