Request for correction/feedback: OpenSciFlow MDAnalysis entry and workflow metadata

[kkkniengLiu]

Hello MDAnalysis maintainers,

I am Kaining Liu, one of the initiators of OpenSciFlow, an early open initiative for modular, reproducible, local-first AI for Science workflows.

We listed MDAnalysis as a related project in our early AI for Science workflow landscape because it is a core trajectory-analysis tool for our first reference workflow:

https://github.com/OpenSciFlow/awesome-ai4s-workflows

We are not claiming any partnership. The goal is to describe existing tools accurately and learn what metadata a workflow system should record before running or citing scientific tools.

Could you help us check two small points?

1. Is our description of MDAnalysis accurate?
2. For a workflow system that may call or cite MDAnalysis, what metadata should be required? For example: input topology/trajectory expectations, environment, validation tests, citation, known limitations, or safety notes for interpreting RMSD/RMSF/Rg outputs.

Relevant draft links:

• Landscape list: https://github.com/OpenSciFlow/awesome-ai4s-workflows
• Plugin manifest draft: https://github.com/OpenSciFlow/plugin-manifest
• Workflow templates draft: https://github.com/OpenSciFlow/workflow-templates

If you prefer that we revise or remove the entry, please say so and we will update it.

Thank you.

[kkkniengLiu]

Follow-up: we added the first draft MDAnalysis plugin manifest here: https://github.com/OpenSciFlow/plugin-manifest/blob/main/examples/mdanalysis-trajectory-analysis/opensciflow.yaml. Feedback on input formats, validation, citation wording, and limitations would be especially helpful.

[orbeckst]

• preferred academic citation:

  R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. MDAnalysis: A Python package for the rapid analysis of molecular dynamics simulations. In S. Benthall and S. Rostrup, editors, Proceedings of the 15th Python in Science Conference, pages 98-105, Austin, TX, 2016. SciPy, doi:10.25080/majora-629e541a-00e

  (Note that if you install duecredit you can also automatically obtain citations for any used code, see https://docs.mdanalysis.org/stable/documentation_pages/references.html#citations-using-duecredit )

• for supported file formats, see

  • Table of supported topology file formats
  • Table of supported trajectory file formats \

• MDAnalysis follows SPEC0 so the latest release is Python >= 3.11