Merge branch 'master' of https://github.com/MDAnalysis/MDAnalysis.github.io into reorder-pages-in-sidebar

Author: namiroues

_includes/sidebar.html

@@ -55,6 +55,11 @@ <h1>
         {% endif %}
       {% endfor %}
     </nav>
+
+    <!-- Donation Button -->
+    <div class="sidebar-donate" style="margin-top: 20px;">
+      {{ site.numfocus.donate_button }}
+    </div>
 
     <p>&copy; {{ site.time | date: '%Y' }}. All rights reserved.</p>
   </div>

_posts/2025-04-13-ugm2025.md

@@ -0,0 +1,17 @@
+---
+layout: post
+title: Announcement and Call for Abstracts for MDAnalysis UGM 2025
+---
+
+We are pleased to announce the [2025 MDAnalysis UGM][ugmPage] (User Group Meeting), taking place on the 9-11th November, 2025, in Arizona, USA at [Arizona State University](https://www.asu.edu/). [Abstracts][abstracts] are welcomed from all areas relevant to MDAnalysis's work, from scientific applications (e.g., biomolecular simulations, soft matter and materials science, drug discovery and more) to the use and development of open source software and tools for data analysis of molecular simulation output. Additionally this UGM will have sessions focusing on ongoing work towards enabling simulation streaming being undertaken at ASU (see our previous [workshop][streaming_workshop] on this topic). When submitting your abstract, you may indicate whether you prefer to give a 15 minute talk, 5 minute lighting talk, or poster presentation.
+
+MDAnalysis strives to be a diverse and welcoming community for all. A limited number of travel bursaries are available to enable those facing financial barriers to attend and present their work. If you would like to apply, please follow the prompts on the [abstract submission form][abstracts].
+
+The deadline for submitting your abstract and/or bursary application is **July 15th, 2025**. Submissions will be reviewed by the end of July 2025; we will contact applicants shortly after.
+
+Follow the [official event page][ugmPage] on our website for the most up-to-date information about the UGM. If you have any questions or special requests, please contact [[email protected]][email].
+
+[abstracts]: https://forms.gle/jfKsiWUDn4TMzX5Q6
+[ugmPage]: https://www.mdanalysis.org/pages/ugm2025/
+[email]: mailto:[email protected]
+[streaming_workshop]: https://www.mdanalysis.org/2024/11/03/ASU_streaming_workshop/

