31 Jul 2024
We are excited to announce the launch of our MDAnalysis Community Survey 2024! Do you or your institution use, develop, contribute to, or sponsor MDAnalysis? Have you attended MDAnalysis workshops or user group meetings? Have you heard about MDAnalysis, but are still learning how to get started or looking for more ways to get involved? If any of these things sound like you, we want to hear from you as part of our valued community! Your feedback is crucial in helping us understand the diverse needs and experiences within our community and guiding our efforts to make MDAnalysis an even more inclusive and welcoming community.
Purpose of the Survey
This survey aims to gather your insights and feedback on various aspects of MDAnalysis, especially about your experiences as a community member and your engagement with the MDAnalysis project.
What will the data be used for?
The information from this survey will help us foster an inclusive and supportive community by:
- Determining preferred MDAnalysis communication channels and developing a content strategy to keep the community informed.
- Informing workshop and event planning efforts to reach diverse audiences based in various time zones across the globe.
- Ensuring MDAnalysis resources are findable and accessible.
Confidentiality and Anonymity
We value your privacy so your responses will be kept confidential and anonymous and only shared with MDAnalysis survey administrators. Demographic information will only be reported in an aggregated format to generate high-level insights.
How to Participate
We invite all members of the MDAnalysis community to participate in the survey. We greatly appreciate your time answering a few questions (around 10 minutes) before August 31st, 2024. Please take a moment to share your thoughts and experiences with us by clicking the following link to access the survey:
Take the Survey
Thank you so much for being a part of the MDAnalysis community. We cannot wait to hear from you!😀
Acknowledgment
This survey was developed as part of an Outreachy project.
The following resources were consulted to aid in the development of this survey:
– @adetutudeborah (Outreachy intern working with MDAnalysis) @jennaswa @micaela-matta (Outreachy mentors)
30 May 2024
MDAnalysis has partnered with CCPBioSim to offer an industry talk on June 19, 2024 from 14:00 - 15:30 BST, presented by MDAnalysis core developer, Richard Gowers (@richardjgowers).
Title: MDAnalysis and Alchemical Simulations
Abstract: MDAnalysis is a popular Python package for the analysis of molecular dynamics simulation data. After introducing the package in broad strokes, this talk will give insight into how this package has been used and extended to process data coming from so-called “alchemical simulations”; where molecules are perturbed through non-physical states to provide estimates of properties such as binding affinities. Topics included will be biopolymer recognition, handling of multistate simulation data and analysing hybrid topology alchemical models.
Although attendance is free, you must register to receive the relevant Zoom information. Check out the CCPBioSim event page to access the registration link and find out more information.
27 May 2024
We are happy to announce that MDAnalysis is hosting three Google Summer of Code (GSoC) contributors - @ljwoods2, @talagayev and @lunamorrow - and an Outreachy intern - @adetutudeborah. MDAnalysis has been accepted as its own organization with GSoC for the fifth year running, and we are excited to be hosting our second-ever MDAnalysis Outreachy internship. We are grateful to Google and Outreachy for granting us the opportunity to get started on four very exciting projects!
GSoC
Streaming trajectory data directly from cloud storage will allow researchers to share their trajectories more easily than ever before, however, rewriting existing trajectory file readers for cloud-streaming would be a slow and complex process. zarrtraj, a trajectory file format based on Zarr storage, presents an alternative which natively supports AWS S3, Google Cloud Buckets, and Azure Blob Storage in addition to reading from a local directory without much added complexity. Lawson’s GSoC 2024 project will be to continue enhancing the ease-of-use, robustness, and efficiency of this format.
Lawson is a computer science student at Arizona State University (ASU) graduating in December 2024. You can find Lawson on GitHub as @ljwoods2 and on LinkedIn. To see updates on the zarrtraj project as well as his other projects you can check out his blog.
The main objective of Valerij’s GSoC project will revolve around the visualization of small molecules in 2D through the application of the MDAnalysis RDKit converter, which allows converting MDAnalysis atomgroups into RDKit objects and benefit from its powerful drawing code to display small molecules. These can then be annotated at the atom level with information associated with the MDAnalysis Universe or arbitrary data in an easy to use interactive display in Jupyter Notebooks.
Valerij is a pharmacy student who graduated from the University of Marburg, where he worked at the Kolb Lab. Valerij is currently a PhD student at the Free University of Berlin in the Wolber Lab with his research revolving around Toll-like receptor antagonists with addition to method development such as OpenMMDL.
You can find Valerij on Github as @talagayev and on LinkedIn. To see the updates on the 2D visualization of small molecules project follow his blog.
Direct interoperability between molecular dynamics software is critical for enabling collaboration, data transfer and easy use by scientists. OpenBabel is a popular toolbox for chemical molecular modelling as it allows conversion, searching, filtering and analysis of chemical data. The ability to interconvert between OpenBabel OBMols and MDAnalysis AtomGroups will enable input and writing of over 100 chemical data file formats.
Luna is a Bachelor of Advanced Science (Honours) student at the University of Queensland (Australia), studying biochemistry, computational sciences and software engineering. Luna currently works as a research assistant in Megan O’Mara’s group at the Australian Institute of Bioengineering and Nanotechnology, where her role involves code creation, maintenance and improvement. She is pursuing a career as a research software engineer. In her down time around university and work, Luna enjoys hiking, going to the gym, reading, buying plants, cuddling her cat Eddie and spending time with her partner and friends.
You can find Luna on GitHub as @lunamorrow and on LinkedIn. To keep up to date with the Extend MDAnalysis Interoperability with OpenBabel project, check out her blog.
Outreachy
MDAnalysis aims to establish clear communication channels to effectively disseminate information, engage the community, and encourage participation. The main objective of Adetutu’s Outreachy project is to develop a social media and communications strategy for MDAnalysis to grow its user and contributor base.
Adetutu will conduct surveys to understand the communication preferences of MDAnalysis developers and users. Based on the survey data, she will recommend the best platforms for discussions and increasing engagement.
Additionally, she will set up an email newsletter to keep the community updated on MDAnalysis news, announcements, and events.
Adetutu Oluwasanmi is a First-Class Microbiology graduate from Lagos State University. She recently completed a 1-year diploma in software engineering at AltSchool Africa, where she gained coding and software development skills.
Her previous roles include social media manager, communications intern, and freelance science writer, giving her a diverse skill set that she brings to her current project.
Adetutu is on GitHub as @adetutudeborah, and on Twitter as @adetutuoluwa2.
She will be documenting her internship journey on her Medium blog. Feel free to check it out for updates on her experience!
— @BradyAJohnston @cbouy @hmacdope @IAlibay @jennaswa @micaela-matta @orbeckst @richardgowers @xhgchen @yuxuanzhuang (mentors and org admins)