Frontiers | The Academic, Societal and Animal Welfare Benefits of Open Science for Animal Science | Veterinary Science

Abstract:  Animal science researchers have the obligation to reduce, refine, and replace the usage of animals in research (3R principles). Adherence to these principles can be improved by transparently publishing research findings, data and protocols. Open Science (OS) can help to increase the transparency of many parts of the research process, and its implementation should thus be considered by animal science researchers as a valuable opportunity that can contribute to the adherence to these 3R-principles. With this article, we want to encourage animal science researchers to implement a diverse set of OS practices, such as Open Access publishing, preprinting, and the pre-registration of test protocols, in their workflows.

 

Interviews with the lab protocol community – insights from an Academic Editor and a reviewer – EveryONE

“What do you think are the benefits of lab protocols for open science?

RK: PLOS ONE journal in collaboration with protocols.io has developed a unique and state-of-the-art platform for publishing lab protocols. This is a well-timed and useful innovation. The development of scientific knowledge is based on a variety of methodological approaches bordering on art. Because of the increasing complexity of scientific methods and their diversity, an appropriate forum or open science platform is needed, where the research community can present the best solution and point out the problems that may be encountered in other laboratories. Such a platform should of course be open, and in this form, it is really effective.

AF: Improving data reproducibility in research is one of today’s most important issues to address. Providing clear and detailed protocols, without limitation of words or space, is an effective way to communicate optimized protocols. This will directly help to improve data reproducibility between labs, as well as provide a thorough record of procedures that have been published in parallel. Improving communication of optimized protocols helps to drive robust research, allowing people to build their own research on already thorough studies, and not spend excessive time optimizing protocols based on poorly executed or explained protocols. …”

Open access methods and protocols promote open science in a pandemic – ScienceDirect

“How open-access methods and protocols publishing advanced the project’s goals

In considering a publication strategy, Milón was motivated by a common feeling of frustration: being fascinated by a new scientific publication and excited to try the new approach in his own lab but ultimately being disappointed to realize that the methods reporting wasn’t quite robust enough to faithfully recreate the experiment. Milón sees this as not only an inconvenience for himself but a broader challenge for research reproducibility. To help prevent challenges to other groups adopting their method, their results were therefore reviewed, polished, and packaged as three freely available scientific documents (Alcántara et al., 2021a; Alcántara et al., 2021b; Mendoza-Rojas, et al., 2021). The development of the method, including detailed reporting of the various optimizations and analytical comparisons that informed each component of the assay was described in Cell Reports Methods (Alcántara et al., 2021b). The methods paper provides the empirical justification for each step of the method and serves as both a general blueprint for future open-source diagnostic methods development and as a more specific template from which future modifications to any given step can be explored….”

Open access methods and protocols promote open science in a pandemic – ScienceDirect

“How open-access methods and protocols publishing advanced the project’s goals

In considering a publication strategy, Milón was motivated by a common feeling of frustration: being fascinated by a new scientific publication and excited to try the new approach in his own lab but ultimately being disappointed to realize that the methods reporting wasn’t quite robust enough to faithfully recreate the experiment. Milón sees this as not only an inconvenience for himself but a broader challenge for research reproducibility. To help prevent challenges to other groups adopting their method, their results were therefore reviewed, polished, and packaged as three freely available scientific documents (Alcántara et al., 2021a; Alcántara et al., 2021b; Mendoza-Rojas, et al., 2021). The development of the method, including detailed reporting of the various optimizations and analytical comparisons that informed each component of the assay was described in Cell Reports Methods (Alcántara et al., 2021b). The methods paper provides the empirical justification for each step of the method and serves as both a general blueprint for future open-source diagnostic methods development and as a more specific template from which future modifications to any given step can be explored….”

Why I am building Arcadia.

“I walked away with the backing to establish a new startup, Trove….

At Trove, we are led by curiosity and remain committed to learning and sharing the knowledge we’ve gained. There is no need to lock up the lessons we’ve learned from others in the tick community. In fact, we have sought their feedback, and we will publish most of our protocols, tools, and datasets without paywalls or delays. It’s the most rigorous any of us have ever had to be, and all of this is in the absence of journals. Our work may ultimately translate into products that could be useful to many more people….

For all these reasons, I have decided to take the best parts of my experiences to build a new research organization called Arcadia Science. I am co-founding Arcadia with yet another fierce woman scientist Prachee Avasthi, who is a leader among leaders in the fight for open science. …”

Clearinghouse Standards of Evidence on the Transparency, Openness, and Reproducibility of Intervention Evaluations | SpringerLink

Abstract:  Clearinghouses are influential repositories of information on the effectiveness of social interventions. To identify which interventions are “evidence-based,” clearinghouses review intervention evaluations using published standards of evidence that focus primarily on internal validity and causal inferences. Open science practices can improve trust in evidence from evaluations on the effectiveness of social interventions. Including open science practices in clearinghouse standards of evidence is one of many efforts that could increase confidence in designations of interventions as “evidence-based.” In this study, we examined the policies, procedures, and practices of 10 federal evidence clearinghouses that review preventive interventions—an important and influential subset of all evidence clearinghouses. We found that seven consider at least one open science practice when evaluating interventions: replication (6 of 10 clearinghouses), public availability of results (6), investigator conflicts of interest (3), design and analysis transparency (3), study registration (2), and protocol sharing (1). We did not identify any policies, procedures, or practices related to analysis plan registration, data sharing, code sharing, material sharing, and citation standards. We provide a framework with specific recommendations to help federal and other evidence clearinghouses implement the Transparency and Openness Promotion (TOP) Guidelines. Our proposed “TOP Guidelines for Clearinghouses” includes reporting whether evaluations used open science practices, incorporating open science practices in their standards for receiving “evidence-based” designations, and verifying that evaluations used open science practices. Doing so could increase the trustworthiness of evidence used for policy making and support improvements throughout the evidence ecosystem.