_posts/2025-05-23-gsoc-students.md

@@ -0,0 +1,71 @@
+---
+layout: post
+title: Google Summer of Code Students 2025
+---
+
+We are proud to announce that MDAnalysis — in [collaboration with Molecular Nodes, ProLIF, and WESTPA](https://github.com/MDAnalysis/mdanalysis/wiki/GSoC-2025-Project-Ideas#collaborations) — 
+is hosting _four_ [Google Summer of Code][gsoc] (GSoC) contributors: @jpkrowe, @nilay-v3rma, @PardhavMaradani, and @yuyuan871111. MDAnalysis has been accepted as its own [organization with GSoC][mda-gsoc] 
+for the sixth year in a row. We are grateful to Google for granting us the opportunity to get started on these four very exciting projects!
+
+## James (Jamie) Rowe: [Integrating MDAnalysis Streaming Analysis within WESTPA Propagators](https://summerofcode.withgoogle.com/programs/2025/projects/SvFaSgr5)
+
+<img
+src="https://avatars.githubusercontent.com/u/28990394?v=4"
+title="James (Jamie) Rowe" alt="James (Jamie) Rowe"
+style="float: left; width: 110px; height: 110px; border-radius: 20px; border: 15px solid white" />
+
+James' project is a collaboration between MDAnalysis and [WESTPA](https://westpa.github.io/westpa/), a toolkit for running Weighted Ensemble simulations. In Weighted Ensemble simulations, many short trajectories are run in parallel and evaluated after each iteration to identify those that have progressed along a predefined coordinate. This analysis step can become a bottleneck, as all trajectories must be loaded and processed before the next iteration can begin. The goal of this project is to use MDAnalysis' trajectory streaming capabilities to analyze trajectories on-the-fly, reducing analysis overhead and decreasing the time between iterations.
+
+James is a 3rd year PhD student at Imperial College London. His PhD project aims to use molecular dynamics to understand how mutations and modifications to the fundamental building blocks of bone, such as collagen, lead to increased fracture risk and compromised mobility. He has recently released an article on [selective rupture in collagen](https://pubs.rsc.org/en/content/articlehtml/2023/cp/d2cp05051j) and a [review article that integrates experimental and computational advances in bone research](https://www.sciencedirect.com/science/article/pii/S0079642525000490).
+
+You can find James on [GitHub](https://github.com/jpkrowe), [LinkedIn](https://www.linkedin.com/in/james-rowe-74018425b/) and [Bluesky](https://bsky.app/profile/jrowe2000.bsky.social).
+
+To find updates on this project, check out his blog [here!](jpkrowe.github.io)
+
+## Nilay Verma: [Enhancing ProLIF Visualizations: A Hybrid Approach for Automated, Customizable 2D Interaction Layout](https://summerofcode.withgoogle.com/programs/2025/projects/XWsglxQM)
+
+<img    
+src="https://github.com/nilay-v3rma.png"
+title="Nilay Verma" alt="Nilay Verma"
+style="float: left; width: 110px; height: 110px; border-radius: 20px; border: 15px solid white" />
+
+Nilay's project focuses on improving the 2D interaction visualizations in [ProLIF](https://github.com/chemosim-lab/ProLIF), a tool for analyzing molecular interactions such as protein–ligand and protein–protein binding. He is enhancing LigNetwork plots by implementing graph-based algorithms to automate residue placement, reduce edge overlaps, and improve overall readability. Additionally, he is exploring the integration of visualization approaches from tools like InteractionDrawer and Flareplot to improve the visual representation of interactions. The goal is to create a more user-friendly and informative visualization tool for researchers.
+
+Nilay is a sophomore at Indian Institute of Technology Gandhinagar (IITGN), pursuing a dual major in B.Tech Computer Science and Materials Science. He is passionate about computational materials science, machine learning, and generative AI and its applications. 
+
+You can find Nilay on [GitHub](https://github.com/nilay-v3rma), [LinkedIn](https://www.linkedin.com/in/nilay-verma-1110a928a/) and his [Portfolio](https://nilay-v3rma.github.io/).
+
+To keep up with his work, you can check out his [gsoc-blog](https://nilay-v3rma.github.io/gsoc-blog/).
+
+## Pardhav Maradani: [Better Interfacing of Blender and MDAnalysis](https://summerofcode.withgoogle.com/programs/2025/projects/9BR8jbvV)
+
+<img
+src="https://avatars.githubusercontent.com/pardhavmaradani"
+title="Pardhav Maradani" alt="Pardhav Maradani"
