Streamlining Molecular Dynamics – Marjan Albooyeh and Chris Jones on FlowerMD
Channel: The Journal of Open Source Software
Date: 2024-03-21

#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 https://github.com/marjanalbooyeh and Chris @chrisjonesBSU https://github.com/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: https://github.com/chrisjonesBSU
- Marjan Albooyeh's GitHub profile: https://github.com/marjanalbooyeh
- The Journal of Open Source Software: https://joss.theoj.org/, https://twitter.com/JOSS_TheOJ, https://blog.joss.theoj.org/
- @arfon: https://fosstodon.org/@arfon, https://www.linkedin.com/in/arfon/, https://github.com/arfon, https://www.arfon.org/
- @abbycabs https://twitter.com/abbycabs, https://hachyderm.io/@abbycabs, https://bsky.app/profile/abbycabs.bsky.social, https://www.linkedin.com/in/abbycabs/, https://github.com/abbycabs, https://abbycabs.github.io/
- Donate to JOSS: https://numfocus.org/donate-to-joss

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