Station1 Frontiers Fellowship Students 2023

Station1 Logo

MDAnalysis is excited to to have participated this year as a host organization for the Station1 Frontiers Fellowship program for the first time. We thank Station1 for supporting two outstanding students, John Ong and Karen Bekhazi, who have been working with us to understand the evolution of heterogeneity between objects in the Protein Data Bank (PDB) PDBx/mmCIF file format. John and Karen’s research will help inform MDAnalysis’s planned extension of interoperability between MDAnalysis and the PDBx/mmCIF format. Keep reading to learn more about John and Karen’s experience, and download their capstone poster here.

John Ong

John Ong

Hello everyone, my name is John Ong, and I was one of the Station1 interns working with MDAnalysis this summer. I am a soon-to-be third-year undergraduate student at the University of Utah studying mathematics and computer science.

MDAnalysis is used widely in the biomolecular sciences and thus is important in research that ultimately aims at improving human health. The PDB is an international repository for experimentally-determined 3D structures of biomolecules, such as proteins and nucleic acids. However, data representation techniques for structures on the PDB often differ, despite the same master format (PDBx/mmCIF). Hence, there exists “dialects” within the PDB’s files.

This summer, Karen and I explored the reasons for the existence of these dialects. Through literature reviews and interviews we’ve carried out with both key members within the PDB and PDB user(s), we’ve found experimental methods, knowledge of proteins, data processing methods, and user error to be the most common contributors to these dialects. We also studied the motivations for format changes and regulations (and the lack thereof) within the PDB and its user base.

All in all, this was a rewarding summer. While we did not achieve as many technical results as we would have liked, studying change has been interesting. I’m honored to have been a mentee of @richardjgowers and @hmacdope, and to have had the support of MDAnalysis and its community this summer.

You can find me on GitHub, LinkedIn and my website!

I hope to be able to continue contributing to this incredible community!

Karen Bekhazi

Karen Bekhazi

Molecular dynamics simulations are capable of generating new trajectory analyses in their own specific output format. This consequently challenges the tools’ further development and widespread use since they are limited to specific formats that can’t be accessed by all users. This summer, our work has mostly focused on the effects of the lack of a standardized format on molecular dynamics’ scientific and social impact. We evaluated the creation of different PDB file formats by drawing parallels between them and notions in the field of linguistics, such as dialects and stemmatics. Our research was also supported by further study of both the PDB and MDAnalysis’s stakeholders.

I am a rising junior at Smith College. I am studying Engineering Sciences and Chemistry, with an interest in biochemistry, biomaterials, and the intersection of biophysics and chemistry. Originally from Beirut, Lebanon, I enjoy running, reading, and watching movie commentaries in my free time.

Here are my LinkedIn and GitHub profiles.

Thank you to the amazing MDAnalysis community and to our mentors, @richardjgowers and @hmacdope, for this summer!

Online Training Workshop Series

MDAnalysis is excited to be kicking off a series of free online training workshops in Fall 2023. The first will be held on October 25, 2023 from 15:00-18:30 UTC.

This online workshop will consist of an introduction to the MDAnalysis Python library, as well as an opportunity for hands-on learning through basic MDAnalysis tutorials. The workshop will be delivered to a small group to allow interactive discussions, questions, and participant engagement. It is designed for beginners to MDAnalysis who already have a working knowledge of Python and know how use shell and notebook environments.

Register soon (places limited)

If you are interested in participating in this workshop, fill out this short application form before September 30, 2023. Selected participants will be notified in early October.

We have a small number of bursaries to enable participation for researchers from underrepresented groups who are facing financial barriers; these can be applied for when completing the application form.

We are looking into organizing the next workshop for Australasian time zones, so also keep an eye out for announcements of future workshops!

— The MDAnalysis Team

UGM 2023 Keynote Speaker Introduction - Cédric Bouysset

We are excited to introduce our next keynote speaker for the MDAnalysis user group meeting (UGM), Dr. Cédric Bouysset (@cbouy), who was a 2020 Google Summer of Code (GSoc) student with MDAnalysis! To learn more about his work on the interoperability between MDAnalysis and RDKit, see his GSoC report.

There is still time to register and submit your abstract (Abstract Deadline: July 7, 2023). An Outstanding Talk Travel Award will be awarded to the best talk given at the UGM to offset travel and accommodation costs. In addition, if you are facing financial barriers to attendance of the UGM, submit your bursary application with your registration form by Friday, June 23, 2023.

Dr. Cédric Bouysset Speaker Card