+style="float: left; width: 110px; height: 110px; border-radius: 20px; border: 15px solid white" />
+
+MDAnalysis has a basic interface with [Blender](https://www.blender.org/) through a popular extension called [Molecular Nodes](https://github.com/BradyAJohnston/MolecularNodes), which allows importing MDAnalysis universes and provides advanced rendering capabilities through a GUI. The ability to script and support advanced visualizations of MDAnalysis results is currently limited. This project attempts to define, prototype and implement various APIs along with an integrated GUI within Blender as part of [GGMolVis](https://github.com/yuxuanzhuang/ggmolvis) and [Molecular Nodes](https://github.com/BradyAJohnston/MolecularNodes) that will together provide advanced visualization capabilities for MDAnalysis.
+
+Pardhav is an undergraduate student from India pursuing a Bachelors in Computer Science and Engineering from Vellore Institute of Technology (Vellore) and a BS in Data Science and Applications from Indian Institute of Technology (IIT) Madras.
+
+You can find Pardhav on GitHub [@PardhavMaradani](https://github.com/PardhavMaradani).
+
+To see updates on this project, you can check out his [blog](https://pardhavmaradani.github.io/categories/gsoc-2025/).
+
+## Yu-Yuan (Stuart) Yang: [MDAnalysis x ProLIF Project 5: H-Bond Interactions from Implicit Hydrogens](https://summerofcode.withgoogle.com/programs/2025/projects/5Otkx8vp)
+
+<img
+src="https://avatars.githubusercontent.com/yuyuan871111"
+title="Yu-Yuan (Stuart) Yang" alt="Yu-Yuan (Stuart) Yang"
+style="float: left; width: 110px; height: 110px; border-radius: 20px; border: 15px solid white" />
+
+[ProLIF](https://github.com/chemosim-lab/ProLIF), a MDAnalysis/RDKit-based tool for identifying protein-molecule interactions in molecular dynamics trajectories, lacks a straightforward method for evaluating hydrogen bonds when only heavy atoms are present. This project introduces an "implicit hydrogen bond (H-bond) interaction method" directly using heavy atom positions to detect H-bonds. This new feature for ProLIF will help many users (especially, beginner-level programming users) compare their experimental and computational structures without explicit hydrogens.
+
+Yu-Yuan (Stuart) graduated from National Taiwan University (Taipei, Taiwan), holding a Bachelor of Science in Agricultural Chemistry, a Bachelor of Engineer in Chemical Engineering, and a Master of Science in Biomedical Electronics and Bioinformatics. He worked on both wet-lab ([WPI fibril microcapsules](https://doi.org/10.1016/j.jtice.2024.105344), [SEA-PHAGE](https://www.linkedin.com/in/yuyuan871111/overlay/1635506597143/single-media-viewer?type=DOCUMENT&profileId=ACoAACiNG10BL5O9KRp8TUNZI_sskb-wj5N80BM&lipi=urn%3Ali%3Apage%3Ad_flagship3_profile_view_base%3BC9cMZG0TSRKfr%2F%2BybMQWPw%3D%3D)) and dry-lab ([FastEval Parkinsonism](https://doi.org/10.1038/s41746-024-01022-x), [Quantum computing for drug discovery](https://doi.org/10.1109/MNANO.2023.3249499), [MD simulations of SARS-CoV-2 omicron variants](https://doi.org/10.1093/bfgp/elac053), [Automated WGS(WES) reporting system](https://github.com/yuyuan871111/NHRI_group4)) projects. [Stuart](https://www.qmul.ac.uk/sbbs/staff/yuyuanyang.html) currently studies for a PhD in [UKRI-AIDD doctoral training programme](https://www.qmul.ac.uk/deri/ukri-aidd-doctoral-training-programme/) in [Richard W. Pickersgill](https://www.qmul.ac.uk/sbbs/staff/richardpickersgill.html)'s and [Arianna Fornili's group](https://afornililab.wordpress.com/) at Queen Mary University of London (London, UK) to explore protein conformations with a computer-vision-based deep learning model. He is pursuing a career as a computational research scientist in drug discovery. During the free time, Stuart enjoys playing volleyball and badminton and sometimes visiting new places and cities with his family and friends.
+
+You can find Stuart on GitHub as @yuyuan871111 and on [LinkedIn](https://www.linkedin.com/in/yuyuan871111/). To keep up to date with his latest projects, check out his [blog](https://yuyuan871111.github.io/blogs/gsoc/).
+
+— @BradyAJohnston @cbouy @fiona-naughton @jeremyleung521 @ljwoods2 @ltchong @orbeckst @talagayev @yuxuanzhuang @IAlibay @jennaswa (@MDAnalysis/gsoc-mentors and org admins)
+
+[gsoc]: https://summerofcode.withgoogle.com
+[mda-gsoc]: https://summerofcode.withgoogle.com/programs/2025/organizations/mdanalysis

