A research article is an orderly summation of a complex and circuitous process. It is characterized by detailed planning, iterative trial and…
Our ongoing partnership with protocols.io led to a new and exciting PLOS ONE article type, Lab Protocols, which offers a new avenue to share research in-line with the principles of Open Science. This two-part article type gives authors the best of both platforms: protocols.io hosts the step-by-step methodology details while PLOS ONE publishes a companion article that contextualizes the study and orchestrates peer review of the material. The end result is transparent and reproducible research that can help accelerate scientific discovery.
Read our interview with protocols.io CEO and co-founder Dr. Lenny Teytelman where he discusses what triggered the concept for the company, how researchers can benefit from this collaboration and how his team settled on such an adorable racoon logo.
For those who are unfamiliar, what is protocols.io?
It is a platform for developing and sharing reproducible methods. It serves both researchers needing secure and private collaboration and those aiming to share their knowledge publicly.
What was the inspiration behind protocols.io? Did you have any particular experiences or issues as a researcher that led to you believing protocol sharing was an under-supported element of the scientific community?
It was a year and a half of my postdoc that went into correcting just a single step of the microscopy methods that I was using. Instead of a microliter of a chemical, the step needed five, and instead of a fifteen-minute incubation with it, it needed an hour. The problem is that this isn’t a new technique but is a correction of a previously-published method. That means I didn’t get any credit for that year and a half, and everyone using this method was either getting misleading results or had to spend one or two years rediscovering what I know—rediscovering what I’d love to share with them, but didn’t have a good way of doing.
This is the experience that led to my obsession with creating a central place to facilitate the sharing of such knowledge, within research groups and companies and broadly with the world.
As authors of PLOS ONE began to share methods, we realized that all researchers and disciplines had a need for a dedicated tool for proper method sharing… We now warmly welcome methods from all fields and disciplines, including psychology, social sciences, clinical, chemistry, and so on.– Lenny Teytelman, CEO and co-founder of protocols.io
Protocols.io launched in 2014 — how were the first few years? How were you able to make yourself known and show that your product is worthwhile and secure for researchers?
Oh, you just touched on a painful topic. I actually gave a talk at a conference in 2018, called The harsh lessons from 4 years of community building at protocols.io. The first years were surprisingly rough. As an academic with zero entrepreneurial experience, I naively expected that once we build the platform, I’d tell my scientist friends that it exists, and through word of mouth, it would go viral. Turns out that it is not how new initiatives work. There is a lot of dedicated work needed to build the trust and visibility and simply let researchers know that you exist.
It took the support of publishers, societies, funders, and Open Science and reproducibility champions to climb out of obscurity. Speaking of that support, the 2017 partnership between PLOS and protocols.io was critical in helping the research community learn about protocols.io.
How has the platform evolved since then? What elements have been consistent and what have been some major changes?
Our vision and mission have not really changed since 2014, but thanks to the constant feedback of the research community and a brilliant CTO and co-founder Alexei Stoliartchouk listening to that input, the product has grown from a rudimentary website to a powerful tool with amazing functionality to support the sharing of the method details and to help in the daily work of the researcher. For a fun comparison of where we were at launch in February 2014, take a look at our Kickstarter video.
One of the early changes was in scope, a year after we launched. We initially thought that this is a platform for experimental wetlab scientists, but soon after launch, requests started to come to expand it to support computational/bioinformatics workflows. And then in 2017, there was another expansion in scope, catalyzed by that same 2017 partnership with PLOS. As authors of PLOS ONE began to share methods, we realized that all researchers and disciplines needed a dedicated tool for proper method sharing. This actually led us to change our welcome page from “Repository for Life Science Methods” to “Repository for Research Methods.” We now warmly welcome methods from all fields and disciplines, including psychology, social sciences, clinical, chemistry, and so on.
How important is the new PLOS ONE Lab Protocol article type to the journey and mission of protocols.io?
