Reproducibility and Transparency by Design | Molecular & Cellular Proteomics

Abstract:  To truly achieve reproducible research, having reproducible analytics must be a principal research goal. Biological discovery is not the only deliverable; reproducibility is an essential part of our research.

[From the body of the paper:] “As mandated data sharing resolves a portion of the overall transparency/reproducibility challenge, the unaddressed issue remains the sharing of analyses….” 

Transparent peer review and open data at Communications Biology | Communications Biology

“As of January 1st 2019, authors submitting manuscripts to Communications Biology can choose to publish the reviewer reports and author replies with their articles. The first articles with associated reviewer reports have now been published, representing an important step in our broader journey toward greater openness….

In addition, we ask that the data underlying plots and graphs in the main figures are available either in the supplementary materials or via an online generalist repository….Given the positive outcome of our trial, we are now making source data mandatory for published papers from today….”

Genetics Research turns a new [open access] leaf… | Genetics Research | Cambridge Core

“[W]e are delighted to announce that from January 2019, Genetics Research will convert to the open access model of publication. Genetics is an area where both authors and funders are showing substantial support for Open Access, with increasing author uptake of OA. It is our belief that converting Genetics Research to open access is the right solution for the journal and for the community. From January 2019, Genetics Research will publish all articles under the Creative Commons Attribution License (CC BY), which permits use, distribution, reproduction and adaptation in any medium, provided the original work is properly cited. Subsequently, an Article Processing Charge (APC) will be payable by authors or their funder on acceptance of their primary research article. In the majority of cases, these costs are paid by the author, his or her institution, or a funder….”

A single, open access journal may prevent the primary publishing problems in the life sciences: Accountability in Research: Vol 0, No 0

Abstract:  Herein, we discuss a novel way to knit current life sciences publishing structures together under the scope of a single life science journal that would countermand many of the issues faced in current publishing paradigms. Such issues include, but are not limited to, publication fees, subscription fees, impact factor, and publishing in more “glamorous” journals for career health. We envision a process flow involving (i) a single, overall, life sciences journal, (ii) divided into sections headed by learned societies, (iii) to whom all scientific papers are submitted for peer review, and (iv) all accepted scientific literature would be published open access and without author publication fees. With such a structure, journal fees, the merit system of science, and unethical aspects of open access would be reformed for the better. Importantly, such a journal could leverage existing online platforms; that is to say, it is conceptually feasible. We conclude that wholly inclusive publishing paradigms can be possible. A single, open access, online, life sciences journal could solve the myriad problems associated with current publishing paradigms and would be feasible to implement.

ORION Call for Novel Co-creation Initiatives | ORION Open Science

“The ORION project is launching a funding call for novel co-creation initiatives to open up research in life sciences and biomedicine. This call will provide funding of up to 100,000€ for a project that brings together a variety of different participants from across a range of sectors to co-create a new project or product based around life sciences research….

Projects should follow Open Science and RRI [Responsible Research & Innovation] principles….”

ORION Call for Novel Co-creation Initiatives | ORION Open Science

“The ORION project is launching a funding call for novel co-creation initiatives to open up research in life sciences and biomedicine. This call will provide funding of up to 100,000€ for a project that brings together a variety of different participants from across a range of sectors to co-create a new project or product based around life sciences research….

Projects should follow Open Science and RRI [Responsible Research & Innovation] principles….”

Improving Zimbabwe’s capacities to effectively use open data on malnutrition

The need to provide better access to timely and accurate data for policy makers, farmers and the private sector to inform agriculture and nutrition interventions and activities, has been widely acknowledged as part of the solution to ending malnutrition.

It is with this in mind that the Zimbabwe Evidence Informed Policy Network, with support from the Global Open Data for Agriculture and Nutrition (GODAN), implemented a 2-day workshop on open data for nutrition and agriculture. Held on 11-12 March 2019 in Harare, Zimbabwe, the objective of the workshop was to develop the skills and knowledge of agriculture and nutrition stakeholders to understand what open data is, the value and benefits of open data, and the intellectual and copyright issues around it….”

Improving Zimbabwe’s capacities to effectively use open data on malnutrition

The need to provide better access to timely and accurate data for policy makers, farmers and the private sector to inform agriculture and nutrition interventions and activities, has been widely acknowledged as part of the solution to ending malnutrition.

It is with this in mind that the Zimbabwe Evidence Informed Policy Network, with support from the Global Open Data for Agriculture and Nutrition (GODAN), implemented a 2-day workshop on open data for nutrition and agriculture. Held on 11-12 March 2019 in Harare, Zimbabwe, the objective of the workshop was to develop the skills and knowledge of agriculture and nutrition stakeholders to understand what open data is, the value and benefits of open data, and the intellectual and copyright issues around it….”

The effect of bioRxiv preprints on citations and altmetrics | bioRxiv

Abstract:  A potential motivation for scientists to deposit their scientific work as preprints is to enhance its citation or social impact, an effect which has been empirically observed for preprints in physics, astronomy and mathematics deposited to arXiv. In this study we assessed the citation and altmetric advantage of bioRxiv, a preprint server for the biological sciences. We retrieved metadata of all bioRxiv preprints deposited between November 2013 and December 2017, and matched them to articles that were subsequently published in peer-reviewed journals. Citation data from Scopus and altmetric data from Altmetric.com were used to compare citation and online sharing behaviour of bioRxiv preprints, their related journal articles, and non-deposited articles published in the same journals. We found that bioRxiv-deposited journal articles received a sizeable citation and altmetric advantage over non-deposited articles. Regression analysis reveals that this advantage is not explained by multiple explanatory variables related to the article and its authorship. bioRxiv preprints themselves are being directly cited in journal articles, regardless of whether the preprint has been subsequently published in a journal. bioRxiv preprints are also shared widely on Twitter and in blogs, but remain relatively scarce in mainstream media and Wikipedia articles, in comparison to peer-reviewed journal articles.

Biodiversidata: an open-access biodiversity database for Uruguay – IRep – Nottingham Trent University

Abstract

Background

The continental and marine territories of Uruguay are characterised by a rich convergence of multiple biogeographic ecoregions of the Neotropics, making this country a peculiar biodiversity spot. However, despite the biological significance of Uruguay for the South American subcontinent, the distribution of biodiversity patterns in this country remain poorly understood, given the severe gaps in available records of geographic species distributions. Currently, national biodiversity datasets are not openly available and, thus, a dominant proportion of the primary biodiversity data produced by researchers and institutions across Uruguay remains highly dispersed and difficult to access for the wider scientific and environmental community. In this paper, we aim to fill this gap by developing the first comprehensive, open-access database of biodiversity records for Uruguay (Biodiversidata), which is the result of a large-scale collaboration involving experts working across the entire range of taxonomic diversity found in the country. 

New information

As part of the first phase of Biodiversidata, we here present a comprehensive database of tetrapod occurrence records native from Uruguay, with the latest taxonomic updates. The database provides primary biodiversity data on extant Amphibia, Reptilia, Aves and Mammalia species recorded within the country. The total number of records collated is 69,380, spanning 673 species and it is available at the Zenodo repository: https:// doi.org/10.5281/zenodo.2650169. This is the largest and most geographically and taxonomically comprehensive database of Uruguayan tetrapod species available to date and it represents the first open repository for the country.