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From Sandra Gesing <sandra.ges...@nd.edu>
Subject Re: GSoC Proposal: In-Situ Molecular Dynamics Data Analysis
Date Mon, 21 Mar 2016 21:05:04 GMT
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 in.

Thanks,
Sandra

------------------------------------------------------------------------------------------------------------
Sandra Gesing
Research Assistant Professor, Department of Computer Science and Engineering
Computational Scientist, Center for Research Computing
University of Notre Dame
http://www3.nd.edu/~sgesing
------------------------------------------------------------------------------------------------------------

On Sat, Mar 19, 2016 at 6:38 PM, Jeffery Kinnison <
Jeffery.D.Kinnison.1@nd.edu> wrote:

> 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 (http://openmm.org/) and the MDTraj analysis
> framework (http://mdtraj.org). 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 <https://folding.stanford.edu/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.
>
> Best,
> Jeff Kinnison
>
>
>
>
>

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