From dc229009035716c2fe094ab869e84e0619fefa86 Mon Sep 17 00:00:00 2001 From: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Date: Tue, 6 May 2025 22:08:34 +0200 Subject: [PATCH 1/8] Draft skeleton intro post for gsoc --- _posts/2025-06-01-gsoc-students.md | 75 ++++++++++++++++++++++++++++++ 1 file changed, 75 insertions(+) create mode 100644 _posts/2025-06-01-gsoc-students.md diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md new file mode 100644 index 00000000..065268f5 --- /dev/null +++ b/_posts/2025-06-01-gsoc-students.md @@ -0,0 +1,75 @@ +--- +layout: post +title: Google Summer of Code Students 2025 +--- + +We are proud to announce that MDAnalysis is hosting _NUMBER_ [Google Summer of Code][gsoc] (GSoC) contributors - +[@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE), [@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE), +[@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE), and [@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE). +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 _NUMBER_ very exciting projects! + +## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) + +NAME + +Write a short description of your project here! + +Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) + +Add where we can find you here! (github, linkedin, twitter, others, etc.) + +Add a link to your blog here! + +## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) + +NAME + +Write a short description of your project here! + +Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) + +Add where we can find you here! (github, linkedin, twitter, others, etc.) + +Add a link to your blog here! + +## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) + +NAME + +Write a short description of your project here! + +Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) + +Add where we can find you here! (github, linkedin, twitter, others, etc.) + +Add a link to your blog here! + +## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) + +NAME + +Write a short description of your project here! + +Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) + +Add where we can find you here! (github, linkedin, twitter, others, etc.) + +Add a link to your blog here! + +— @BradyAJohnston @cbouy @fiona-naughton @jeremyleung521 @ljwoods2 @ltchong @orbeckst @talagayev @yuxuanzhuang @IAlibay @jennaswa (mentors and org admins) + +[gsoc]: https://summerofcode.withgoogle.com +[mda-gsoc]: https://summerofcode.withgoogle.com/programs/2025/organizations/mdanalysis From c027c737678c2a25b47bb2deb26bfb3a45b83675 Mon Sep 17 00:00:00 2001 From: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Date: Fri, 9 May 2025 09:01:37 +0200 Subject: [PATCH 2/8] Add collaborations and contributor names/project titles --- _posts/2025-06-01-gsoc-students.md | 24 +++++++++++------------- 1 file changed, 11 insertions(+), 13 deletions(-) diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md index 065268f5..33b38650 100644 --- a/_posts/2025-06-01-gsoc-students.md +++ b/_posts/2025-06-01-gsoc-students.md @@ -3,17 +3,15 @@ layout: post title: Google Summer of Code Students 2025 --- -We are proud to announce that MDAnalysis is hosting _NUMBER_ [Google Summer of Code][gsoc] (GSoC) contributors - -[@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE), [@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE), -[@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE), and [@GITHUB_HANDLE](https://github.com/GITHUB_HANDLE). -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 _NUMBER_ very exciting projects! +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! -## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) +## James Rowe: [Integrating MDAnalysis Streaming Analysis within WESTPA Propagators](https://summerofcode.withgoogle.com/programs/2025/projects/SvFaSgr5) NAME Write a short description of your project here! @@ -24,11 +22,11 @@ Add where we can find you here! (github, linkedin, twitter, others, etc.) Add a link to your blog here! -## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) +## Nilay Verma: [Enhancing ProLIF Visualizations: A Hybrid Approach for Automated, Customizable 2D Interaction Layout](https://summerofcode.withgoogle.com/programs/2025/projects/XWsglxQM) NAME Write a short description of your project here! @@ -39,11 +37,11 @@ Add where we can find you here! (github, linkedin, twitter, others, etc.) Add a link to your blog here! -## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) +## Pardhav Maradani: [Better Interfacing of Blender and MDAnalysis](https://summerofcode.withgoogle.com/programs/2025/projects/9BR8jbvV) NAME Write a short description of your project here! @@ -54,11 +52,11 @@ Add where we can find you here! (github, linkedin, twitter, others, etc.) Add a link to your blog here! -## NAME: [PROJECT TITLE](https://summerofcode.withgoogle.com/programs/2025/projects/PROJECT_URL) +## Yu-Yuan (Stuart) Yang: [MDAnalysis x ProLIF Project 5: H-Bond Interactions from Implicit Hydrogens](https://summerofcode.withgoogle.com/programs/2025/projects/5Otkx8vp) NAME Write a short description of your project here! From 5d1b763c4af7882b0800c5cd39c378116ab7eff4 Mon Sep 17 00:00:00 2001 From: "Yu-Yuan (Stuart) Yang" Date: Tue, 20 May 2025 19:52:08 +0100 Subject: [PATCH 3/8] Gsoc intro - Stuart (#35) * Stuart intro * Update _posts/2025-06-01-gsoc-students.md Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * Update 2025-06-01-gsoc-students.md --------- Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> --- _posts/2025-06-01-gsoc-students.md | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md index 33b38650..6a495f7c 100644 --- a/_posts/2025-06-01-gsoc-students.md +++ b/_posts/2025-06-01-gsoc-students.md @@ -55,17 +55,15 @@ Add a link to your blog here! ## Yu-Yuan (Stuart) Yang: [MDAnalysis x ProLIF Project 5: H-Bond Interactions from Implicit