Transition to Open Science - an interview with Dr. Jiajia Sun (Part 2)

Liz Maag-Capriotti
November 24, 2021

Accelerate Research

This goal of global collaborative science can seem ambitious and daunting to a single researcher, but there are several achievable benefits that open-science practices can provide. Open source helps to accelerate knowledge and discoveries because researchers are no longer required to reinvent or reimplement standard resources. Dr. Sun gave an example of how two of his graduate students are using SimPEG, an open-source Python package for geophysics, to develop their research code. “SimPEG has tremendously accelerated [their] research since they just use it to implement [their ideas],” he said. “Without SimPEG they would be years behind what they have achieved today.”

Using such open-source packages gives researchers access to more than previously written code. Open-source code is built within a group of researchers who communicate, collaborate, and contribute. Dr. Sun and his students are not only using SimPEG, but are contributing members of its open-source community. The SimPEG group host weekly community meetups to discuss code development and implementation, as well as a monthly seminar series where community members present their ongoing research.

The SimPEG group shares their weekly community meetups and monthly seminar series on their Curvenote team profile.

SimPEG community members use Curvenote to take meeting notes, collaborate on snippets of code in Jupyter, and share their notes and seminar videos. Their material is available on their public Curvenote profile. Dr. Sun was glad that he and his students could share their ongoing research projects within the seminar series and hopes that other students, “will be inspired by how we do our research and use open source.”

Communicating earlier and often throughout the research cycle can provide a variety of benefits, especially to early career researchers. Creating code within an open-source package forces developers to write quality code that others will be able to read, use, and edit in the future. Early career researchers can gain valuable experience, participate in meaningful reviews, and be exposed to new productivity tools and practices within these groups.

By sharing ongoing research projects beyond a small group of co-authors, researchers receive corrective and instructive feedback that can influence a project’s trajectory and results. Often the feedback provided after journal submission or publication is overlooked as researchers feel that project is complete and have moved on to other subjects.

The content privacy settings on Curvenote provide opportunities for researchers to share their ideas with the public or with only a select group of collaborators. Dr. Sun gave an example, “My student might want to share with me or the whole SimPEG team. I think that would be a really good thing. First of all it protects the students. You aren’t sharing with the whole world but my student is stepping out of my small group and engaging with more people.”

Maximize Impact

Dr. Sun and his graduate students have also made an effort to share their data and code along with their publications. “What we do when we first submit our manuscript is to also publish code on an open-source repository like Zenodo, so when the reviewers and editors get our manuscript they will immediately have access to our code and they can reproduce our figures.”

Dr. Sun also mentioned the recent addition of a preprint service to their open-science workflow, “Just a few days ago we submitted a paper to JGR (Journal of Geophysical Research) and they offer a service to transfer your papers to ESSOAr (Earth and Space Science Open Archive).”

Sharing the additional information along with their publications is a “good way to maximize the impact of your work,” Dr. Sun expressed. This fact was evident when he and his student published a paper in the Journal of Geophysical Research: Solid Earth (Nurindrawati & Sun, 2020) in September of 2020 and shared their data and code, using Zenodo. “In just 4 weeks there were 400 downloads!”, he continued, “If you talk about real impact, this is real impact!”

As scientists, we often think of the impact of our research in number of citations, but how often do we actually implement, reproduce, or even fully read a scholarly article before we cite it? Sharing the building blocks of our research allows others to better understand, contribute to, and expand the science. We discussed how Curvenote links its writing platform and the Jupyter coding environment and its potential to improve how we conduct and share our open science.

Dr. Sun commented, “Curvenote can do so many things: version control, [Jupyter] Notebook, text, documentation, image creation. It has almost all the features that researches would need to develop, document, communicate and collaborate on their projects and all these features are integrated into one unified framework.”

Challenges or Limitations?

Even with a long list of benefits, there was still the question of challenges or limitations of open science. Is it possible to still contribute or make use of open-source materials when working within exclusive research contracts?

“There are certain situations where you can’t do open source because of an agreement or contract,” Dr. Sun said. He added that he was fortunate to not currently be limited by these constraints, and even with industry sponsored projects there are ways to contribute back to open projects. “All the work is done in an open-source framework; it’s just that we can’t publish our results.”

A commonly debated disadvantage to open science is the idea of being “scooped.” When asked about these concerns, Dr. Sun said, “different people have different interests, focuses, hypotheses, tests and questions they want to answer” and a research project is much more than a single idea or method. He explained, “you can scoop my method but are you going to focus on the same study area, and try to answer the same geological questions that I am interested in? Probably not.”

Open science changes the cadence in which researchers openly collaborate. New forms of sharing such as Curvenote, GitHub, and Zenodo, and publishing such as preprints and digital archives, allow registration and comprehension of methods or ideas much earlier in a research cycle. All of science is based on the evolution and adaptation of ideas, sharing earlier and more transparently can increase impact.

Open Future

After our discussion it’s easy to understand how Dr. Sun can be so passionate and enthusiastic about the open-science, open-source, and open-education practices and communities. Sharing information earlier and often throughout the research process accelerates the discoveries and conclusions we are able to make collectively. By getting feedback sooner, we can implement these ideas, improve our skills as researchers and expand the impact of our work.

When early career researchers participate in open science they learn valuable skills and practices that can only serve to benefit them throughout their career. In regards to promoting open-science among his students, Dr. Sun commented, “these skills are transferable and especially helpful for those students who end up working in a non-geoscience-related industry. Quite a few of my students are now data scientists instead of geoscientists. The skills mentioned above are currently not in the curriculum [but] will serve them well even if they want to switch their career.”

A variety of tools exist to conduct open science. Zenodo makes it possible to link a publication to shared code and data. GitHub serves as a repository for open-source coding packages and freely available datasets. When publishing papers, open-access journals and preprint services, such as arXiv, allow readers earlier access to ideas.

As the open-science movement continues to grow, Curvenote is being designed to integrate and expand on these tools to serve researchers throughout their workflows: promoting reproducibility and open science. Today, researchers can version control Jupyter Notebooks and integrate directly with collaborative tools for technical writing. Results and findings remain linked and reproducible, all of which can remain private, be shared publicly on Curvenote, or exported to preprint services. By supporting reproducibility and allowing granular controls on privacy throughout the research process, we aim to support scientists and researchers as they accelerate and share their discoveries — no matter where they are on their open-science journeys.

Cover photo by Hunter Harritt on Unsplash.

Part 1

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