GSoC 2026 Intro + Question: Edison (SF Bay Area), interested in the WESTPA dashboard (Project 5)

[edison16a]

Hi everyone, I’m Edison from the U.S. (San Francisco Bay Area).

I’m a student interested in Computer Science & Biomedical Engineering. I’m excited to start contributing to MDAnalysis.

Background and Programming Languages

• Python (NumPy), JavaScript/TypeScript (Next.js), HTML/CSS, Swift, and some ML/AI experience.
• This is my first year applying to GSoC, and I am excited about open source and want to be more involved.
• I have experience writing tests in hackathon/internship projects, and I’m comfortable debugging and iterating based on feedback.

Projects

FlameSense - Winner of Los Altos Hacks 2025
Competed against 350+ competitors. Built a wildfire-risk prediction system using a sequential neural network trained on historical burn data and real-time weather inputs (temperature, humidity, wind) to forecast spread for emergency planning. Built in HTML/CSS, Python, and utilized a .keras model

SensePlan - Winner of Luma A2A - Agents Hackathon 2025
Competed against 130+ professional adult engineers. Built an autonomous AI agent that discovers relevant medical clinics or health services via web data, evaluates options based on user preferences, and places appointments end-to-end using programmatic voice calls (Bright Data + VAPI).

CallSense - Winner of Milpitas Hacks 2025
Competed against 150+ competitors. Built an AI assistant for 911 call centers that transcribes live emergency calls, extracts critical details, prioritizes incidents by urgency, and suggests targeted follow-up questions to support faster, more accurate dispatch decisions.

CS Experience

Software Engineer Intern at Tanius Technology (Trading Firm): Worked on data analysis and systems (e.g., analyzing relationships in market data; built an iOS app + a C# web server)

Why computational physics/chemistry/materials means a lot to me

I’ve had severe food allergies since I was a child. I’ve been interested in biology/chemistry and medical science because I’ve wanted to learn more about molecular interactions. I’m especially interested in software projects that help analyze simulations to eventually benefit the scientific community and research.

Scientific experience

• UCLA Applications of Nanoscience: Gained wet lab experience across biopolymers, microfluidics, nanotoxicity, water filtration, and prototyping a nanotech wound-care gel (“NanoKnit”). My project involved simulation/data analysis work, and I’m interested in contributing to MDAnalysis.
• Stanford Inspiring Future Scientists through Shadowing: Collaborated with Stanford Ph.D. candidate researchers in chemistry, biology, and genetics, assisting with experimental setup and observing advanced instrumentation and simulations.

Interest area (Project 5 - WESTPA)

I’m interested in Project 5: Dashboard for tracking WESTPA simulation progress.

From what I understand, WESTPA is a Python framework for weighted ensemble simulations and analysis. It is designed to scale and interface with different stochastic dynamics engines. I am excited to build a GUI/CLI dashboard to better track progress and estimate completion time.

What I’m planning to do next

I plan to work through the WESTPA Getting Started docs and tutorials and read up on how progress reporting is handled.

Questions

For Project 5, should the WESTPA progress dashboard be implemented in the WESTPA repo, in MDAnalysis, or as a separate package?

Thank you so much, looking forward to it!
@jeremyleung521 @ltchong @nilay-v3rma

[jeremyleung521]

Welcome.

Regarding this:

For Project 5, should the WESTPA progress dashboard be implemented in the WESTPA repo, in MDAnalysis, or as a separate package?

Ideally sitting within the westpa/westpa repo, which may or may not require changes to MDA depending on the implementation. It ultimately depends on the scope of your project, which you should describe/define/pitch in your proposal. Your justifications and ability to weigh the pros/cons is what we're hoping to see. :)

[edison16a]

Hi Jeremy,

Thanks for the guidance, I really appreciate it. I’m excited to continue looking into WESTPA and to begin planning the proposal.

For any future questions about the project, would you prefer that I continue replying in this thread or open a new discussion?

Thanks,
Edison

[jeremyleung521]

Feel free to stick to this thread. It makes it easier for me to track.

[edison16a]

Hi Jeremy,

I have gotten the WESTPA CLI installed and running locally and used it to generate a west.h5 file. I also started looking into what progress indicators and time estimates the dashboard can report from the information WESTPA records. I confirmed west.h5 contains the expected groups like iterations and summary.

Next, I plan to look into what information can be gathered via WESTPA’s work managers such as ZMQ and data managers.