Hydrogens](https://summerofcode.withgoogle.com/programs/2025/projects/5Otkx8vp) Yu-Yuan (Stuart) Yang -Write a short description of your project here! - -Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) +[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. -Add where we can find you here! (github, linkedin, twitter, others, etc.) +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. -Add a link to your blog here! +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 (mentors and org admins) From 2003f5ee010490114a29c54e530a003b16b8f9b8 Mon Sep 17 00:00:00 2001 From: Pardhav Maradani <66913993+PardhavMaradani@users.noreply.github.com> Date: Wed, 21 May 2025 00:23:33 +0530 Subject: [PATCH 4/8] Intro for Pardhav Maradani (#36) * Intro for Pardhav Maradani * Add link to Blender Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * Spell out institute name Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> --------- Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> --- _posts/2025-06-01-gsoc-students.md | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md index 6a495f7c..55f2c347 100644 --- a/_posts/2025-06-01-gsoc-students.md +++ b/_posts/2025-06-01-gsoc-students.md @@ -40,17 +40,17 @@ Add a link to your blog here! ## Pardhav Maradani: [Better Interfacing of Blender and MDAnalysis](https://summerofcode.withgoogle.com/programs/2025/projects/9BR8jbvV) Pardhav Maradani -Write a short description of your project here! +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. -Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) +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. -Add where we can find you here! (github, linkedin, twitter, others, etc.) +You can find Pardhav on GitHub [@PardhavMaradani](https://github.com/PardhavMaradani). -Add a link to your blog here! +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) From 5d3b869c4cf9977a397598ea46b31b2f9c10e2c1 Mon Sep 17 00:00:00 2001 From: Nilay Verma <144618541+nilay-v3rma@users.noreply.github.com> Date: Wed, 21 May 2025 00:24:21 +0530 Subject: [PATCH 5/8] GSoC Intro - Nilay (#37) * GSoC Intro - Nilay * Update _posts/2025-06-01-gsoc-students.md Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> * Update 2025-06-01-gsoc-students.md for Nilay --------- Co-authored-by: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> --- _posts/2025-06-01-gsoc-students.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md index 55f2c347..89d4f8be 100644 --- a/_posts/2025-06-01-gsoc-students.md +++ b/_posts/2025-06-01-gsoc-students.md @@ -24,18 +24,18 @@ Add a link to your blog here! ## Nilay Verma: [Enhancing ProLIF Visualizations: A Hybrid Approach for Automated, Customizable 2D Interaction Layout](https://summerofcode.withgoogle.com/programs/2025/projects/XWsglxQM) -Nilay Verma -Write a short description of your project here! +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. -Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) +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. -Add where we can find you here! (github, linkedin, twitter, others, etc.) +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/). -Add a link to your blog here! +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) From c462698b9d239b108af8e6149a3df5c70ac7cf69 Mon Sep 17 00:00:00 2001 From: Jamie Rowe Date: Thu, 22 May 2025 08:39:24 +0100 Subject: [PATCH 6/8] Added James Rowe introduction (#38) --- _posts/2025-06-01-gsoc-students.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md index 89d4f8be..aacd8c8e 100644 --- a/_posts/2025-06-01-gsoc-students.md +++ b/_posts/2025-06-01-gsoc-students.md @@ -10,17 +10,17 @@ for the sixth year in a row. We are grateful to Google for granting us the oppor ## James Rowe: [Integrating MDAnalysis Streaming Analysis within WESTPA Propagators](https://summerofcode.withgoogle.com/programs/2025/projects/SvFaSgr5) James Rowe -Write a short description of your project here! +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. -Write something about yourself here! (affiliation, background, interests - work and/or personal, etc.) +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). -Add where we can find you here! (github, linkedin, twitter, others, etc.) +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). -Add a link to your blog here! +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) From 088a10cf3f4e16f658d04b032c357ac2f041ccee Mon Sep 17 00:00:00 2001 From: Jenna M Swarthout Goddard <38287809+jennaswa@users.noreply.github.com> Date: Thu, 22 May 2025 09:40:30 +0200 Subject: [PATCH 7/8] Add (Jamie) to @jpkrowe's heading line --- _posts/2025-06-01-gsoc-students.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md index aacd8c8e..5000d175 100644 --- a/_posts/2025-06-01-gsoc-students.md +++ b/_posts/2025-06-01-gsoc-students.md @@ -7,7 +7,7 @@ We are proud to announce that MDAnalysis — in [collaboration with Molecular No 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 Rowe: [Integrating MDAnalysis Streaming Analysis within WESTPA Propagators](https://summerofcode.withgoogle.com/programs/2025/projects/SvFaSgr5) +## James (Jamie) Rowe: [Integrating MDAnalysis Streaming Analysis within WESTPA Propagators](https://summerofcode.withgoogle.com/programs/2025/projects/SvFaSgr5) Date: Thu, 22 May 2025 09:42:34 +0200 Subject: [PATCH 8/8] Tag gsoc-mentors team --- _posts/2025-06-01-gsoc-students.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/_posts/2025-06-01-gsoc-students.md b/_posts/2025-06-01-gsoc-students.md index 5000d175..9571808b 100644 --- a/_posts/2025-06-01-gsoc-students.md +++ b/_posts/2025-06-01-gsoc-students.md @@ -65,7 +65,7 @@ Yu-Yuan (Stuart) graduated from National Taiwan University (Taipei, Taiwan), hol 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 (mentors and org admins) +— @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