cRegulome: an R package for accessing microRNA and transcription factor-gene expression correlations in cancer [PeerJ]

Abstract:  Background

Transcription factors and microRNAs play a critical role in regulating the gene expression in normal physiology and pathological conditions. Many bioinformatics tools were built to predict and identify transcription factor and microRNA targets and their role in the development of diseases including cancers. The availability of public access high-throughput data allows researchers to make data-driven predictions.

Implementation

Here, we developed an R package called cRegulome to access, manage and visualize data from open source databases. The package provides a programmatic access to the regulome (transcription factor and microRNA) expression correlations with target genes of different cancer types. It obtains a local instance of Cistrome Cancer and miRCancerdb databases and provides classes and methods to query, interact with and visualize the correlation data.

Availability

cRegulome is available on the comprehensive R archive network (CRAN) and the source code is hosted on GitHub as part of the ROpenSci on-boarding collection, https://github.com/ropensci/cRegulome.

Open Research Funders Group Welcomes Howard Hughes Medical Institute as Newest Member — Open Research Funders Group

The Open Research Funders Group (ORFG) is excited to announce the addition of the Howard Hughes Medical Institute (HHMI) as its newest member. HHMI is an independent philanthropy that supports basic biomedical scientists and educators with the potential for transformative impact. HHMI has long viewed the sharing of research materials and tools as a fundamental responsibility of the scientific endeavor. The ORFG is pleased to add the Howard Hughes Medical Institute to the growing roster of research funders working to enable the open sharing of research outputs….”

Mindray Signs Patient Safety Movement’s Open Data Pledge & Becomes 90th Company to Join to Improve Patient Safety | Business Wire

The Patient Safety Movement Foundation (PSMF) announced today that the global medical device developer and manufacturer Mindray has become the 90th company to sign the PSMF’s Open Data Pledge, demonstrating its commitment to improving patient safety through data sharing….”

Mindray Signs Patient Safety Movement’s Open Data Pledge & Becomes 90th Company to Join to Improve Patient Safety | Business Wire

The Patient Safety Movement Foundation (PSMF) announced today that the global medical device developer and manufacturer Mindray has become the 90th company to sign the PSMF’s Open Data Pledge, demonstrating its commitment to improving patient safety through data sharing….”

eLife welcomes Michael Eisen as Editor-in-Chief | For the press | eLife

“eLife is pleased to announce Michael (Mike) Eisen as its new Editor-in-Chief.

A world leader in advocacy for open science, Eisen, from University of California, Berkeley, and the Howard Hughes Medical Institute (HHMI), was chosen following a worldwide search and selection process. In addition to his scientific achievements as an HHMI Investigator and Professor of Molecular and Cell Biology, he has demonstrated outstanding leadership and commitment to reforming research comunication for the benefit of scientists and society….”

Big pharma is embracing open-access publishing like never before

“Scientists who work in the pharmaceutical industry have begun to publish a higher proportion of their papers open access than academics who aren’t in industry, according to an analysis.

In a literature analysis, researchers found that the proportion of open-access papers published by 23 large drug companies, such as Pfizer and Roche, almost doubled between 2009 and 2016, and has overtaken the proportion of freely available papers published generally in medicine-related fields. The study was posted to the SocArXiv preprint server on 7 February1….”

roduction and uptake of Open Access publications involving the private sector: the case of big pharma