 

Methods as a scientific asset – The Official PLOS Blog

“Clear, complete, and open methods increase credibility and support lasting impact. Documenting and sharing methodologies has interrelated scientific and reputational benefits for individuals and the community. 

Making methods public creates a positive impression. Having the option to review detailed methods increases readers’ trust, whether or not they consult the documentation. 
Researchers can more easily reproduce results with detailed open methods. Authors who want to apply the method in their own research can do so more efficiently if the approach is described in detail and easy to find online.
Strong, easy-to-follow methods are more likely to be used in future research, and by extension more likely to be cited, bringing fresh eyes to the original and helping it to remain relevant over time….”

Public access to protocols of contemporary cancer randomized clinical trials | Trials | Full Text

Abstract:  Access to randomized clinical trial (RCT) protocols is necessary for the interpretation and reproducibility of the study results, but protocol availability has been lacking. We determined the prevalence of protocol availability for all published cancer RCTs in January 2020. We found that only 36.1% (48/133) of RCTs had an accessible protocol and only 11.3% of RCTs (15/133) had a publicly accessible protocol that was not behind a paywall. Only 18.0% (24/133) of RCTs were published in conjunction with the protocol on the journal website. In conclusion, few cancer RCTs have an accessible research protocol. Journals should require publication of RCT protocols along with manuscripts to improve research transparency.

 

Communicating reusable research with peer-reviewed protocols from PLOS ONE and protocols.io

“Register below for our up-coming webinar where PLOS, protocols.io and the research community will introduce an innovative new publishing option that gives researchers recognition for their contributions to developing and optimising research methods, and advances open science. Developed with researchers and in partnership with the protocols.io team, Lab Protocol articles in PLOS ONE consist of two interlinked components that together describe peer-reviewed, reusable methods.

 

This webinar will cover:

The importance of sharing peer-reviewed protocols and methods to advance open science and meet researchers’ needs

A new, innovative partnership between protocols.io and PLOS ONE

An overview of the options for publishing protocols and methods at PLOS ONE

How peer-reviewed protocols at PLOS ONE complement other types of publication

The researcher perspective and experience with sharing and reusing verified methodologies

Questions from the audience and discussion with panelists…”

Day One Project: Re-envisioning Reporting of Scientific Methods

“The information contained in the methods section of the overwhelming majority of research publications is insufficient to definitively evaluate research practices, let alone reproduce the work. Publication—and subsequent reuse—of detailed scientific methodologies can save researchers time and money, and can accelerate the pace of research overall. However, there is no existing mechanism for collective action to improve reporting of scientific methods. The Biden-Harris Administration should direct research-funding agencies to support development of new standards for reporting scientific methods. These standards would (1) address ongoing challenges in scientific reproducibility, and (2) benefit our nation’s scientific enterprise by improving research quality, reliability, and efficiency. …

Common standards are already proving invaluable for the recognition and reuse of open data. The same principles could be applied to open methods….

Compliance could be achieved through a combination of “push” incentives from publishers and “pull” incentives from funders. As is already happening for open-data standards, federal agencies can require researchers to adhere to open-methods standards in order to receive federal funding, and scientific journals can require researchers to adhere to open-methods standards in order to be eligible for publication….”  

Dockstore: enhancing a community platform for sharing reproducible and accessible computational protocols | Nucleic Acids Research | Oxford Academic

Abstract:  Dockstore (https://dockstore.org/) is an open source platform for publishing, sharing, and finding bioinformatics tools and workflows. The platform has facilitated large-scale biomedical research collaborations by using cloud technologies to increase the Findability, Accessibility, Interoperability and Reusability (FAIR) of computational resources, thereby promoting the reproducibility of complex bioinformatics analyses. Dockstore supports a variety of source repositories, analysis frameworks, and language technologies to provide a seamless publishing platform for authors to create a centralized catalogue of scientific software. The ready-to-use packaging of hundreds of tools and workflows, combined with the implementation of interoperability standards, enables users to launch analyses across multiple environments. Dockstore is widely used, more than twenty-five high-profile organizations share analysis collections through the platform in a variety of workflow languages, including the Broad Institute’s GATK best practice and COVID-19 workflows (WDL), nf-core workflows (Nextflow), the Intergalactic Workflow Commission tools (Galaxy), and workflows from Seven Bridges (CWL) to highlight just a few. Here we describe the improvements made over the last four years, including the expansion of system integrations supporting authors, the addition of collaboration features and analysis platform integrations supporting users, and other enhancements that improve the overall scientific reproducibility of Dockstore content.