Soon after our launch, when I realized that things don’t just “go viral”, I began to think a lot about incentives. It occurred to me some time in 2015 that it would be amazing if researchers had a way of turning their protocols into peer reviewed papers. I was looking at the F1000Research model and wondering if we could add peer review to protocols.io. The problem was that our scope was so broad, we would need thousands of academic editors to be able to support the peer review — essentially we’d have to build PLOS ONE. Then, in 2017 when we started working with PLOS, I realized, “We don’t have to build PLOS ONE! It already exists; we just need to partner!”
And while this partnership is a big deal for protocols.io, I am particularly excited about it because of what it can do for reproducibility and Open Science. As I said when we announced the launch, “We’re thrilled to extend our partnership with PLOS by launching this new modular article type. This will provide authors with all of the benefits of rigorous peer review, plus a dynamic and interactive platform to present their protocols, with support for videos and precise details that are important for adopting and building upon the published methods.”
What type of research does not need to be as fast as possible? Do malaria or pediatric cancer patients somehow have the luxury of time? Can our planet afford delays in climate research? Open and rapid sharing as we see today for COVID-19 must be the norm, not an exception.– Lenny Teytelman, on the importance of Open Science
PLOS and protocols.io have similar mission statements and nearby offices: how did this collaboration with PLOS start?
Many people assume that our collaboration with PLOS is a consequence of me being co-advised as a graduate student by Professor Michael Eisen, co-founder of PLOS. That actually is not the case. It is true that as soon as I realized in 2012 that something like protocols.io needs to be built, I called Professor Eisen, described the idea, and said, “PLOS should build such a platform.” But he replied, “PLOS is a publisher, not a software developer. You need to build it.”
So in fact, it is the Chief Science Officer of PLOS, Dr. Veronique Kiermer, who is the key early lead on the PLOS/protocols.io connection. Dr. Kiermer was the founding editor of Nature Methods and has a passion for reproducibility and a deep appreciation for the essential role that protocols play in the research cycle. We met at an Open Access mixer in San Francisco when she had just moved to PLOS. As I showed her what we had built, she asked countless questions of “can it do this and that” and I showed her the “yes” answers right on my phone. She got excited and said, “This is exactly what I always dreamed of. We should do something together!”
What has the COVID-19 pandemic taught you about the importance of Open Science and supporting collaborative research opportunities?
I’ve been stunned by the extent of rapid sharing and collaborative spirit in the research world, united against the COVID-19 pandemic. It is how you ideally imagine science working. It is how science should work. We’ve seen a remarkable level of rapid method sharing in the SARS-CoV-2 group. But it’s not just the methods; researchers are sharing data, preprints, code in precisely the way that accelerates and amplifies everyone’s efforts around the globe.
I am simultaneously inspired by what I see and frustrated that this isn’t yet the norm. I’ve been watching the world and publishers declare in 2015 that rapid sharing and immediate Open Access are essential for Ebola research. Then the same in 2016 for Zika. Then 2019 for all research related to the opioid crisis. In 2020 and 2021 it’s COVID-19. It’s frustrating that we make exceptions for pandemics and crises and then go back to the traditional stunted way of sharing.
What type of research does not need to be as fast as possible? Do malaria or pediatric cancer patients somehow have the luxury of time? Can our planet afford delays in climate research? Open and rapid sharing as we see today for COVID-19 must be the norm, not an exception.
What’s next for protocols.io? (How can you continue to help scientists adopt Open Science activities?)
The beautiful part of our growth (we have over 9,000 public protocols now and have been roughly doubling every year since our launch), is that with increased sharing and researchers on protocols.io we also have received more feedback and requests than ever. As more requests and suggestions come in, our appetite for improving and enhancing the platform only increases. It’s kind of like with research itself – each answer leads to more questions and more thirst for experiments.
We are also genuinely excited about the PLOS ONE Lab Protocols and we look forward to the first papers being published and to the future developments in this partnership. We’re just getting started.
Bonus Question: How did you decide on the cute raccoon logo?
Too many reasons to list here! Read this Twitter thread to find out!