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---
layout: default
permalink: /
---
<section id="home-slider">
<div class="container">
<div class="row">
<div class="main-slider">
<div class="slide-text">
<h1>In Situ Data Analytics for Next Generation Molecular Dynamics Workflows</h1>
</div>
<div id="slide-logo-container">
<div id="slide-logo-inner-container">
<div id="slide-logo-images-container">
<img src="images/slider/logo-q1.png" class="slider-q1" alt="slider image">
<img src="images/slider/logo-q2.png" class="slider-q2" alt="slider image">
<img src="images/slider/logo-q3.png" class="slider-q3" alt="slider image">
<img src="images/slider/logo-q4.png" class="slider-q4" alt="slider image">
</div>
<img src="images/slider/logo-name.png" class="slider-name" alt="slider image">
</div>
</div>
</div>
</div>
</div>
<div class="preloader"><i class="fa fa-sun-o fa-spin"></i></div>
</section>
<!--/#home-slider-->
<section id="services">
<div class="container">
<div id="testimonial-container">
<div class="row">
<h1 class="padding-top bold title text-center">About Analytics4MD</h1>
<div class="text-center" style="padding: 20px">
This project tackles the data challenge of data analysis of molecular dynamics simulations on the
next-generation supercomputers by:
</div>
<div class="col-md-6">
<div class="testimonial">
<div class="media wow scaleIn" data-wow-duration="500ms" data-wow-delay="300ms">
<div class="pull-left" style="margin-right: 10px">
<span class="fa-stack fa-1x">
<i class="fa fa-square fa-stack-2x" style="color: orangered"></i>
<i class="fa fa-angle-double-down fa-stack-1x fa-inverse"></i>
</span>
</div>
<div class="media-body">
<span style="font-size: 18px">Creating new in situ methods</span>
to trace molecular events such as conformational changes, phase transitions, or binding
events in molecular dynamics simulations at runtime by locally reducing knowledge on
high-dimensional molecular organization into a set of relevant structural molecular
properties
</div>
</div>
<div class="media wow scaleIn" data-wow-duration="500ms" data-wow-delay="300ms">
<div class="pull-left" style="margin-right: 10px">
<span class="fa-stack fa-1x">
<i class="fa fa-square fa-stack-2x" style="color: royalblue"></i>
<i class="fa fa-cog fa-stack-1x fa-inverse"></i>
</span>
</div>
<div class="media-body">
<span style="font-size: 18px">Integrating simulation and analytics into complex
workflows</span>
for runtime detection of changes in structural and temporal molecular properties
</div>
</div>
</div>
</div>
<div class="col-md-6">
<div class="testimonial">
<div class="media wow scaleIn" data-wow-duration="500ms" data-wow-delay="300ms">
<div class="pull-left" style="margin-right: 10px">
<span class="fa-stack fa-1x">
<i class="fa fa-square fa-stack-2x" style="color: yellowgreen"></i>
<i class="fa fa-database fa-stack-1x fa-inverse"></i>
</span>
</div>
<div class="media-body">
<span style="font-size: 18px">Designing new data representations and extend unsupervised
machine learning techniques</span>
to accurately and efficiently build an explicit global organization of structural and
temporal molecular properties
</div>
</div>
<div class="media wow scaleIn" data-wow-duration="500ms" data-wow-delay="300ms">
<div class="pull-left" style="margin-right: 10px">
<span class="fa-stack fa-1x">
<i class="fa fa-square fa-stack-2x" style="color: darkslategrey"></i>
<i class="fa fa-graduation-cap fa-stack-1x fa-inverse"></i>
</span>
</div>
<div class="media-body">
<span style="font-size: 18px">Developing new curriculum material, online courses, and
online training material targeting data analytics</span>
</div>
</div>
</div>
</div>
</div>
<div class="text-center" style="padding: 20px">
The project's harnessed knowledge of molecular structures' transformations at runtime can be used
to steer simulations to more promising areas of the simulation space, identify the data that
should be written to congested parallel file systems, and index generated data for retrieval
and post-simulation analysis. Supported by this knowledge, molecular dynamics workflows such as
replica exchange simulations, Markov state models, and the string method with swarms of trajectories
can be executed <i>from the outside</i> (i.e., without reengineering the molecular dynamics
code)
</div>
</div><!--/#testimonial-container-->
</div>
</section>
<section id="software">
<div class="container">
<div class="row">
<div class="col-lg-12 padding-top wow fadeInLeft" data-wow-duration="1000ms" data-wow-delay="300ms">
<h1 class="bold title text-center">Get the A4MD Software</h1>
<div class="text-center" style="padding: 20px">
Download A4MD software here: <a href="https://github.com/Analytics4MD/A4MD">Github Repository</a>
</div>
</div>
</div>
</div>
</section>
<section id="publications">
<div class="container">
<div class="row">
<div class="col-lg-12 padding-top wow fadeInLeft" data-wow-duration="1000ms" data-wow-delay="300ms">
<h1 class="bold title text-center">Selected Publications</h1>
<div class="row" style="padding-top: 20px">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Harshita Sahni, Hector Carrillo-Cabada, Ekaterina Kots, Silvina Caino-Lores, Jack Marquez,
Ewa Deelman, Michel Cuendet Harel Weinstein, Michela Taufer, and Trilce Estrada
<b>Online
Boosted Gaussian Learners for in-situ Detection and Characterization of Protein Folding
States
in Molecular Dynamics Simulations</b>
<i>In Proceedings of the 19th IEEE International Conference
on e-Science (eScience)</i>
(2023).
