protocols.io use on mobile devices - sciNote blog (1)

Integration Between SciNote ELN and protocols.io Will Enable Users To Seamlessly Optimize Their Research Methods

 3 min read

Have you ever spent months correcting or adjusting one step of a previously published method? Do you often run into “Contact author for details” or “… we used a slightly modified version of the method…” sections?

We are speaking with Lenny Teytelman, cofounder of protocols.io – a collaborative research platform that is taking the process of scientific discovery to the next level by allowing researchers to share protocols, communicate possible corrections and optimize research methods. Available for every scientist today, this open access repository of research protocols is both free to read and free to publish. We will share with you the story behind it and discuss what will sciNote electronic lab notebook users be able to do once it is connected with protocols.io.

How did a postdoc struggle bring to life one of the greatest research platforms today? A platform that is changing the way we communicate research?

The motivation for our effort goes back to the beginning of my postdoc at MIT. I spent a year and a half correcting a single step of a microscopy method. It turned out that instead of a microliter of an enzyme we needed 5 and instead of a 15-minute incubation we needed an hour. However, as this discovery was not a new technique but a correction of a previously-published method, I had no way to get credit for this work. More importantly, all of the scientists using this method would either get misleading results or would have to waste 1-2 years re-discovering what I know. (For those wondering, yes, I did share these details on protocols.io.)

However, as we got going, we quickly realized that keeping protocols up-to-date is the second problem to solve. The first issue is that when we publish, we don’t usually share the full details necessary for replicating and following up on the work. The Materials & Methods sections of journals are full of things like “we used a slightly modified version of the protocol reported in paper X” or “contact author for details”. In fact, the recent publication of the first results of the Reproducibility Project: Cancer Biology showed that missing the critical details of the protocols is a huge problem for reproducibility. As Ed Yong wrote in The Atlantic when reporting on these results,

The hardest part, by far, was figuring out exactly what the original labs actually did. Scientific papers come with methods sections that theoretically ought to provide recipes for doing the same experiments. But often, those recipes are incomplete, missing out important steps, details, or ingredients. In some cases, the recipes aren’t described at all; researchers simply cite an earlier study that used a similar technique.”

So over the past two years, a lot of our focus has been on pushing for a shift in the way we communicate our research. We’ve been working on connecting with journals to encourage authors to share the explicit protocols as they submit their research papers for peer review. The ice is finally starting to melt.

 

How can scientists share and discover up to date protocol knowledge via protocols.io?

Instead of several paragraphs describing some of our coolest features, here is a 90-second video summarizing them in a way more entertaining fashion:

sciNote ELN and protocols.io decided to connect. Can you tell us a bit more about that?

I should share a tidbit from our history regarding electronic lab notebooks (ELNs). Since our mobile protocols.io apps on iOS and Android make it possible to follow a protocol step-by-step as you do an experiment and to keep track of specific changes, there is an ELN component to our product. This was part of protocols.io from day one, and at first, we even had plans to expand it into a full-featured ELN. Luckily, we understood fairly quickly that focus is critical for startups. It’s hard enough to build a protocol repository and get people to use it. It is insanely hard to build a good ELN. To do both for the same startup is impossible. So, instead, we added public APIs to allow any existing ELN to connect to us and vice versa. As I mentioned above, we’re big fans of sciNote and look forward to the collaboration and to sciNote becoming the first digital notebook to connect to protocols.io.

What will sciNote ELN users be able to do once it is connected with protocols.io?

We are planning to start with a simple integration so that sciNote electronic lab notebook users can seamlessly connect to their protocols.io account to see their protocols and journal records while working inside sciNote.

Later on, we hope to enable bidirectional integration between our platforms. That is, we hope to let the scientists also export from sciNote to protocols.io to create new protocols and to see their sciNote lab notebook records easily when working in protocols.io. Ultimately, we dream of a flow when you click an “add to manuscript” button on sciNote or protocols.io and it automatically adds the protocol to the paper’s Materials & Methods and pulls up the figures from the experiment run with that protocol for insertion in the the Results section.

The broad mission of protocols.io and sciNote is the same – to save scientists time and make their work more reproducible and efficient. Without a doubt, integration of sciNote and protocols.io will help to move a little bit closer towards that goal.

 

By Lenny Teytelman (protocols.io) & Tea Pavlek (sciNote LLC)

Leave us a comment:

2 Comments Published

by Jarral Ryter , post on 17 January 2018 |

Are these two systems connected yet? curious.

by Tea Pavlek , post on 18 January 2018 |

Dear Jarral,

yes! You can find more information about the integration and how to use protocols.io with sciNote here: https://scinote.net/blog/scinote-now-integrated-protocols-io/

We would be glad to hear your feedback, ideas and suggestions.
Feel free to contact us anytime.

Kind regards,
Tea from sciNote