UAB Condor Pilot

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=== Molecular Docking ===
 
=== Molecular Docking ===
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Molecular docking is a process for discovering an ideal orientation between two molecules, the receptor and the ligand.  There are a number of approaches which can be taken to explore how ligand (drug) can bind to a receptor (protein). The approach used in this pilot was a conformational space search using genetic algorithms which  evolve the orientation of the molecules to find the most likely orientation for docking to occur, as implemented by the [http://autodock.scripps.edu/ AutoDock application from The Scripps Research Institute].
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This virtual screening of protein-drug interactions is computationally intense and can incorporate large databases of chemical compounds.  This makes it an ideal candidate for finding as many compute resources as possible to leverage during the screening process. The structure of this workflow using AutoDock analyzes each receptor-ligand pair can independently, making it an ideal candidate for leveraging the loosely couple collection of computers made available through the Condor scheduler.
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Molecular docking is the computational part of a much larger workflow that involves discovery of the protein structure via X-ray crystallography. This process is nicely described in this [hcp://vimeo.com/7643687 video describing X-ray crystallography] at the Institute of Molecular and Cell Biology in Strasbourg, France.  Similar facilities at Argonne National Laboratory are used by researchers at UAB's [http://www3.ccc.uab.edu/index.php?option=com_content&view=article&id=167&Itemid=190 Center for Biophysical Sciences and Engineering] to explore the structure of proteins.
  
 
== Components of Pilot ==
 
== Components of Pilot ==

Revision as of 14:58, 31 May 2012

The UAB Condor Pilot explored the utility to research applications of aggregated unused compute cycles harvested from many computers. The pilot established a demonstration spare-cycle compute fabric using the Condor scheduler and compared the performance of a molecular docking workflow on this fabric and several larger production Condor fabrics to the performance of the same workflow running on our campus compute cluster Cheaha.

The UAB Condor Pilot successfully demonstrated the value of harvested unused compute cycles to the molecular docking workflow. The results suggest that similar applications, especially those that can scale by repeating the same task on distinct data sets, will likewise benefit from the abundant compute resources that can be harvested via a Condor compute fabric. The UAB Condor Pilot ended in May 2012 with the presentation of our results (pdf) at Condor Week 2012.

Contents

Background

Condor

Molecular Docking

Molecular docking is a process for discovering an ideal orientation between two molecules, the receptor and the ligand. There are a number of approaches which can be taken to explore how ligand (drug) can bind to a receptor (protein). The approach used in this pilot was a conformational space search using genetic algorithms which evolve the orientation of the molecules to find the most likely orientation for docking to occur, as implemented by the AutoDock application from The Scripps Research Institute.

This virtual screening of protein-drug interactions is computationally intense and can incorporate large databases of chemical compounds. This makes it an ideal candidate for finding as many compute resources as possible to leverage during the screening process. The structure of this workflow using AutoDock analyzes each receptor-ligand pair can independently, making it an ideal candidate for leveraging the loosely couple collection of computers made available through the Condor scheduler.

Molecular docking is the computational part of a much larger workflow that involves discovery of the protein structure via X-ray crystallography. This process is nicely described in this [hcp://vimeo.com/7643687 video describing X-ray crystallography] at the Institute of Molecular and Cell Biology in Strasbourg, France. Similar facilities at Argonne National Laboratory are used by researchers at UAB's Center for Biophysical Sciences and Engineering to explore the structure of proteins.

Components of Pilot

Condor Testbeds

Autodock Workflow

Participants

Performance Comparison

Conclusions

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