MDAKits are standalone packages containing code using MDAnalysis components that solve a specific scientific problems or in some form enhances the functionality of MDAnalysis core library. An MDAKit can be written by anyone and hosted anywhere.
The MDAKits team (@ianmkenney, @lilyminium, @fiona-naughton, @IAlibay, @orbeckst) will work with you on creating an MDAKit.
An MDAKit can be registered in the MDAKits registry and thus be advertised to the whole MDAnalysis community. They will also be continuously tested against the latest released version and the current development version of the core MDAnalysis library so that users and developers have an up-to-date view of the code health of an MDAKit.
For more details, see our intro blog post on MDAKits and the MDAKits paper:
Irfan Alibay, Lily Wang, Fiona Naughton, Ian Kenney, Jonathan Barnoud, Richard J Gowers, and Oliver Beckstein.. MDAKits: A framework for FAIR-compliant molecular simulation analysis. In Meghann Agarwal, Chris Calloway, and Dillon Niederhut, editors, Proceedings of the 22nd Python in Science Conference (SCIPY 2023), pages 76–84, Austin, TX, 2023. doi: 10.25080/gerudo-f2bc6f59-00a.
Pick an idea for a stand-alone feature you, or others, want to see
possible through MDAnalysis - see the list of
project ideas below!
We encourage you to discuss any ideas in the lead-up to the hackathon -
look for proposed projects marked [Project] on the
UGM issue tracker, and join our Discord server
to follow the discussion on the #hackathon channel.
Read our guide on making an MDAKit (https://mdakits.mdanalysis.org/makingakit.html). We also recommend watching our accompanying video tutorial which demonstrates the complete process of creating and adding an MDAKit to the registry.
Some other things to keep in mind:
- Use the MDAnalysis API: MDAnalysis features a mature API aimed to promote extensibility. We recommend you see how our collection of base classes and other existing tools could simplify your Kit and present a consistent interface to potential users; e.g. AnalysisBase for trajectory-based analysis https://userguide.mdanalysis.org/stable/examples/analysis/custom_trajectory_analysis.html
- Using external packages: Many tools and analyses have already been implemented as stand-alone tools or in other packages. It’s worth checking to see what’s available - it may be easier to include an external tool as a dependency than to make a Kit “from scratch”. Keep in mind how easy it would be to install and move data between MDAnalysis and the external implementation, and make sure to check the licence before including it in your Kit.
At the hackathon, the MDAKits team will be around to answer any questions you may have about making and registering an MDAKit. While we do not require collaboration, we do encourage you to make use of this opportunity being surrounded by other enthusiastic MDAnalysis contributors.
If you’ve ever performed (or want to perform) any analysis/trajectory manipulation with MDAnalysis that is not already directly implemented, chances are that others will too, and could benefit from the creation of an MDAKit!
If you already have code for this - awesome! You can jump right into turning your code into an MDAKit.
If you have an idea but don't yet have code (or it's a work-in-progress) - that's also awesome! Here is your opportunity to get things rolling.
In both cases, we recommend you share your idea ahead of the hackathon
by raising an issue on the UGM issue tracker (include
[project] in the title, and provide an overview of what your Kit will
do and any current progress towards this). This will give you a dedicated
space to share and discuss your idea, get feedback, and
find interested attendees willing to help make your Kit a reality.
Also post on the #hackathon discord channel and link
the issue.
See the list of Project Ideas. Pick an idea from this list, or use it to inspire your own Kit idea. Once you've identified a project you'd like to work on, you can comment as such on the project's associated issue on the UGM issue tracker. See who else is interested, and form a team to tackle the issue together!