Researchers reject APC-based OA publishing as promoted by Plan S – For Better Science

“Lynn Kamerlin, Bas de Bruin and their colleagues have been the most vocal critics of Plan S from the very beginning, braving continuous opposition from certain OA leaders. Now that final Plan S guidelines were released, the chemists publish this Open Letter expressing their worry about a possible dystopian OA future….”

Researchers warn open access Plan S may still be too rushed, despite one-year delay | News | Chemistry World

The funders behind Plan S – an ambitious set of policies that aims to speed up the transition to open access publishing – have released updated guidelines that delay implementing the plan for a year and provide more clarity on transformative publishing agreements.

The revisions have attracted mixed reactions from chemists, some of whom welcome the clarity while others worry it will harm their careers.

COAlition S – the group of funders behind Plan S – has said the plan will now come into effect in 2021 rather than the proposed 2020 date to give publishers more time to shift their business models. While many researchers agree this is necessary, some say it still does not allow enough time for the scientific community to adapt….”

Envisioning data sharing for the biocomputing community | Interface Focus

Abstract:  The scientific community is facing a revolution in several aspects of its modus operandi, ranging from the way science is done—data production, collection, analysis—to the way it is communicated and made available to the public, be that an academic audience or a general one. These changes have been largely determined by two key players: the big data revolution or, less triumphantly, the impressive increase in computational power and data storage capacity; and the accelerating paradigm switch in science publication, with people and policies increasingly pushing towards open access frameworks. All these factors prompt the undertaking of initiatives oriented to maximize the effectiveness of the computational efforts carried out worldwide. Taking the moves from these observations, we here propose a coordinated initiative, focusing on the computational biophysics and biochemistry community but general and flexible in its defining characteristics, which aims at addressing the growing necessity of collecting, rationalizing, sharing and exploiting the data produced in this scientific environment.

novel open access web portal for integrating mechanistic and toxicogenomic study results | Toxicological Sciences | Oxford Academic

Abstract:  Applying toxicogenomics to improving the safety profile of drug candidates and crop protection molecules is most useful when it identifies relevant biological and mechanistic information that highlights risks and informs risk mitigation strategies. Pathway-based approaches, such as GSEA, integrate toxicogenomic data with known biological process and pathways. Network methods help define unknown biological processes and offer data reduction advantages. Integrating the two approaches would improve interpretation of toxicogenomic information. Barriers to the routine application of these methods in genome-wide transcriptomic studies include a need for “hands-on” computer programming experience, the selection of one or more analysis methods (e.g. pathway analysis methods), the sensitivity of results to algorithm parameters, and challenges in linking differential gene expression to variation in safety outcomes. To facilitate adoption and reproducibility of gene expression analysis in safety studies, we have developed Collaborative Toxicogenomics (CTox), an open-access integrated web portal using the Django web framework. The software, developed with the Python programming language, is modular, extensible and implements “best-practice” methods in computational biology. New study results are compared to over 4,000 rodent liver experiments from Drug Matrix and open TG-GATEs. A unique feature of the software is the ability to integrate clinical chemistry and histopathology-derived outcomes with results from gene expression studies, leading to relevant mechanistic conclusions. We describe its application by analyzing the effects of several toxicants on liver gene expression and exemplify application to predicting toxicity study outcomes upon chronic treatment from expression changes in acute-duration studies.

novel open access web portal for integrating mechanistic and toxicogenomic study results | Toxicological Sciences | Oxford Academic

Abstract:  Applying toxicogenomics to improving the safety profile of drug candidates and crop protection molecules is most useful when it identifies relevant biological and mechanistic information that highlights risks and informs risk mitigation strategies. Pathway-based approaches, such as GSEA, integrate toxicogenomic data with known biological process and pathways. Network methods help define unknown biological processes and offer data reduction advantages. Integrating the two approaches would improve interpretation of toxicogenomic information. Barriers to the routine application of these methods in genome-wide transcriptomic studies include a need for “hands-on” computer programming experience, the selection of one or more analysis methods (e.g. pathway analysis methods), the sensitivity of results to algorithm parameters, and challenges in linking differential gene expression to variation in safety outcomes. To facilitate adoption and reproducibility of gene expression analysis in safety studies, we have developed Collaborative Toxicogenomics (CTox), an open-access integrated web portal using the Django web framework. The software, developed with the Python programming language, is modular, extensible and implements “best-practice” methods in computational biology. New study results are compared to over 4,000 rodent liver experiments from Drug Matrix and open TG-GATEs. A unique feature of the software is the ability to integrate clinical chemistry and histopathology-derived outcomes with results from gene expression studies, leading to relevant mechanistic conclusions. We describe its application by analyzing the effects of several toxicants on liver gene expression and exemplify application to predicting toxicity study outcomes upon chronic treatment from expression changes in acute-duration studies.

