JOSSCast: Open Source for Researchers

Streamlining Molecular Dynamics – Marjan Albooyeh and Chris Jones on FlowerMD

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#6: Marjan Albooyeh and Chris Jones chat with Arfon and Abby about their experience building FlowerMD, an open-source library of recipes for molecular dynamics workflows.

Marjan and Chris are both grad students in Dr. Jankowski’s lab at Boise State University where they use molecular dynamics to study materials for aerospace applications and organic solar cells.

Before joining the lab, Marjan was a machine learning researcher. Chris learned to code when the lab’s glove-box went down and he never looked back.

You can follow them both on GitHub: Marjan @marjanalbooyeh and Chris @chrisjonesBSU.

See the show notes: https://blog.joss.theoj.org/2024/03/josscast-6-streamlining-molecular-dynamics

Episode highlights:

  • [00:00:12] Introduction to FlowerMD and its creators, Marjan Albooyeh and Chris Jones.
  • [00:02:54] Explanation of molecular dynamics simulation process and applications.
  • [00:05:10] Insights into FlowerMD's development process and design goals.
  • [00:09:26] Target audience for FlowerMD and its usability for researchers.
  • [00:11:30] Importance of reproducibility in research facilitated by FlowerMD.
  • [00:16:18] Challenges faced building FlowerMD.
  • [00:19:52] Experiences with the JOSS review process.
  • [00:22:39] Contribute to FlowerMD!
  • [00:24:08] Future plans for FlowerMD and building a research community.

    • Links:

    • JOSS paper: https://joss.theoj.org/papers/10.21105/joss.05989
    • FlowerMD repository: https://github.com/cmelab/flowerMD
    • Chris Jones's GitHub profile: @chrisjonesBSU
    • Marjan Albooyeh's GitHub profile: @marjanalbooyeh
    • The Journal of Open Source Software (Twitter/X, blog)
    • @arfon on (fosstodon, Linkedin, GitHub, website)
    • @abbycabs on (Twitter/X, hachyderm, bsky, Linkedin, GitHub, website)
    • Donate to JOSS

      • See the show notes: https://blog.joss.theoj.org/2024/03/josscast-6-streamlining-molecular-dynamics


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      Supercharge your research with the latest scientific software showcased in the Journal of Open Source Software (JOSS). Hear directly from authors on their work, their motivations, and new ways open source software can accelerate your work.

      Hosted by editor-in-chief Arfon Smith and founding editor Abby Cabunoc Mayes, each episode features an interview with different authors of published papers in JOSS. Tune in to learn about the latest developments in research software engineering and open science, and how they are changing the way research is conducted.

      New episodes every other Thursday.

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      JOSSCast: Open Source for ResearchersBy The Journal of Open Source Software