<!-- <a href="https://scitech.isi.edu/wordpress/wp-content/papercite-data/pdf/do2020iccs.pdf"
target="_blank">[link]</a> -->
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Silvina Caino-Lores, Michel A. Cuendet, Jack Marquez* Trilce Estrada, Ewa Deelman, Harel
Weinstein, and Michela Taufer.
<b>Runtime Steering of Molecular Dynamics Simulations Through
In Situ Analysis and Annotation of Collective Variables</b>
<i>In Proceedings of Platform for Advanced
Scientific Computing (PASC) Conference</i>
(2023).
<!-- <a href="https://ieeexplore.ieee.org/document/8859247/" target="_blank">[link]</a> -->
</div>
</div>
<div class="row" style="padding-top: 20px">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Tu Mai Anh Do, Lo ̈ıc Pottier, Rafael Ferreira da Silva, Silvina Ca ́ıno-Lores, Michela Taufer,
and Ewa Deelman.
<b>Performance Assessment of Ensembles of In Situ Workflows under Re-
source Constraints.</b>
<i>Journal of Concurrency and Computation: Practice and Experience (CCPE).</i>
(2023).
<!-- <a href="https://ieeexplore.ieee.org/document/8859247/" target="_blank">[link]</a> -->
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Silvina Caino-Lores, Michel Cuendet, Trilce Estrada, Ewa Deelman, Harel Weinstein, and Taufer,
Michela.
<b>High-Throughput In-Situ Workflows for Ensemble Molecular Dynamics.</b>
<i>In Proceedings
of the 18th IEEE International Conference on e-Science (eScience)</i>
(2022).
<!-- <a href="https://ieeexplore.ieee.org/document/8859247/" target="_blank">[link]</a> -->
</div>
</div>
<div class="row" style="padding-top: 20px">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Tu Mai Anh Do, Loic Pottier, Rafael Ferreira da Silva, Frederic Suter, Silvina Ca ́ıno-Lores*,
Michela Taufer, and Ewa Deelman.
<b>Co-Scheduling Ensembles of In Situ Workflows.</b>
<i>In Pro-
ceedings of the 17th Workshop on Workflows in Support of Large-Scale Science (WORKS)</i>
(2022).
<!-- <a href="https://scitech.isi.edu/wordpress/wp-content/papercite-data/pdf/do2020iccs.pdf"
target="_blank">[link]</a> -->
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Michela Taufer, Ewa Deelman, Rafael Ferreira da Silva, Trilce Estrada, Mary Hall, and Miron
Livny.
<b>A Roadmap to Robust Science for High-throughput Applications: The Developers’ Per-
spective.</b>
<i>In Proceedings of the IEEE Cluster Conference (CLUSTER)</i>
(2021).
<!-- <a href="https://ieeexplore.ieee.org/document/8859247/" target="_blank">[link]</a> -->
</div>
</div>
<div class="row" style="padding-top: 20px">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Michela Taufer, Ewa Deelman, Rafael Ferreira da Silva, Trilce Estrada, and Mary Hall
<b>A
Roadmap to Robust Science for High-throughput Applications: The Scientists’ Perspective.</b>
<i>In
Proceedings of the 20th IEEE International Conference on eScience</i>
(2021).
<!-- <a href="https://scitech.isi.edu/wordpress/wp-content/papercite-data/pdf/do2020iccs.pdf"
target="_blank">[link]</a> -->
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Tu Mai Anh Do, Lo ̈ıc Pottier, Silvina Ca ́ıno-Lores, Rafael Ferreira da Silva, Michel A. Cuen-
det, Harel Weinstein, Trilce Estrada, Michela Taufer, and Ewa Deelman.
<b>A Lightweight
Method for Evaluating in situ Workflow Efficiency</b>
<i>J. Comput. Sci. Elsevier</i>
(2021).