For the proposal, I am planning to prioritize reliable progress and ETA reporting with a minimal UI first. I’m setting richer MDAnalysis streaming visualization as a further goal.

For long-standing WESTPA users, does that prioritization match what users would most want to see between status reports? I appreciate your help & feedback!

Thanks,
Edison

[edison16a]

Hi Jeremy,

Progress Update:

I looked through WESTPA’s work managers related to run progress, such as the ZMQ work manager and data_manager.py.
I see that west.h5 holds completed iteration data (iterations, summary, segment weights, pcoord), while the work managers hold data closer to the running simulations.

Proposal Questions:

I’m planning to start drafting my proposal and have a couple of questions.

For the proposal, I am planning to prioritize reliable progress reporting. Better UI and MDAnalysis streaming visualization are further goals.

For long-standing WESTPA users, does that prioritization match what users would most want to see between status reports?
Also, for long-running WESTPA simulations, what progress indicators do users typically care about the most in practice (for example, iteration count, segment completion within an iteration, etc.)?

I appreciate your help & feedback!

Edison
@jeremyleung521 @ltchong @nilay-v3rma

[jeremyleung521]

Segment completion within an iteration and estimated iteration count are both important, but the latter is difficult to estimate.

Won't be commenting on pre-proposal content too much (comments come after preproposal get selected) but I'd say you're on a good track.

[edison16a]

Thanks! Much appreciated!

[edison16a]

Hi @jeremyleung521 !

I have completed the project proposal draft, and I am planning to submit it this week.

Would you like to take a look at it before I submit it through GSoC?

Best,
Edison

[jeremyleung521]

Hi @edison16a, unfortunately, the pre-proposal submission deadline has passed (March 9th, 2026) (and I don't think I see your submission) so you won't be able to apply to join GSoC 2026 w/ MDAnalysis this year. Feel free to look at other organizations that are still open. As always, you're welcome to contribute to MDAnalysis + WESTPA (+ Molecular Nodes)'s open source code bases!

https://www.mdanalysis.org/2026/02/19/gsoc2026/#information-for-prospective-gsoc-contributors

[edison16a]

Hi @jeremyleung521

Thank you for letting me know. I sadly missed the pre-proposal deadline.

I had misunderstood the timeline and thought March 16 was the key date as that is when the main GSoC application portal opens, so I had been planning around that. That was my mistake.

I installed and ran the WESTPA CLI locally, generated a west.h5 file, looked through relevant parts of the WESTPA codebase related to progress reporting, and drafted a proposal for Project 5. I wanted to ask respectfully if there is any possibility at all that something could still be done for this year, or if there is any alternate path to still be considered. I understand the deadline may be firm, but I would really appreciate it if there is any flexibility.

I sincerely appreciate your guidance and your time. My proposal and resume have been drafted and are ready to submit today. I put in a lot of effort and really hope there is a chance to be considered.

Thanks,
Edison

[edison16a]

@jeremyleung521 I have shared my proposal below. I would appreciate it if you could take a look and hope that it can be accepted.

I apologize for my misunderstanding of the deadline (please see my message above).

Link to proposal: https://docs.google.com/document/d/10o9dVb5m1WejxKDTaHP13oucbog6CIdPXMwOguukiOU/edit?usp=sharing

[jeremyleung521]

@jeremyleung521 I have shared my proposal below. I would appreciate it if you could take a look and hope that it can be accepted.

I apologize for my misunderstanding of the deadline (please see my message above).

Link to proposal: https://docs.google.com/document/d/10o9dVb5m1WejxKDTaHP13oucbog6CIdPXMwOguukiOU/edit?usp=sharing

Hi @edison16a, unfortunately that's not a decision for me to make. Google is very keen on fairness and so the preproposal deadline has to be firm. We've turned away many candidates already and it wouldn't be fair otherwise.

If the project ends up not taken by a GSOC collaborator by May, you're welcome to work on it (it's open source after all!) but obviously we wouldn't be able to mentor you as closely as a GSoC collaborator would have (and without all the perks of GSoC).

[edison16a]

Hi @jeremyleung521

Thanks for the clarification. I completely understand.

I’ve really enjoyed working on this over the past month and appreciate your feedback while I was iterating on the proposal.

If there’s any possibility to be involved, I’d be very excited to.

If the project remains open, I’d love to stay involved and contribute, and I appreciate your guidance and offer to mentor.

Thanks again for your time and support.
@ltchong @nilay-v3rma