What the Chemical Industry Didn’t Want You to Know

Tucked away in an Oregon barn for decades was a collection of internal documents, correspondence, and chemical safety studies detailing the lengths the chemical industry took to conceal the dangers of their products.  

The documents in this collection—dubbed the “Poison Papers”—allege fraudulent chemical safety testing, corporate concealment of chemical dangers, and collusion between the industry and the regulators who were supposed to be protecting the public and environment. Commonly used herbicides like Roundup (glyphosate), dicamba, atrazine, and 2,4-D feature prominently among the papers, as do nearly every large chemical corporation. 

Now, thanks to the combined efforts of the Center for Media and Democracy (CMD) and the Bioscience Resource Project (BRP), this collection is available online for the first time….

The Poison Papers are the digitization of about three tons of files from litigation against Monsanto, litigation involving some of the Dow Chemicals products, open records requests, and Freedom of Information Act requests to the federal government as well as state agencies. It represents documents that were discovered over the past 40 years but some of the documents, including scientific studies, are older than that because they are from litigation….”

American Chemical Society and Max Planck institutes partner on transformative open access plan – American Chemical Society

The Publications Division of the American Chemical Society (ACS) and the Max Planck Gesellschaft (MPG) announced today a collaborative open access strategic partnership that will advance shared goals for open science and enhance convenience for the MPG researcher and author community. Effective from the outset of 2019, the four-year transformative agreement provides researchers affiliated with Max Planck institutes the opportunity to disseminate immediately, under an open access license, 100 percent of their research articles upon acceptance and publication by a peer-reviewed ACS journal. MPG researchers also benefit from full reader access to all ACS Publications journals and Chemical & Engineering News….”

American Chemical Society and Max Planck institutes partner on transformative open access plan – American Chemical Society

The Publications Division of the American Chemical Society (ACS) and the Max Planck Gesellschaft (MPG) announced today a collaborative open access strategic partnership that will advance shared goals for open science and enhance convenience for the MPG researcher and author community. Effective from the outset of 2019, the four-year transformative agreement provides researchers affiliated with Max Planck institutes the opportunity to disseminate immediately, under an open access license, 100 percent of their research articles upon acceptance and publication by a peer-reviewed ACS journal. MPG researchers also benefit from full reader access to all ACS Publications journals and Chemical & Engineering News….”

Open-access chemistry textbooks gain popularity

“In October 2018, the US Department of Education gave LibreTexts, an OER portal based at the University of California, Davis, a $4.9 million grant to develop free, open textbooks in targeted subjects, including chemistry. The goal for the chemistry materials is to develop resources that will enable schools to offer an ACS-approved bachelor’s degree with zero cost for textbooks. ACS evaluates programs to determine whether they meet the guidelines established by the society’s Committee on Professional Training. The consortium developing LibreTexts includes 11 institutions beyond UC Davis, plus the California State University system. The consortium and its predecessor, ChemWiki, previously received funding from the US National Science Foundation….

Professors who want to use LibreTexts can use the existing materials as is, or they can mix and match the various textbooks available to make their own. The consortium currently contains 61 chemistry textbooks, 58 of which are in English and 3 of which are in Spanish.

Brett McCollum, a chemistry professor at Mount Royal University, in Canada, adopted LibreTexts for one section of his general-chemistry class in 2015. After a successful trial run, his department adopted it for all sections of both semesters of general chemistry the following year….

Rather than linking to existing LibreTexts pages, McCollum replicates those pages on his own course pages within LibreTexts and edits them to fit the focus of his class. “Having that freedom to tailor the book was really valuable to me,” he says….

McCollum envisions a future with most OER development funded by governments. In Canada, most provinces already have an OER initiative, he says. “Canada sees this as an important path forward for equity and for enabling students from diverse backgrounds to engage more fully in higher education,” McCollum says. “We have a vision of sharing nationally and internationally” the materials from the OER initiatives….

One thing that differentiates OpenStax from commercial publishing is the OER provider doesn’t need to constantly release new editions of its books to keep ahead of a used-book market. OpenStax books are available free to students electronically or for a nominal cost if a student prefers to have a printed version….”

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….”