events.md

@@ -4,7 +4,7 @@ title: Events
 order: 7
 ---
 
-MDAnalysis hosts and participates in various **community-driven events, user group meetings (UGMs), and workshops** to foster collaboration and learning.
+MDAnalysis hosts and participates in various **community-driven events, user group meetings (UGMs), workshops, and hackathons** to foster collaboration and learning.
 
 This page provides information on **upcoming and past events**, including **UGMs, workshops, and talks**. Whether you're a developer, researcher, or new to the field, these events provide opportunities to engage with and contribute to the MDAnalysis ecosystem.
 

pages/ugm2025.md

@@ -0,0 +1,165 @@
+---
+layout: page
+title: UGM 2025
+order: 5
+---
+
+## When and Where
+
+The 2025 MDAnalysis UGM (User Group Meeting) will be held in-person across 3 days, 9th-11th November, 2025, at at [Arizona State University](https://www.asu.edu/).
+
+### Address
+[Center for Biological Physics and Department of Physics](https://cbp.asu.edu/)
+Arizona State University
+Tempe, AZ 85287
+
+## What to Expect
+The UGM will bring together users of the MDAnalysis package from different communities. Our goal is to foster an opportunity to connect interdisciplinary researchers and developers across biomolecular simulations, soft matter, materials science and more. Whether you are a new MDAnalysis contributor, an MDAnalysis core developer, or a researcher using (or interested in using) MDAnalysis for your work in academia or industry, this UGM is for you.
+
+You can expect:
+* Keynote talks from experts in the molecular dynamics simulations space (see [Keynote Speakers](https://www.mdanalysis.org/pages/ugm2025/#Keynote-Speakers) below)
+* Talks related to developing and using MDAnalysis for diverse scientific applications (see [Program](https://www.mdanalysis.org/pages/ugm2025/#Program) below)
+* A focus on recent simulation streaming work being undertaken at ASU
+* Tutorials diving into new features
+* Direct access to the [MDAnalysis core developer team][coredev] to help shape future development of MDAnalysis
+* Networking opportunities to foster new collaborations
+* A hackathon and other social outings
+
+## Registration
+In-person attendance will be $100 per attendees, and online attendance will be free; see the registration button below.
+
+<a href="https://forms.gle/bPvVTMpzBkyCRtNA7" target="_blank" style="background:#FF9200;padding:10px;margin:10px 0px;text-align:center;text-decoration:none;font-size:16pt;color:#000000;display:inline-block;border-radius:3px">Register</a>
+
+## Keynote Speakers
+
+Keynote speakers will be announced soon.
+
+## Program
+
+A finalized agenda will be available closer to the event date. The UGM will include a mix of talks, tutorials, and a hackathon where attendees can expect 15 minute talks, 5 minute lighting talks, and poster presentations. A streaming focused hackathon will provide attendees to an opportunity to incorporate this new feature into their workflow.
+
+## Travel and Accommodation
+
+*Participants are expected to make their own travel and accommodation arrangements.*
+
+[Tempe][] is part of the "Valley of the Sun" metropolitan area, which encompasses
+[Phoenix][], the 5th most populous city in the US. Today the area is home to more
+than 4.8 million people and encompasses the ancient lands of the Akimel O'odham
+(Pima), Maricopa, and Tohono O'odham tribes.
+
+### Airport
+
+**Phoenix Sky Harbor** [PHX][] airport has direct connections to all major hubs
+in the US.
+
+PHX airport is 5.5 miles (10 minutes by car/rideshare) from the workshop venue
+
+### Public transport (Light Rail)
+
+The [Valley Metro Light Rail][Light Rail] connects the airport to Tempe along a
+West-East axis. If your destination is near a Light Rail stop then
+public transport works well:
+
+1. Take the free [PHX Sky Train][] from the terminal to the **44th St/Washington**
+Metro Rail stop.
+2. Walk from the Sky Train stop to the Light Rail stop (all inside the 44th St
+Sky Train structure)
+3. Buy a ticket at the ticket machine near the exit escalators to the Light
+Rail stop.
+4. At the [44th St/Washington stop][LightRail44thSt] (Stop #10018) take the
+*east-bound* Light Rail (direction Mesa, Gilbert Rd/Main St).
+5. The stop closest to the Hyatt Place Hotel and the workshop venue is
+**University Dr/Rural Rd** (Stop #10023). If you want to get off closer to
+downtown Tempe get off one stop earlier at **Veterans Way/College Ave** (Stop #10025)
+6. Walk to your destination.
