Compliance with ethical rules for scientific publishing in biomedical Open Access journals indexed in Journal Citation Reports | proLéka?

Abstract:  This study examined compliance with the criteria of transparency and best practice in scholarly publishing defined by COPE, DOAJ, OASPA and WAME in Biomedical Open Access journals indexed in Journal Citation Reports (JCR). 259 Open Access journals were drawn from the JCR database and on the basis of their websites their compliance with 14 criteria for transparency and best practice in scholarly publishing was verified. Journals received penalty points for each unfulfilled criterion when they failed to comply with the criteria defined by COPE, DOAJ, OASPA and WAME. The average number of obtained penalty points was 6, where 149 (57.5%) journals received ? 6 points and 110 (42.5%) journals ? 7 points. Only 4 journals met all criteria and did not receive any penalty points. Most of the journals did not comply with the criteria declaration of Creative Commons license (164 journals), affiliation of editorial board members (116), unambiguity of article processing charges (115), anti-plagiarism policy (113) and the number of editorial board members from developing countries (99). The research shows that JCR cannot be used as a whitelist of journals that comply with the criteria of transparency and best practice in scholarly publishing.

Essential Open Source Software for Science – Chan Zuckerberg Science Initiative – Medium

We followed two guiding principles in creating this opportunity:

  • First, we didn’t want to limit funding to pure software development. Open source is more than just writing code. It includes improving documentation, addressing usability, managing the project, and building community. We want to provide opportunities in whatever form will help make the computational foundations of biological research more usable and robust….
  • Second, we wanted to be inclusive in defining the scope of what counts as essential software for biomedical research. The proposed work does not need to be tied to novel research. Additionally, both domain-specific software and foundational tools and infrastructure used across several domains of science will be eligible to apply, so long as they have some impact in biomedical science. Such foundational tools can range from data structures to numerical computation libraries to toolkits for workflow execution and reproducibility. These tools play a critical role, often acting as dependencies for more domain-specific tools….”

Coming Soon: Essential Open Source Software for Science – Chan Zuckerberg Initiative

The Chan Zuckerberg Initiative will soon invite applications for open source software projects that are essential to biomedical research. Applicants can request funding between $50k and $250k for one year. This RFA is the first of a series. CZI will invite applications during three distinct cycles, with rounds beginning June 18, 2019; mid-December 2019; and mid-June 2020. Read our Medium post to learn more….”

Electronic Lab Notebooks | Harvard Biomedical Data Management

Lab notebooks are good for writing down procedures, observations, conclusions and for drawing flow charts and diagrams by hand. However, in order to accommodate the increase of digital data collected, researchers have taped instrumentation and computer printouts onto the pages of their notebooks, or cross-referenced larger data sets by recording file names and locations in the notebook.

An ELN (electronic lab notebook) is a software tool that in its most basic form replicates an interface much like a page in a paper lab notebook. In this electronic notebook you can enter protocols, observations, notes, and other data using your computer or mobile device. This offers several advantages over the traditional paper notebook.

The number of available ELN tools is increasing and the functions of each are quickly changing. As a result, it may be confusing to evaluate all of the advantages and limitations of each when looking for the right solution for your project.

The Electronic Lab Notebook Matrix has been created to aid HMS researchers in the process of identifying a usable Electronic Lab Notebook solutions to meet their specific research needs. Through this resource, researchers can compare and contrast the numerous solutions available today, and also explore individual options in-depth….”

If Research Libraries and Funders Finance Open Access: Moving Beyond Subscriptions and APCs | Willinsky | College & Research Libraries

Abstract:  Following the examples of SCOAP3, in which libraries fund open access, and eLife, in which funding agencies have begun to directly fund open access scholarly publishing, this study presents an analysis of how creatively combining these two models might provide a means to move toward universal open access (without APCs). This study calculates the publishing costs for the funders that sponsor the research and for the libraries that cover unsponsored articles for two nonprofit biomedical publishers, eLife and PLOS, and the nonprofit journal aggregator BioOne. These entities represent a mix of publishing revenue models, including funder sponsorship, article processing charges (APC), and subscription fees. Using PubMed filtering and manual-sampling strategies, as well as publicly available publisher revenue data, the study found that, in 2015, 86 percent of the articles in eLife and PLOS acknowledge funder support, as do 76 percent of the articles in the largely subscription journals of BioOne. Such findings can inform libraries and funding agencies, as well as publishers, in their consideration of a direct-payment open access model, as the study (a) demonstrates the cost breakdown for funder and library support for open access among this sample of X articles; (b) posits how publishing data-management organizations such as Crossref and ORCID can facilitate such a model of funder and library per-article open access payments; and (c) proposes ways in which such a model offers a more efficient, equitable, and scalable approach to open access across the disciplines than the prevailing APC model, which originated with biomedical publishing.

Should I publish in an open access journal? | The BMJ

An “author pays” publishing model is the only fair way to make biomedical research findings accessible to all, say Matthew Kurien and David S Sanders, but James J Ashton and R Mark Beattie worry that it can lead to bias in the evidence base towards commercially driven results….”

Research assistant (temporary) posting: online research for preprint server directory – ASAPbio

We are seeking temporary research assistance (online, remote) for a project to survey biomedical preprint servers for current scholarly practices.

Dr Jamie Kirkham, University of Liverpool and Dr Naomi Penfold, ASAPbio, are leading a research project to survey current scholarly publishing practices by preprint servers for biomedical and health sciences. We are seeking assistance to complete the initial research process, which involves structured online research to identify practices as stated on preprint server websites….”

Abstract: Potential predatory journals are colonizing the ICMJE recommendations list of followers



The International Committee of Medical Journal Editors (ICMJE) has expressed its concerns about predatory journals using the list of ICMJE Recommendations (ICMJE-R) followers to “gain the appearance of legitimacy.” We assessed the presence of potential predatory journals on the ICMJE-R list and their adherence to ICMJE recommendations.


A random sample of 350 journals from the estimated 3,100-3,200 biomedical journals listed as ICMJE-R followers was chosen. Data collected from the ICMJE and journal webpages in English were: adherence to six ICMJE-R policies/requirements, year of journal’s listing as ICMJE-R follower, discipline covered, publisher and its country of origin and existence of article processing charge. Potential predatory journal was considered as one open access journal not being a member of a recognized listing in COPE, DOAJ, OASPA, AJOL and/or INASP.


Thirty-one percent of journals were considered to be potentially predatory; 94% of them were included in the ICMJE-R list in 2014-2018. Half were published in the United States and 62% were devoted to medicine. Adherence to five of the six policies/requirements was infrequent, ranging from 51% (plagiarism) to 7% (trial registration). Seventy-two percent of journals mentioned a policy on authors’ conflicts of interest. Information on article processing charge was available for 76% journals and could not be found for 22%. Authorship policy/ instructions were significantly more present in journals with publishers from India than from the USA (53% vs 30%; p = 0.047), with no differences in the other five policies.


Predatory journals should be deleted from the ICMJE-R list of followers to prevent misleading authors. ICMJE-R following journals need to be reevaluated with pre-defined published criteria.

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….”

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….”