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Paper: Analyzing Particle Systems for Machine Learning and Data Visualization with freud #471

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@bdice
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commented May 22, 2019

This paper introduces applications of the freud particle data analysis library for machine learning and data visualization tasks in computational molecular sciences.

We plan to include a few minor updates to the content and benchmarks/figures following our next release of the package.

Thanks in advance to reviewers!

bdice and others added some commits May 17, 2019

Update 36_bradley_dice.rst
Restructure introduction
Merge pull request #1 from bdice/vyas_intro_rewrite
Update 36_bradley_dice.rst
@stsievert

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commented May 25, 2019

I'll be reviewing this paper! I'm curious to learn more.

(note: http://procbuild.scipy.org/)

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Here's an initial review. It's been interesting to see examples of the software required to analyze and generate figures for particle simulations.

I'm curious on what exactly this software does and what inputs and outputs are required for this software. Most of my review is focused around that, with a couple small style nits.

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@harunaabdu

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commented Jun 11, 2019

In summary, the authors tried in introducing a python library called “freud” for the analysis of particles data from molecular dynamic simulations.

Based on the initial review I made the following points about the paper.

  • The authors are seeming to be excited and expert in using freud python library, and ready to communicate the work with other researchers.
  • The topic is relevant to the conference and will contribute to the body of knowledge with a little modification.
  • The quality of the writing conveys the information that furthers the knowledge or research of the readers, but some little adjustment needs to be made as commented by stsievert.
  • The work has advanced the state of the data visualization in a scientific domain, the practice of scientific computing itself, and another subject area within the scope of the conference.
  • The authors also provide Github link to the complete source code
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commented Jun 11, 2019

Thanks @harunaabdu and @stsievert, I'll apply these suggestions and get back to you soon!

bdice added some commits Jun 19, 2019

Merge pull request #5 from bdice/reviewer_comments
Additional code comments.
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commented Jun 19, 2019

@stsievert @harunaabdu Thanks again for your review. We have applied the changes you suggested and some edits suggested by coauthors on the paper.

We considered the data flow figure you mentioned, @stsievert - we revised that text instead, which may clarify the concept enough. Let us know if we should still consider adding a figure there.

bdice added some commits Jun 21, 2019

Merge pull request #6 from bdice/reviewer_comments2
Address additional comments.
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commented Jun 22, 2019

@bdice feel free to @ your reviewers when you feel this is ready for a second look 😄

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commented Jun 23, 2019

@stsievert @harunaabdu - this is ready for a second look when you're able. Thanks! 👍

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commented Jun 23, 2019

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