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From "Pierce, Marlon" <>
Subject Re: GSoC Proposal: In-Situ Molecular Dynamics Data Analysis
Date Mon, 21 Mar 2016 21:06:31 GMT
HI Jeff,

Please go ahead and start a draft proposal in the GSOC 2016 site.



From: Sandra Gesing <<>>
Reply-To: "<>" <<>>
Date: Monday, March 21, 2016 at 5:05 PM
To: "<>" <<>>
Subject: Re: GSoC Proposal: In-Situ Molecular Dynamics Data Analysis

Dear Jeff,

I have seen that you included in your description also Jupyter as benefit from your project.
Jupyter is planned to come in via a different project but you can leave all the other benefits


Sandra Gesing
Research Assistant Professor, Department of Computer Science and Engineering
Computational Scientist, Center for Research Computing
University of Notre Dame

On Sat, Mar 19, 2016 at 6:38 PM, Jeffery Kinnison <<>>
Good evening,

I have been communicating with Suresh and Marlon about creating a gateway for Molecular Dynamics
(MD) simulation and analysis software, specifically the OpenMM software package (
and the MDTraj analysis framework ( MD studies typically require hundreds
to thousands of independent simulations distributed over a cluster to gather sufficient data,
with simulations running for days, weeks, months, or longer, depending on the size of the
molecule. Because of these considerations, tools are needed for creating and distributing
simulations, monitoring simulations as they run, and performing certain actions as events
occur during simulation.

The goal of this project is to extend Apache Airavata in the following ways:

  *   monitoring running simulations for user-defined events
  *   performing user-defined actions when an event occurs
  *   monitoring system resources
  *   streaming partial simulation results and system resource usage

I have previously collaborated on a piece of software called Folding@Work (named for Folding@Home<>),
which distributes simulations and returns partial results for analysis, which could serve
as a prototype for the functionality described above.

This project is being considered as a Google Summer of Code proposal, and I would appreciate
any comments or suggestions to improve these ideas.

Jeff Kinnison

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