Dear Biomolecular NMR Spectroscopists,
Last year, the CCPN team published a proposal to include specifications for dynamics experiments in the NMR Exchange Format on the NEF Github page. This would make it easier for dynamics data to be exchanged between different software packages and deposited in the BMRB.
Video Introduction
Since the proposal document itself is around 18 pages long in total and necessarily relatively dense, we have prepared a short 12-minute video to introduce and provide an overview of our proposal on YouTube: https://youtu.be/EgKxyYmwEMA
Feedback
We are keen to receive feedback from a wide range of researchers involved in recording and analysing biomolecular NMR dynamics experiments and writing software to analyse such data, so that we can improve the proposal and move towards having it accepted by the NEF Consortium.
Email: you are welcome to be in touch with Geerten Vuister and/or Vicky Higman directly if you have any suggestions or comments. We are also happy to meet up for discussions on Zoom if that would be helpful.
CCPN Forum: you are welcome to add comments and feedback to this forum thread.
NEF Github page: you are welcome to post something directly to the NEF Github page.
Open Zoom Meeting: we will be hosting an open Zoom meeting on Thursday 22 January at 8:00 New York / 13:00 London / 14:00 Berlin / 18:30 New Delhi / 22:00 Tokyo (please contact us for details or see the international magnetic resonance mailing list). This will be a chance to make comments in advance of the BMRB’s data retreat at the end of January when we will also be presenting and discussing this proposal. We may add further open Zoom meetings (at different times of day) in February if there is sufficient interest.
In order to structure the session, we are suggesting the following topics for discussion, before moving to a more open conversation:
- Short introduction
- Does it make sense to use a single saveframe for all experiment types (in contrast to the BMRB)?
- Is it sensible to have a save frame which connects rates directly with the data they originate from? Is duplication of information outweighed by ease of accessing it? Should it be mandatory or not?
- Does the proposal adequately account for the ways in which people record their data on a practical level in the form of either pseudo-3D or series of 2D experiments?
- Controlled vocabulary: would anyone like to propose alternative terms or move the proposal to using an existing controlled vocabulary?
- How can we encourage the community to increase deposition rates (of all types of data)?
- Open questions/discussion
If you would like us to add any topics to this outline, then do contact us before the session.
We hope to create a summary of the session to be available to anyone who is not able to attend.
Perspective Article
You may also be interested in our Perspective article in the Journal of Biomolecular NMR which accompanied our publication of the NEF Dynamics proposal. In it we argue that the deposition of increasing amounts of NMR data (including dynamics data) is of particular importance in the age of AI/ML.
Implementation
Gary Thompson has already implemented the NEF dynamics proposal in his NEF Pipelines software using a temporary namespace.
The CCPN team are currently working on implementing the NEF dynamics proposal in our new AnalysisDynamics software using the same temporary namespace. The software will enable full Model Free analysis and more, includes a plugin for the ChemEx software by Guillaume Bouvignies and is currently in the beta testing phase.
We hope to hear back from many of you!
Vicky Higman, Geerten Vuister, Eliza Płoskoń and Gary Thompson