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Xuan Yu, a man with a mission to bring Open Science to the Earth [Sciences]

Part of my job at ScienceOpen is, and this might come as a surprise, advocating Open Science practices. It’s very easy to get bored of my own voice and ideas though, and I love hearing the perspectives and experiences of others. By listening to others about their Open Science adventures, and taking on board what they have to say and learning from them, we become stronger ourselves and as part of a community, and understand how to put things into practice more easily. This is why the Open Science Stars series exists, and why it’s so important! The next interview in the series is with Xuan Yu, and is our first with an Earth scientist, which is very exciting! Enjoy!

Credit: Xuan Yu
Credit: Xuan Yu

Hi Xuan! When did you first hear about ‘open science’? What was your first reaction, do you remember?

When I joined the OntoSoft committee meeting in March, 2015, I was introduced the concept of ‘open science’. I was not convinced by the concept, because there are usually many individual preference-based methods involved in most of geoscience projects.

It seems like much of the global push for open science comes from the Life Sciences. How are things in the Earth Sciences in terms of awareness and solutions?

Earth Sciences are slowing moving towards transparent, reproducible, and open culture. Many funding agencies and publishers have made actions to promote open science.

Can you tell us about some of the strategies you’ve developed for sharing data and software in geoscience? What drives your commitment to this?

I would like to recommend the strategy of transparent publication in geoscience. Sharing data and software with journal articles will draw wide attention and be practical. Because: 1) background information about the data and software has been explained in the article, which increases data transparency, 2) a scientific story in the article will lead readers to the data and software, which promotes the utility of the data. Specifically, there are four key steps in transparent publication of geoscience: persistent, linked, user-friendly, and sustainable (PLUS).

  • Persistent: Data, software, and authors should be persistently (i.e., consistently) identifiable. The process of the research (including data and software) should be assigned with persistent unique identifiers (e.g., data and software can be uploaded to online repositories with DOIs or PURLs (Permanent Uniform Resource Identifiers)).
  • Linked: Data and software should be linked in the computational workflow so that the software can be understood and reused by the readers. These links should include any intermediate data derived from the original data that represent essential information in the final figures of the article.
  • User-friendly: The software should be packaged with documentation and instructions so that readers can decide if the software can be reused in their work, and, if applicable, know how to apply it. It is important to be mindful of your audience and consider cross-disciplinary readers.
  • Sustainable: Authors are recommended to register anORCID (Open Researcher and Contributor ID), so that readers can track research updates. Software should be maintained at repositories (e.g.,GitHubCRAN, and CodePlex) so that further development can be achieved (e.g., users will be notified when the software is updated and authors will receive suggestions and comments regarding next version of the software).

Sharing data and software with journal articles will draw wide attention and be practical

A reader asked me about data and code in one of my previously published papers. And then he doubted the reproducibility of the results shown in the paper. I spent more than 3 months to guide him through each data processing pipeline to reproduce the final results. To avoid such problems in future publications, I decided to pay attention to transparency and reproducibility in the preparation of my future manuscripts.

I decided to pay attention to transparency and reproducibility in the preparation of my future manuscripts

How has the research community generally responded to this progressive action from you?

There are diverse responses. Some scholars agreed it is good practice to explore possible solutions for research reproducibility. Some scholars argued that it is difficult to apply widely across the scientific community.

Do you have any advice for researchers wishing to engage their communities with open research practices?

Try to promote open research practices among different levels of scientists, different communities according to their roles (e.g. publisher, funding agencies, conferences.), and different disciplines. When the engaging target is specified, it will be easier to develop and implement practices.

How important is open sharing of data in research aspects such as hydrology and other aspects of Earth system research? Why would there be any resistance to sharing in these fields?

Hydrologic data and models are important for researchers. We often ask corresponding authors for data and models to test our new methods or hypotheses. Sharing data and models require time and effort to explain the meaning and processing pipelines. Sometimes, research institutions or funding agencies have different policies on data and model sharing.

What are the biggest barriers to open science in the Earth Sciences? And how can we help overcome these?

First the practice is not clear. We need to inspire the motivation and incentive of open science and then develop best practices applicable in each discipline.

We need to inspire the motivation and incentive of open science and then develop best practices applicable in each discipline

How can we engage younger generations in these issues, and get them invested in open research at an earlier age?

I don’t know. [EdAppreciate the honesty! It’s a difficult question.]

You’ve given numerous talks about open science all across the USA. Has the response to these generally been positive?

No, there are both concerns and agreements.

What are the key messages that you try and communicate about open science?

I tried to convey that research facilities and methods are changing, funding agencies and journals are change, therefore, it’s the perfect time to think about open science.

How can platforms like ScienceOpen help younger researchers develop their skills in open research? What other tools or platforms would you recommend to researchers?

It is good to provide latest information on open research for each discipline. Maybe launch some programs or competitions to increase the involvements and experiences on open research.

Where do you see the future of scholarly communication? What steps are needed to get there?

The future of scholarly communication should be adapted to the requirement of researchers and development of modern technology. First, we need to inspire each researcher pay attention to the effectiveness of scholarly communication. Second, we need to bring discussions between communication professionals and research scientists to guide and develop the future of scholarly communication

We need to inspire each researcher pay attention to the effectiveness of scholarly communication

Whose responsibility do you think it is to lead this change?

Maybe the funding agencies should take the leading role.

Do you have any advice for younger researchers looking to start a career in academia?

No. But I do need advice for how to start a career in academia.

Thank you, Xuan! As a geologist, it’s great to see you championing so many great initiatives in the field! 🙂

Xuan Yu

Dr. Xuan Yu is one of 15 Distinguished Lecturers in the NSF EarthCube Program. His Distinguished Lecturer Tour was launched in 2016 on research transparency and the modern publication strategy for geoscientists. These lectures have been presented at University of Delaware, University of Pennsylvania, USGS, University of Maryland, Michigan State University, Princeton University, University of Florida, and University of Central Florida. Xuan holds a B.S. in Hydrogeology from China University of Geosciences and an M.S. in water resources engineering from China Institute of Water Resources and Hydropower Research. Xuan earned his Ph.D. in Civil Engineering from the Pennsylvania State University. He is currently a postdoctoral researcher in the Department of Geological Sciences at the University of Delaware.

1 thought on “Xuan Yu, a man with a mission to bring Open Science to the Earth [Sciences]”

  1. This is an interesting interview — especially because (as the you both mention) discussions re: ‘Open Science’ are not super common in Earth Sciences. Though there are several ‘open science’ solutions for us (as a discipline) that Dr. Yu mentions (repositories for code, figures and data), a major barrier in my mind is the lack of a dedicated preprint service for Earth Science/Geoscience. The EGU/Copernicus journals have ‘discussion papers’ when you submit (part of their open review pipeline) and depending on the research topic one can submit to biorxiv, peerj preprints, or arxiv…. But there is no dedicated preprint service just for earth scientists… seems strange in 2016…

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