<!-- <a href="https://scitech.isi.edu/wordpress/wp-content/papercite-data/pdf/do2020iccs.pdf"
target="_blank">[link]</a> -->
</div>
</div>
<div class="row" style="padding-top: 20px">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Hector Carrillo-Cabada, Jeremy Benson, Asghar Razavi, Brianna Mulligan, Michel A. Cuendet, Harel
Weinstein, Michela Taufer, and Trilce Estrada.
<b>A Graphic Encoding Method for Quantitative Classification of Protein Structure and
Representation of Conformational Changes</b>
<i>IEEE/ACM Transactions on Computational Biology and Bioinformatics (IEEE/ACM TCBC).</i>
(2020).
<a href="https://ieeexplore.ieee.org/document/8859247/" target="_blank">[link]</a>
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Tu Mai Anh Do, Loic Pottier, Stephen Thomas, Rafael Ferreira da Silva, Michel A. Cuendet, Harel
Weinstein, Trilce Estrada, Michela Taufer, and Ewa Deelman.
<b>A Novel Metric to Evaluate In Situ Workflows</b>
<i>In Proceedings of the International Conference on Computational Science (ICCS), pp. 1 –
14.</i>
(2020).
<a href="https://scitech.isi.edu/wordpress/wp-content/papercite-data/pdf/do2020iccs.pdf"
target="_blank">[link]</a>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Michela Taufer, Trilce Estrada, and Travis Johnston.
<b>A Survey of Algorithms for Transforming Molecular Dynamics Data into Metadata for In Situ
Analytics based on Machine Learning Methods</b>
<i>Issue of Philosophical Transactions A., 378(2166):1-11.</i>
(2020).
<a href="https://royalsocietypublishing.org/doi/full/10.1098/rsta.2019.0063"
target="_blank">[link]</a>
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Michela Taufer, Stephen Thomas, Michael Wyatt, Tu Mai Anh Do, Loïc Pottier, Rafael Ferreira da
Silva, Harel Weinstein, Michel A. Cuendet, Trilce Estrada, and Ewa Deelman.
<b>Characterization of In Situ and In Transit Analytics of Molecular Dynamics Simulations for
Next-generation Supercomputers</b>
<i>In Proceedings of the IEEE eScience Conference, pp.1-12.</i>
(2019).
<a href="https://ieeexplore.ieee.org/document/9041757" target="_blank">[link]</a>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Trilce Estrada, Jeremy Benson, Hector Carrillo-Cabada, Asghar M. Razavi, Michel A. Cuendet,
Harel Weinstein, Ewa Deelman, and Michela Taufer.
<b>Graphic Encoding of Proteins for Efficient High-Throughput Analysis</b>
<i> In Proceedings of the 9th ACM Conference on Bioinformatics, BCB, pp. 315 – 324. Washington,
DC, USA. August 29 - September 1. </i>
(2018).
<a href="https://dl.acm.org/doi/pdf/10.1145/3233547.3233607" target="_blank">[link]</a>
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Rafael Ferreira da Silva, Scott Callaghan, Tu Mai Anh Do, George Papadimitriou, and Ewa Deelman.
<b>Measuring the Impact of Burst Buffers on Data-Intensive Scientific Workflows</b>
<i>Future Generation Computer Systems, 101, 208-220 (2019).</i>
<a href="http://dx.doi.org/10.1016/j.future.2019.06.016" target="_blank">[link]</a>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Asghar M. Razavi, George Khelashvili, and Harel Weinstein.
<b>A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine
Transporter</b>
<i>Scientific Reports, 7</i>
(2017).
<a href="https://www.nature.com/articles/srep40076" target="_blank">[link]</a>
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Rafael Ferreira da Silva, Rosa Filgueira, Lia Pietri, Ming Jiang, Rizos Sakellariou, Ewa
Deelman.
<b>A Characterization of Workflow Management Systems for Extreme-scale Applications</b>
<i>Future Generation Computer Systems, 75,</i>
228-238 (2017).
<a href="http://www.sciencedirect.com/science/article/pii/S0167739X17302510">[link]</a>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer.
<b>In situ data analytics and indexing of protein trajectories.</b>
<i>Journal of Computational Chemistry, 38</i>
(16), 1419-1430, (2017).
<a href="https://www.ncbi.nlm.nih.gov/pubmed/28093787" target="_blank">[link]</a>
</div>
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Michel A. Cuendet, Harel Weinstein, and Michael V. LeVine.
<b>The Allostery Landscape: Quantifying Thermodynamic Couplings in Biomolecular Systems</b>
<i>Journal of Chemical Theory and Computation, 12</i>
(12), 5758-5767, (2016).
<a href="http://pubs.acs.org/doi/abs/10.1021/acs.jctc.6b00841" target="_blank">[link]</a>
</div>
</div>
<div class="row">
<div class="col-xs-12 col-sm-6 publication">
<i class="fa fa-file-text-o"></i>
Travis Johnston, Boyu Zhang, Adam Liwo, Silvia Crivelli, Michela Taufer.
