In this interview, Prof. Chong discusses her current research endeavors, the crucial role of open access in both science and software, and how open-source software has enabled greater collaboration and reproducibility in her field.
As part of an ongoing series here on ACS Axial, we’re interviewing authors and librarians from around the world to find out more about their research, their published work, and the impact that open science is having on a changing landscape of research communication. This time, we talked with Lillian Chong, Professor of Chemistry at the University of Pittsburgh.
I believe that all science should be available to the community.
Good morning, Professor Chong. Could you tell us about your lab’s current research focus?
I work in the field of computational biophysics, and we focus on the simulation of pathways and rates for barrier-crossing processes called rare events. Examples of rare events include protein binding and protein folding, and all kinds of other interesting processes on biologically relevant time scales.
You published a paper with ACS at the end of 2023, "LPATH: A semi-automated Python tool for clustering molecular pathways." How would you summarize that for someone unfamiliar with the area?
When we think about how a biological process happens, it is all about the pathways that a system takes from an initial state to a final state. If you're looking at two protein partners binding one another, it would be going from the unbound to the bound state, and the different pathways they take between these states. It's a challenge to analyze all those pathways once you have them, because they could be different lengths and there can be different routes. There are many methods for clustering structures of biomolecules, but relatively few methods for clustering pathways.
That was the goal of our paper, and I had a very creative graduate student in my lab at the time who explored the literature for methods in linguistics. He came across a technique for plagiarism detection in text, and he used this technique to score the similarity between pairs of pathways where each pathway was represented as a text string of different states that were visited at regular intervals. Based on these scores, he clustered the pathways into distinct classes or routes.
Your article was published in the Journal of Chemical Information and Modeling—how was the experience?
It was great. Also, I think it is an excellent feature of the Journal of Chemical Information and Modeling to have an Application Note section, which is an avenue for software developers to receive credit for their work. I think these articles are a great way to communicate how to use various software tools with the community, encouraging open science.
Your article was published open access under your institution's agreement with ACS. How did you discover this option was available to you?
The university sent an email to let all the faculty know about the institution’s agreement. When I submitted my paper through the author portal, it was easy to select the open access option and have it approved by my institution. It worked seamlessly.
What are your thoughts on open access as a concept?
I'm a strong proponent of open access in both science and software. For more than a decade, my lab has been developing an open-source software package for rare event sampling, called WESTPA. Our software has facilitated efforts by many groups. I think the trend of developing open-source software has made the field more collaborative and facilitates reproducibility in science.
I believe that all science should be available to the community.I think it's a great trend that Federal funding agencies have required people to be open about their science. As a result, there are more and more software packages available that are open source, and developers are encouraged to design them to be modular so that they're interoperable, so that our packages can all play off of each other: for instance, my lab software can be used with any dynamics engine—whichever your favorite one is—for running molecular dynamics simulations, and you can use it with any analysis tool. Open source software greatly facilitates collaborations—not just in terms of the software, but in terms of methods development and ambitious applications in the sciences.
What are your views on other open science workflows like open data, preprints, and transparent peer review?
I think preprints are great. We post preprints from my lab, and it's a great way to get feedback from more than just the people who would do the peer review for your work. And I think it's also great for the submission of grants when making certain preprints available to the reviewers can be helpful.
Where do you see open access in 10 years' time?
In my simulation community, one of the current challenges is that molecular simulations have been generating larger and larger data sets. In the near term I'd hope that we a repository where researchers can deposit their data sets. These can be tens or even hundreds of terabytes in size, and they're very valuable for the scientific community to analyze with their own methods. Currently there's no straightforward way to share these large data sets except for repositories where one can upload data for just a few pathways generated by a simulation.
I like that more journals are using transparent peer review—publishing the conversations that happen between reviewers, authors, and editors. I think that's very educational for students and postdocs to see, as well as people who are new to a field, as these conversations help inform readers about key issues that experts value in that research area.
Finally: what do you think you'd be doing if you weren't a researcher?
I love writing! It is one of the many aspects of the job that I enjoy about being a researcher. Outside of work, I have been part of a creative writing group that meets regularly for many years now. So if I wasn't a researcher, I think I'd be a writer!
Check out the other interviews in this series:
Ian Cousins, Stockholm University
Hongxia Duan, TU Eindhoven
Vojtěch Vaněček, Institute of Physics, Czech Academy of Sciences
Louise Otting, TU Delft
Kristine Horvat, University of New Haven
David W. McCamant, University of Rochester
Fernando Sartillo Piscil, Benemérita Universidad Autónoma de Puebla
Sue Cardinal, University of Rochester
Rubén Mendoza-Cruz, Universidad Nacional Autónoma de México