+
+### Car/rideshare
+
+To get from the airport to anywhere in Tempe either take a cab (traditional or self-driving
+Waymo) or rideshare (Lyft, Uber).
+
+### ASU Venue
+
+The workshop will be held in the Student Success Center in the Department of
+Physics at [Arizona State University][ASU] (room PSF 186 in the [Physical Sciences F
+building][PSF]). The address is
+
+  Department of Physics  
+  Arizona State University  
+  Physical Sciences F Building  
+  550 E Tyler Mall, PSF 186  
+  Tempe, AZ 85287  
+  USA
+ 
+Paid parking is available in the [Tyler Street Parking
+Structure][TylerStParking] and other on-campus parking structures.
+
+## Support for international travel
+Attendees requiring a letter clarifying the purpose of travel should [contact the MDAnalysis project manager][email]. 
+
+## Meals
+We will provide breakfast and lunch during the event. More information on local food options and group outings will be added soon!
+
+## Health and Safety
+We are committed to providing a safe, comfortable, and healthy environment for the MDAnalysis UGM and have looked to local and international entities and other organizations in the open source community to develop onsite safety measures for UGM attendees.
+
+### COVID-19 Testing
+
+*Testing Positive for COVID-19*
+
+Individuals who are COVID-positive should not attend the UGM. If you receive a positive COVID-19 test result during the UGM, please [notify the MDAnalysis UGM organizing committee][ugm_email] and do not return to the event while you are still COVID-positive.
+
+### Face Coverings
+Face coverings are not required, but are welcomed. We view face coverings as a personal choice and will support attendees in their choice to wear or not to wear a face covering.
+
+
+## Code of Conduct
+All members of the MDAnalysis community and participants in this UGM are expected to abide by the MDAnalysis [Code of Conduct][coc] (CoC).
+
+If you are attending the UGM and wish to make a report, you may contact the [CoC Committee members](https://www.mdanalysis.org/pages/team/#roles) or other event staff/organizers so that they can take any [appropriate immediate response](https://numfocus.org/code-of-conduct-archive/response-and-enforcement-events-meetups). If you would prefer not to do that, please [submit a report][coc_report] to MDAnalysis.
+
+## Who to Contact
+If you have any questions or special requests related to the UGM, you may [contact the organizing committee][ugm_email].
+
+## Sponsors
+A special thanks to our supporters:
+
+<br>
+<a href="https://chanzuckerberg.com/">
+<img
+src="/public/images/CZI_Logo.jpg"
+title="Chan Zuckerberg Initiative Logo" alt="Chan Zuckerberg Initiative Logo"
+style="float: left; height: 5em; " />  
+<a/> 
+
+<br>
+<a href="https://www.nsf.gov/">
+<img
+src="/public/images/nsf.jpg"
+title="National Science Foundation" alt="National Science Foundation"
+style="float: left; height: 5em; " />
+</a>
+
+<br>
+<a href="{{site.numfocus.sponsored_project}}">
+<img
+src="/public/images/numfocus-sponsored.png"
+title="NumFOCUS Fiscally Sponsored Project Logo" alt="NumFOCUS Fiscally Sponsored Project Logo"
+style="float: left; height: 5em; " />
+</a>
+
+
+[coredev]: https://www.mdanalysis.org/about/#mdanalysis-core-developers
+[email]: mailto:[email protected]
+[coc]: https://www.mdanalysis.org/pages/conduct/](https://www.mdanalysis.org/conduct/#mdanalysis-code-of-conduct-and-community-guidelines
+[coc_report]: https://docs.google.com/forms/d/e/1FAIpQLSeID-DiFMbXAHFeeiNgPKiCoa3FwA5I_92xE9cqlZB-3J49zA/viewform?c=0&w=1
+[ugm_email]: mailto:[email protected]
+[TylerStParking]: https://www.google.com/maps/place/Tyler+Street+Parking+Structure,+E+Tyler+St,+Tempe,+AZ+85281/@33.4210869,-111.9324732,17.76z/data=!4m15!1m8!3m7!1s0x872b08ddcbad3a1d:0x34be1bc111135fe9!2sF+Wing,+550+E+Tyler+Mall,+Tempe,+AZ+85287!3b1!8m2!3d33.4209987!4d-111.9313753!16s%2Fg%2F11rvvz0ng!3m5!1s0x872b08e77dae3579:0x666a75efc5dbe1d3!8m2!3d33.4207391!4d-111.9282154!16s%2Fg%2F11bvtdqdr_?entry=ttu
+[HyattPlace]: https://www.hyatt.com/en-US/hotel/arizona/hyatt-place-tempe-phoenix-university/phxzt
+[Tempe]: https://www.tempe.gov/
+[Phoenix]: https://www.phoenix.gov/
+[ASU]: https://www.asu.edu
+[PHX]: https://www.skyharbor.com/
+[Light Rail]: https://www.valleymetro.org/maps-schedules/rail
+[PHX Sky Train]: https://www.skyharbor.com/ground-transportation/phx-sky-train/
+[LightRail44thSt]: https://valleymetro.org/maps-schedules/RAIL?location=44th%20St/Washington,%20East%20Washington%20Street,%20Phoenix,%20AZ,%20USA