An interview with protocols.io: CEO Lenny Teytelman on partnering with PLOS – The Official PLOS Blog

“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….”

An interview with protocols.io: CEO Lenny Teytelman on partnering with PLOS – The Official PLOS Blog

“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….”

Assessment of transparency indicators across the biomedical literature: How open is open?

Abstract:  Recent concerns about the reproducibility of science have led to several calls for more open and transparent research practices and for the monitoring of potential improvements over time. However, with tens of thousands of new biomedical articles published per week, manually mapping and monitoring changes in transparency is unrealistic. We present an open-source, automated approach to identify 5 indicators of transparency (data sharing, code sharing, conflicts of interest disclosures, funding disclosures, and protocol registration) and apply it across the entire open access biomedical literature of 2.75 million articles on PubMed Central (PMC). Our results indicate remarkable improvements in some (e.g., conflict of interest [COI] disclosures and funding disclosures), but not other (e.g., protocol registration and code sharing) areas of transparency over time, and map transparency across fields of science, countries, journals, and publishers. This work has enabled the creation of a large, integrated, and openly available database to expedite further efforts to monitor, understand, and promote transparency and reproducibility in science.

 

 

What’s Next for Open Science – Making the Case for Open Methods – The Scholarly Kitchen

“But data alone is not enough, and an enormous hole in the open science movement has been the lagging attention paid to the reporting of research methodologies. Being able to review the data behind a study does indeed allow one to see if a researcher’s analysis and the conclusions drawn are accurate for that dataset. But it does little to validate the quality and accuracy of the dataset itself. If I don’t know how you got that data, I have no idea if it’s any good, and I certainly don’t stand any chance of replicating it.

A big problem here is that the scant information offered by most journals’ Materials and Methods sections is insufficient to have any chance of repeating what the original authors did. Often when describing a technique, an author will merely cite a previous paper where they used that technique…which also cites a previous paper, which also cites a previous paper and the wild goose chase is on. This lack of detailed methodology reporting is something of an anachronism, driven by decades of a print-dominant publication model aimed at reducing the number of pages in journal issues, along with a lack of incentives to improve methods reporting.

As open data requires the public availability of the data behind any published research conclusions, so open methods would require the public availability of detailed documentation of the procedures used to gather and analyze those data. Like open data, this can happen through a variety of routes — publication of the method as a standalone paper cited by the research paper, detailed documentation of the methods used in the paper itself (or its supplementary materials), or citation of a deposited documentation of the method in a repository such as protocols.io….”

Submit your Lab and Study Protocols to PLOS ONE! – The Official PLOS Blog

“PLOS ONE’s array of publication options that push the boundaries of Open Science continues to expand. We’re happy to announce two new article types that improve reproducibility and transparency, and allow researchers to receive credit for their contributions to study design: Lab Protocols and Study Protocols. 

These new article types complement other Open Science developments at PLOS ONE, such as Registered Reports, and support PLOS’ mission to accelerate progress in science and medicine. Adding reliable and accessible methods that can be built upon to the scientific record, Lab and Study Protocols support robust, reproducible science.  As reproducible science helps accelerate discoveries, such contributions deserve notice. …”

Open Methods: How to receive credit, encourage reproducibility and acknowledge your peers – Countway LibCal – Harvard Library. Countway Library of Medicine

“Research papers and protocol organization in labs often lack detailed instructions for repeating experiments. protocols.io is an open-access platform for researchers to create step-by-step, interactive and dynamic protocols that can be run on mobile or web. Researchers can share protocols with colleagues, collaborators, the scientific community or make them public, with ease and efficiency.

Come learn about protocols.io, navigate credit and acknowledgement, and see how your colleagues at Harvard are using this platform!

Join this webinar for a discussion of:

How do you balance sharing early to help others against sharing prematurely while not being misleading before the method is robust and verified?

Will journals object if you share full protocols before submitting a paper?

Can you share a protocol that was previously published in a journal?

 

Part 1: Protocol Sharing and Collaborating with Human Tumor Atlas Network (HTAN)
Connor Jacobson, Research Assistant, Laboratory of Systems Pharmacology, Harvard Medical School
Madison Tyler, Research Associate, Laboratory of Systems Pharmacology, Harvard Medical School

Part 2: Copyright, credit, scooping: the tricky details of protocol-sharing
Lenny Teytelman, PhD, CEO and Cofounder, protocols.io …”

Towards FAIR protocols and workflows: the OpenPREDICT use case [PeerJ]

Abstract:  It is essential for the advancement of science that researchers share, reuse and reproduce each other’s workflows and protocols. The FAIR principles are a set of guidelines that aim to maximize the value and usefulness of research data, and emphasize the importance of making digital objects findable and reusable by others. The question of how to apply these principles not just to data but also to the workflows and protocols that consume and produce them is still under debate and poses a number of challenges. In this paper we describe a two-fold approach of simultaneously applying the FAIR principles to scientific workflows as well as the involved data. We apply and evaluate our approach on the case of the PREDICT workflow, a highly cited drug repurposing workflow. This includes FAIRification of the involved datasets, as well as applying semantic technologies to represent and store data about the detailed versions of the general protocol, of the concrete workflow instructions, and of their execution traces. We propose a semantic model to address these specific requirements and was evaluated by answering competency questions. This semantic model consists of classes and relations from a number of existing ontologies, including Workflow4ever, PROV, EDAM, and BPMN. This allowed us then to formulate and answer new kinds of competency questions. Our evaluation shows the high degree to which our FAIRified OpenPREDICT workflow now adheres to the FAIR principles and the practicality and usefulness of being able to answer our new competency questions.

 

Publish your Registered Report on F1000Research

“We believe that the value of science is in the rigor of the method, not the appeal of the results – an ethos at the heart of our publishing model. Choosing to publish your research as a Registered Report puts this into practice, by shifting the focus away from the results and back to the research question. Registered Reports can be used for research in almost any field of study, from psychology and neuroscience, to medicine or ecology.

 

Registered Reports on F1000Research follow a two-stage process: firstly, the Study Protocol (Stage 1) is published and peer-reviewed by subject experts before data collection begins. Then, once the research has been completed, the Research Article (Stage 2) is published, peer reviewed, and awarded a Registered Report badge.

 

F1000Research is the first publisher to combine the Registered Reports format with an open, post-publication peer review model. Alongside our open data policy, this format enhances credibility, and takes transparency and reproducibility in research to the next level….”