These Two Former Researchers Are Laser-Focused on Bettering Research Communications

July 10, 2019 Chris Graf

Picture this…

…an information scientist trains at the University of California, Los Angeles (UCLA) then begins a postdoc in astrophysics at Harvard. He becomes increasingly frustrated by 20th-century authoring software that does nothing for the kind of collaboration he and his fellow researchers need so they can capture and communicate the 21stcentury science they’re doing. So, he starts writing some software. 

Cut to…

…a few thousand miles away, at the University of Cambridge, UK, a computational biologist is feeling the same frustration, questioning why journals still “flatten” tables and figures for the web pages they publish, seemingly stuck in their 18th century print-like paradigm. He believes that breaking out of that print-like paradigm will enable more insights and knowledge sharing that will, in turn, accelerate the pace of discovery. He too begins coding software.


Alberto Pepe (our information scientist and astrophysicist) and Matias Piipari (our computational biologist), whose startup companies, Authorea and Manuscripts joined Atypon and Wiley, bringing their laser focus and expertise around solving these issues for researchers. Their goal has always been to simplify how researchers communicate, get organized and collaborate, thus accelerating the pace of science and discovery.

Alberto Pepe is Director of Product at Atypon and is involved in building tools and initiatives for open research. Previously at Harvard University, UCLA, University College London, and CERN, he holds 30+ publications in network analysis, scientific communication, and computational astrophysics.




Matias Piipari is Senior Product Director – Collaborative Research and Authoring Tools at Atypon and is passionate about creating software products. As a computational biologist at the University of Cambridge and Imperial College London, his work bridges the gap between academia and software development.




We're delighted that Alberto and Matias were able to spare some time to talk to us about their journeys and how they see open research progressing.

Q. What was the first thing you did when you walked in the door at Wiley?

Alberto: I believe that the first thing I did when I walked in the door at Wiley was ask around for the best espresso coffee shop in Hoboken. I’m still looking! Jokes aside, I wanted to get to know the people I would be working with. Bear in mind that this was my first job in the corporate world, after several years spent in academia, and then as an entrepreneur. So, I set-up meetings with people within Atypon and Wiley to just chat and find out about their day-to-day work, their processes, their ambitions, and the company culture. I was also curious about overall interest within the company in open access, open science, transparent and reproducible research, data sharing, open peer review, and even startup culture, user-centered product development, and pixel-perfect design. I’m happy to say that I made many friends pretty quickly! 

Q. You say, “I was also curious about overall interest within the company in open access, open science, transparent, reproducible research, data sharing, open peer review, and even startup culture, user-centered product development, and pixel-perfect design.” What stuck out in your mind?

Alberto: I was encouraged by many colleagues, including some in the Executive Leadership Team, to maintain solid bridges both with initiatives happening in academic research and in the startup world. In other words, I was asked - to my surprise - to keep a foot in research and to understand the attitudes and day-to-day practices of researchers, especially the tech-savvy early adopters who are making a difference when it comes to open science and reproducibility. Similarly, I was asked to foster an attitude, work ethic, and passion within my team similar to what I had found in startups.

Q. How did that first step set you up for the mission you brought with you, to simplify things for researchers?

Alberto: I’m a firm believer that the road towards more modern and efficient research publishing is paved with collaboration and synergy. It is essential to embrace an open culture of communication and cooperation among colleagues and across business units and to bring that same attitude even when interacting with entities outside of Wiley. The next generation of tools and platforms for research publishing will be built in an open ecosystem which requires the cooperation of companies, startups, funding agencies, universities, and publishers. 

Q. And how has that kind of “collaboration and synergy” worked for you, Matias?

Matias: To me, it boils down to fostering a super competent, supportive and passionate team and a product development process where actual researcher needs are heard. This is what we are here for, and the product design and feature set, and ultimately user excitement, emerges from that. I feel super fortunate to work on a team of heavy hitters like Alberto and the wider Atypon and Wiley teams to combine our technologies and approaches to create new, exciting collaborative experiences for scientists.

Q. The research and scholarly communications world is changing pretty fast. What about the problems that you’re addressing? How have they evolved since you walked in the door? Or are they pretty much still the same?

Alberto: We definitely did not experience a "Kuhnian" paradigm shift in the world of research and scholarly communication in the last year, but there are many positive signs pointing in the right direction. 