<b>In-Situ Data Analysis of Protein Folding Trajectories.</b>
<i>arXiv:1510.08789,</i>
(2015).
<a href="https://arxiv.org/abs/1510.08789" target="_blank">[link]</a>
</div>
</div>
</div>
</div>
</div>
</section>
<section id="team">
<div class="container">
<div id="team-carousel" class="carousel slide wow fadeIn" data-ride="carousel" data-wow-duration="400ms"
data-wow-delay="400ms">
<div class="row padding-top">
<h1 class="title text-center wow fadeInDown" data-wow-duration="500ms" data-wow-delay="300ms">Meet the
Team</h1>
<p class="text-center wow fadeInDown" data-wow-duration="400ms" data-wow-delay="400ms">Analytics4MD is a
collaborative effort between the University of Delaware, the University of Southern California, and
the Joan and Sanford I. Weill Medical College of Cornell University.</p>
<div class="col-sm-2 col-xs-6">
<div class="team-single-wrapper">
<div class="team-single">
<div class="person-thumb">
<img src="images/about/taufer.jpg" class="img-responsive" alt="">
</div>
<div class="social-profile">
<ul class="nav nav-pills">
<li><a href="mailto:mtaufer@utk.edu"><i class="fa fa-envelope"></i></a></li>
<li><a href="https://www.eecs.utk.edu/people/faculty/dr-michela-taufer/"
target="_blank"><i class="fa fa-link"></i></a></li>
</ul>
</div>
</div>
<div class="person-info">
<h2>Michela Taufer</h2>
<p><strong style="color: #666">PI.</strong> Professor in the Department of Electrical
Engineering & Computer Science at University of Tennessee Knoxville</p>
</div>
</div>
</div>
<div class="col-sm-2 col-xs-6">
<div class="team-single-wrapper">
<div class="team-single">
<div class="person-thumb">
<img src="images/about/deelman.png" class="img-responsive" alt="">
</div>
<div class="social-profile">
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<li><a href="mailto:deelman@isi.edu"><i class="fa fa-envelope"></i></a></li>
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<h2>Ewa Deelman</h2>
<p><strong style="color: #666">Co-PI.</strong> Research Professor in the Computer Science
Department at University of
Southern California</p>
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<h2>Rafael Ferreira da Silva</h2>
<p><strong style="color: #666">Co-PI.</strong> Research Assistant Professor in the Computer
Science Department at University of
Southern California</p>
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<h2>Harel Weinstein</h2>
<p><strong style="color: #666">Co-PI.</strong> Director of the Institute for Computational
Biomedicine at Weill Cornell Medical
College of Cornell University</p>
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<h2>Michel Cuendet</h2>
<p><strong style="color: #666">Co-PI.</strong> Instructor of Computational Biomedicine at
Weill Medical College of Cornell
University</p>
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<h2>Trilce Estrada</h2>
<p><strong style="color: #666">Co-PI.</strong> Assistant Professor in the Computer Science
Department at the University of New
Mexico</p>
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<h2>Travis Johnston</h2>
<p>Research Scientist for AI in HPC</p>
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<h2>Asghar Razavi</h2>
<p>Postdoctoral Associate in Physiology and Biophysics at Weill Cornell Medical
College of Cornell University</p>
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<h2>Loïc Pottier</h2>
<p>Computer Scientist at the University of Southern California</p>
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<h2>Silvina Caino-Lores</h2>
<p>Postdoctoral Research Associate, University of Tennessee, Knoxville</p>
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<h2>Ekaterina Kots</h2>
<p>Postdoctoral Associate, Weill Cornell Medical School</p>
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<h2>Tu Mai Anh Do</h2>
<p>Graduate Research Assistant at the University of Southern California</p>
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<h2>Michael Wyatt</h2>
<p>Research Assistant, University of Tennessee, Knoxville</p>
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<h2>Hector Alexis Carrillo Cabada</h2>
<p>Graduate Research Assistant at the University of New Mexico</p>
</div>
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<h2>Ian Lumsden</h2>
<p>Graduate Research Assistant, University of Tennessee, Knoxville</p>
</div>
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<div class="person-info">
<h2>Jack Marquez</h2>
<p>Research Assistant Professor at University of Tennessee Knoxville</p>
</div>
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<div class="person-info">
<h2>Stephen Thomas</h2>
<p>Post-Doctoral Research Associate at University of Tennessee Knoxville</p>
</div>
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<div class="person-info">
<h2>Harshita Sahni</h2>
<p>Graduate Student at University of New Mexico</p>
</div>
</div>
</div>
</div>
</div>
</div>
</section>
<!--/#team-->