Vision Based Scalable Workflow Development using Web Services

Vision Based Scalable Workflow Development

using Web Services

Jane Ren

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Overview

Introduction to Using Web Services with VisionADT Library NodesVirtual Screening WorkflowThings to Know about VisionHands On Exercises

Using PrepareReceptor from Adt libRunning virtual screening workflowUsing VirtualScreening from Adt libBuilding PDB2PQR macro / library nodeBuilding Autodock workflowBuilidng NAMD workflow

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Mac Users…Make sure your Keyboard & Mouse settings are configure this way, so that your mouse can act like a Windows mouse.

Apple -> System Preferences… -> Keyboard & Mouse

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Loading Web Services Library

QuickTime™ and a decompressor

are needed to see this picture.

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Loading ws.nbcr.net Web Services



After loading the ws library, the new nodes for Web Services appear here.

These are some ofthe web services from

http://ws.nbcr.net

http://ws.nbcr.net/

http://ws.nbcr.net/

http://ws.nbcr.net/

http://ws.nbcr.net/

http://ws.nbcr.net/

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ws.nbcr.net Web ServicesThe web services you just loaded are exactly the same as the ones on http://ws.nbcr.net.

http://ws.nbcr.net/opal2/GetServicesList.do



http://ws.nbcr.net/

http://ws.nbcr.net/

http://ws.nbcr.net/

http://ws.nbcr.net/

http://ws.nbcr.net/

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Loading the ADT Library

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ADT Library Nodes for Virtual Screening

New Adt lib nodes appeared

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ADT Lib Node documentation

You can put your cursor over a node to see its documentation.

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PrepareReceptor Node

The PrepareReceptor node creates the PDBQT file based on the input PDB file.



Input - path to PDB file

Output - PDBQT file (can be URL or local path)

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Inside PrepareReceptor Node

Two Major StepsRun PDB2PQR web service.

This step is skipped if an appropriate PQR file exists on the local machine.

Run PrepareReceptor web service.

Output is URL to PDBQT

PDB2PQR and PrepareReceptor are skipped if an appropriate PDBQT file exists on the local machine.

Output is PDBQT path on local machine.

Macro that runsPDB2QR web service.

Macro that runsPrepareReceptor

web service

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PrepareReceptor Web ServiceOpen the PrepareReceptor parameter panel

Click on PrepareReceptorClick on PrepareReceptorWSDouble click on PrepareReceptorOpalService_ws_nbcr_net

Parameter C (preserve all input charges. ie do not add new charges, default is gasteiger charges) is NOT checked by default with MGL Tools release 1.5.6 revision 32. This may change in the next MGLTools release.

The previous PDB2PQR step is used to add hydrogen charges.You should check/Uncheck this option based on your needs.



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ComputeGrids Node



ComputeGrids prepare sthe GPF with the ligand library and then runs the Autogrid web service.

https://www.nbcr.net/pub/wiki/index.php?title=Virtual_Screening_Libraries

contains information about the current ligand libraries on kryptonite.nbcr.net.

ligand library name Receptor PDBQT file GPF template

URL to Autogrid results

https://www.nbcr.net/pub/wiki/index.php?title=Virtual_Screening_Libraries

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Inside ComputeGrids Node

Check if GPF template path is valid.

Exit if not

Run PrepareGPF web service based on the template GPF.

Run Autogrid web service

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AutodockVS Node



Run Autodock virtual screening with the ligand library.

Ligand library nameTarball of Autogrid results.This can be a URL also. DPF template

URL to Autodock virtual screening results

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Inside AutodockVS Node

Check if DPF template path is valid.

If not, then exit

Run Autodock virtual screening web service.

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Virtual Screening Node



This VirtualScreening node runs the entire virtual screening experiment. It is simply a combination of PrepareReceptor, ComputeGrids, and AutodockVS.

Ligand library name Input - path to PDB file GPF template DPF template


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Inside the VirtualScreening Node

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Using Vision

TypesBy default, a generic node/macro node port has the type None.It is good practice to change None to a real type such as int or string.

