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From Jeffery Kinnison <Jeffery.D.Kinniso...@nd.edu>
Subject Re: GSoC Proposal: In-Situ Molecular Dynamics Data Analysis
Date Mon, 21 Mar 2016 21:28:24 GMT
I created it a few minutes ago.

Best,
Jeff K.

On Mon, Mar 21, 2016 at 5:06 PM, Pierce, Marlon <marpierc@iu.edu> wrote:

> HI Jeff,
>
> Please go ahead and start a draft proposal in the GSOC 2016 site.
>
> Thanks,
>
> Marlon
>
> From: Sandra Gesing <sandra.gesing@nd.edu>
> Reply-To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> Date: Monday, March 21, 2016 at 5:05 PM
> To: "dev@airavata.apache.org" <dev@airavata.apache.org>
> 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 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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