Vision Based Scalable Workflow Development using Web Services

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Vision Based Scalable Workflow Development using
Web Services

• Jane Ren

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Overview

• Introduction to Using Web Services with Vision
• ADT Library Nodes
• Virtual Screening Workflow
• Things to Know about Vision
• 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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Mac Users

• Make sure your Keyboard Mouse settings are
  configure this way, so that your mouse can act
  like a Windows mouse.
• Apple -gt System Preferences -gt Keyboard Mouse

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Loading Web Services Library
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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 of the web services
from http//ws.nbcr.net
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ws.nbcr.net Web Services

• The web services you just loaded are exactly the
  same as the ones on http//ws.nbcr.net.
• http//ws.nbcr.net/opal2/GetServicesList.do

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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 Steps
• Run 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 runs PDB2QR web service.
Macro that runs PrepareReceptor web service
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PrepareReceptor Web Service

• Open the PrepareReceptor parameter panel
• Click on PrepareReceptor
• Click on PrepareReceptorWS
• Double 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?titleVirt
  ual_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
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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.

Tarball of Autogrid results. This can be a URL
also.
Ligand library name
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
URL to Autodock virtual screening results
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Inside the VirtualScreening Node
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Using Vision

• Types
• By 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 Toggle
• By 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 dont 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.

This node will be highlighted for a couple of
seconds.
Type the node here
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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
ligand library name
Input - path to PDB file
GPF template
DPF template
URL to Autodock virtual screening results
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Exercise - Building a Simple PDB2PQR Macro

• Edit --gt Create Macro
• Use PDB2PQR as macro name
• Drag Pdb2pqrOpalService_ws_nbcr_net node to the
  macro.

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Exercise - Building a Simple PDB2PQR Macro

• 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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Exercise - Building a Simple PDB2PQR Macro

• 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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Exercise - Building a Simple PDB2PQR Macro

• 4. Add an input file in the main network

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Exercise - Building a Simple PDB2PQR Macro

• Try the Web Browser Node

macro
Open the URL in default web browser
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Saving PDB2PQR Macro
Right Click
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Saving the Macro

• In MyDefaultLib
• /.mgltools/1.5.6/Vision/UserLibs/MyDefaultLib/Mac
  ro
• In ADT Lib
• mgl_install/1.5.6/MGLToolsPckgs/AutoDockTools/Vis
  ionInterface/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/

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Building NAMD Workflow

• Mirume runs NAMD on teragrid

Number of processors
namd command
All input files
Open stdout.txt in Web browser
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GetInputFiles Macro Node
Get absolute path
Get all inputs from this directory
Make this files a list
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Useful Links

• MGLTools Home page
• http//mgltools.scripps.edu/
• MGL Rocks roll documentation
• http//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?titleNBCR
  _Summer_Institute_2009
• See section 1.7.4