Abstract:  Over the last years Open Access has been ranked very high on science policy agenda’s both internationally as well as nationally. This resulted in many national mandates and international guidelines on OA publishing of scientific results. One of the reasons OA has been pushed so strongly by science policy is found in the argument that what is financed publicly, should be publicly available. This argument, also known as the ‘tax payers argument’ is used to support and legitimize the push for open accessibility, not only of scientific publications, but also of the underlying research data, in order to guarantee the nonacademic sector, with lower degrees of accessibility to otherwise ‘behind-the-paywall’ information, access to outcomes of scientific research in the public sector. In this study we will focus on the developments in the OA publishing in one particular institutional sector, the private sector. Business enterprises represent the main sector in terms of R&D investments. According to Eurostat, in the year 2016 this sector represented 65% of the total R&D expenditures within the EU28. While objectives and incentives in the private sector might not always been aligned with the disclosure of research results in the open scientific literature, there is no doubt that this is the main actor when it comes to R&D performance. Within the business sector, we will focus our study in the pharmaceutical sector, by selecting a number of large pharmaceutical companies. Pharmaceutical companies represent an interesting case of study, given that is it one of the most R&D intensive industries, while it si also known for its shift in R&D orientation, from an in-house focus in the development of R&D towards a model much more open and collaborative, with more interactions with academic partners and other companies. Despite the importance of industrial R&D, until now it remains relatively understudied how private sector institutions which are active in R&D have embraced the OA movement, hence it remains relatively unknown how the private sector adapts to and can benefit from the new paradigm of open scholarship. Our objective is to shed more light on the extent to which big pharma both has been publishing in OA and also has been benefiting from OA publications to build their own research.

Production and uptake of Open Access publications involving the private sector: the case of big pharma

Abstract:  Over the last years Open Access has been ranked very high on science policy agenda’s both internationally as well as nationally. This resulted in many national mandates and international guidelines on OA publishing of scientific results. One of the reasons OA has been pushed so strongly by science policy is found in the argument that what is financed publicly, should be publicly available. This argument, also known as the ‘tax payers argument’ is used to support and legitimize the push for open accessibility, not only of scientific publications, but also of the underlying research data, in order to guarantee the nonacademic sector, with lower degrees of accessibility to otherwise ‘behind-the-paywall’ information, access to outcomes of scientific research in the public sector. In this study we will focus on the developments in the OA publishing in one particular institutional sector, the private sector. Business enterprises represent the main sector in terms of R&D investments. According to Eurostat, in the year 2016 this sector represented 65% of the total R&D expenditures within the EU28. While objectives and incentives in the private sector might not always been aligned with the disclosure of research results in the open scientific literature, there is no doubt that this is the main actor when it comes to R&D performance. Within the business sector, we will focus our study in the pharmaceutical sector, by selecting a number of large pharmaceutical companies. Pharmaceutical companies represent an interesting case of study, given that is it one of the most R&D intensive industries, while it si also known for its shift in R&D orientation, from an in-house focus in the development of R&D towards a model much more open and collaborative, with more interactions with academic partners and other companies. Despite the importance of industrial R&D, until now it remains relatively understudied how private sector institutions which are active in R&D have embraced the OA movement, hence it remains relatively unknown how the private sector adapts to and can benefit from the new paradigm of open scholarship. Our objective is to shed more light on the extent to which big pharma both has been publishing in OA and also has been benefiting from OA publications to build their own research.

A proposal for the future of scientific publishing in the life sciences

Abstract:  Science advances through rich, scholarly discussion. More than ever before, digital tools allow us to take that dialogue online. To chart a new future for open publishing, we must consider alternatives to the core features of the legacy print publishing system, such as an access paywall and editorial selection before publication. Although journals have their strengths, the traditional approach of selecting articles before publication (“curate first, publish second”) forces a focus on “getting into the right journals,” which can delay dissemination of scientific work, create opportunity costs for pushing science forward, and promote undesirable behaviors among scientists and the institutions that evaluate them. We believe that a “publish first, curate second” approach with the following features would be a strong alternative: authors decide when and what to publish; peer review reports are published, either anonymously or with attribution; and curation occurs after publication, incorporating community feedback and expert judgment to select articles for target audiences and to evaluate whether scientific work has stood the test of time. These proposed changes could optimize publishing practices for the digital age, emphasizing transparency, peer-mediated improvement, and post-publication appraisal of scientific articles.