Using Bioapp

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Introduction to Opal Services

Bioapp-use-services.png

After a successful configuration the VM is running and is accessible on the internet. Point your browser to
http://YOUR-VM-FQDN/opal2/dashboard?command=serviceList
You should see a page with an Opal Dashboard similar to the picture on the right. The Dashboard enables one to use applications that are deployed on the server as a web services.

The left column of the page presents names of the available services, and the right column lists WSDL URLs for programmatic access to the same services. For the web access we do not use WSDL URLs, they are here for information only.

A service can be used by clicking on its name which opens a submission form with entries. On the submission form all required entries are labeled and where appropriate all default parameters are set. More information about input parameters can be obtained by clicking on Show/Hide help link on each service form

The next few sections provide a short tutorial for using each service.

VM Opal Services

Autogrid

This service calculates the map grids that can be used by autodock service. It requires 3 inputs:
1. grid parameter file name
2 log file name (a string of alphanumeric characters, no spaces)
3. pdbqt input file

Example inputs File:Autogrid-inputs.tar.gz

After the required values are filled in, click on the Submit button (left). This opens aform with submission results and URL where the job results can be viewed (right).

Bioapp-use-autogrid.png
Bioapp-use-autogrid-result.png


Autodock

This service runs autodock on a single receptor and a single ligand using the the map grids that were calculated by autogrid service. It requires 4 inputs:

1. Parameter Filename: diversity00001.dppf
2. Name of log file: alphanumeric
3. Ligand PDBQT file: diversity00001.pdbqt 4. URL where to fetch the MAP file (use autogrid output URL from Autogrid service)
Make sure the URL is accessible and the format is similar to http://your.server/opal-jobs/appautogrid_4.2.31347329645264242412444

Example inputs File:Autodock-inputs.tar.gz

Gromos clustering

coming soon


TrajQR clustering

coming soon


PDB2PQR

coming soon


Prepare Receptor

This service is used to transform a pdb file into a pdbqt file, which can be used for Autogrid.
It takes 1 input which can be specified in one of the 2 ways:

1. either upload PDB file
2. or specify a URL from which to upload pdb file

First, make a choice by selecting a radio button and then fill in a specified field.

Example inputs File:Prep-receptor-inputs.tar.gz

Vina Screening

coming soon