Right click on the port and choose edit. Select a replacement for None from the data type drop down menu.Click on Apply and then OK.



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Using Vision

Immediate Run ToggleBy default, the toggle is turned on. This means you have immediate run behavior.

If you change the input of a node. Then the node may start running automatically before you click on the run button.

You can turn the toggle off by clicking on the toggle button.

You can also save your network with toggle off Next time your play with your network it will have the immediate run behavior turned off.



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Using Vision

If you don’t know where a node is, then simply type the node name in the search box. The node will be highlighted for a couple of seconds if it is found.



Type the node here

This node will be highlighted for a couple of seconds.

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Using Vision

If the straight lines that are connecting nodes are too hard to see, then spline connections.

Click on Edit

Click on Spline Connections



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Debugging Web Services

You can view the web service log in the Vision terminal. The log may contain helpful URLs.If you do not have a terminal open, then you need to click on the Python IDEL shell icon from ADT or PMV.





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Hands On Exercises

Using PrepareReceptor from Adt lib

Running virtual screening workflow

Using VirtualScreening from Adt lib

Building PDB2PQR macro / library node

Building Autodock workflow

Builidng NAMD workflow

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Exercise - Simple PrepareReceptor



Get File Browser from the Input column in Standard library.Browse a PDB file.

Get PrepareReceptor from Adt library.

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Exercise - Run Entire Virtual Screening Workflow



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Exercise - Play with VirtualScreening



Input - path to PDB file GPF template DPF template


ligand library name

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Exercise - Building a Simple PDB2PQR Macro

Edit --> Create MacroUse PDB2PQR as macro name

Drag Pdb2pqrOpalService_ws_nbcr_net node to the macro.


are needed to see this picture. QuickTime™ and a decompressor


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Double click on the PDB2PQR Web service node

Enter output.pqr as the output_file

Right click on inFile and then click on Unbind Wiget.

This will create an input port for the web service node.



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3. Get the result URL



This will return a list of all URLs, including input PDB, output PQR, stdout.txt, etc.

Get the first URL in the list

Get URL of the directory that Contains all the output files.

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4. Add an input file in the main network



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Try the Web Browser Node


are needed to see this picture.macro

Open the URL in default web browser

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Saving PDB2PQR Macro



Right Click

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Saving the MacroIn MyDefaultLib

~/.mgltools/1.5.6/Vision/UserLibs/MyDefaultLib/Macro

In ADT Lib$mgl_install/1.5.6/MGLToolsPckgs/AutoDockTools/VisionInterface/Adt/Macro



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Exercise: Building Autodock Workflow



Load http://mirume.nbcr.net/opal2 ws first.Mirume uses the CSF scheduler and will run Autodock on multiple hosts.

Input is a URL to the virtual screening files right before the Autodock step.http://kryptonite.nbcr.net/app1249000660642/

http://mirume.nbcr.net/opal2

http://kryptonite.nbcr.net/app1249000660642/

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Building NAMD Workflow



namd command

All input files

Number of processors

Open stdout.txt inWeb browser

Mirume runs NAMD on teragrid

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GetInputFiles Macro Node



Get absolute path

Get all inputs fromthis directory

Make this files a list

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Useful Links

MGLTools Home pagehttp://mgltools.scripps.edu/

MGL Rocks roll documentationhttp://www.nbcr.net/software/doc/mgl-roll/rocks-5.0/

See sections 4.9 and 4.10 for virtual screening documenation

NBCR 09 Summer Institute wiki on virtual screening workflows

https://www.nbcr.net/pub/wiki/index.php?title=NBCR_Summer_Institute_2009

See section 1.7.4

http://mgltools.scripps.edu/

http://www.nbcr.net/software/doc/mgl-roll/rocks-5.0/

https://www.nbcr.net/pub/wiki/index.php?title=NBCR_Summer_Institute_2009

Vision Based Scalable Workflow Development using Web Services

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