Preprints were already a thing a year ago, but over the past few months, their popularity and use have increased substantially in disciplines outside of the physical and biological sciences. Importantly, in the last year most funding agencies (NIH and NASA, for example) have allowed funded researchers to cite their interim research products (preprints) and claim them as products of their funding. This is BIG for researchers. 

Another one is peer review - which has always seemed like the one part of academic publishing most resistant to any change. However, over the past few months, I personally noticed some grassroots initiatives, led by authors and editors alike, aiming at openly publishing peer review reports and alongside peer reviewed publications. 

Something is moving.

Q. What can you share with us about the progress you’re making? What’s already emerged from your product development work, ready for researchers to try out on Authorea and Manuscripts?

Alberto: We are keeping on developing Authorea and Manuscripts with authors and researchers in mind. Manuscripts cover the entire content creation process by offering a modern, simple online and offline platform for creating complex scholarly documents in a simple manner. Authorea is more oriented towards publication, with a focus on open research, lightweight publishing, and preprinting. It enables fast, seamless publication of all kinds of research outputs: articles, data sets, code, figures, slides, and micro-publications. Right now, we’re working on ways to create journal-branded preprint sites and connecting them to submission and peer review systems.

Q. You’ve shared some nice details about Authorea there, and to make that all feel real, is there any chance you can share a few images or links to help bring what we’re doing with Authorea alive?

Alberto: I can point to a couple of recent blog posts which detail the file hosting feature and preprinting:

We also have a new cool preprint server that recently appeared on Authorea here.

As for a service we’re building for articles that are under review, I can only share one design for now. It’s very rough and a work in progress


Q. Similarly, is there anything you can share about Manuscripts, Matias?

Matias: We have focused a lot of our efforts thus far on creating a really pleasant, simple, collaborative writing workflow that will feel familiar to Word and Google Docs users, but which offers scholarly powers lacking in these tools. To share some examples, we offer a powerful citation workflow, cross referencing, a built-in equation editor, and most excitingly, the ability to create computationally reproducible figures. In fact, we have already used the new collaborative web-based version of Manuscripts (that supersedes the Mac-based version my company developed before joining Wiley) to write a conference paper about the product – this paper, written in Manuscripts with Alberto and Alf Eaton (the brains behind the new editor), describes in a lot more detail our approach to tackling scholarly authoring needs.

There is an early test version of Manuscripts here that we’d love to get feedback on.

If you feel like geeking out, since we’re developing this product as an open source effort, you can also check out a lot of the project’s source code on open feature requests and bug trackers here. And, here is what our document editing tools look like, along with the document templates we have from thousands of supported journals:

Q. What’s your vision? Let’s look into your crystal ball for a moment. And without giving it all away, what do you think will become real in the next couple of years, and what’s your ambition?

Alberto: Our vision is to enable researchers to disseminate their research outputs in a timely, safe (and legal) fashion. With the phrase “research outputs” we are as inclusive as we could possibly be; researchers should be able to publish anything that deserves to be part of the scholarly record - not just flat, print-ready PDF articles. We are giving researchers tools to allow them to publish data, figures, dynamic visualizations, code and get credit for them; they can get a DOI for their work and get cited! This new incarnation of Authorea allows publishers to host and manage these rich contents in an entirely fresh new way. In a way, what Matias and I are working on our explorations and experiments that offer a glimpse into what the future of publishing could (and will) be like.

Matias: I second Alberto. What we want to accomplish is turning the research outputs that are reviewed and consumed to more than just static pictures of science – whilst the article of today is not going to disappear anytime soon, the future of publishing involves computationally reproducible, dynamic, interactive media. What we’re building are glimpses of the web-oriented, modern authoring and publishing workflows that are necessary for that.

Thanks, Alberto and Matias! That’s brilliant! You’ve explained how your approach will enable Wiley to support the “open research” and “open science” practices we’re seeing emerge from growing numbers of researchers, with the backing of their research funders and policy-makers. You’ve shown us how your ambitions will simplify how researchers communicate and get organized. We look forward to seeing more as your work progresses, and to enabling researchers to share their new knowledge in the most impactful and open ways.

About the Author

Chris Graf

Director, Research Integrity and Publishing Ethics at Wiley // Director, Research Integrity and Publishing Ethics at Wiley, and is Co-Chair of COPE, Committee on Publication Ethics (an elected and voluntary position for which he will serve a 2-year term). Chris leads initiatives at Wiley that focus on transparency, research integrity and publishing ethics.

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