This document discusses issues with reproducibility and open access in scientific research. It notes studies showing that over 50% of published studies cannot be repeated, and major pharmaceutical companies could only validate around 25% of preclinical studies. It argues that the current publishing system, dominated by for-profit publishers, boxes in academic knowledge and prioritizes profits over open access. The document advocates for cultural and technological changes like open access policies, altmetrics, and software for reproducible research to help make science more open.
Reproducibility, preregistration, etc.: Making good science even betterAlex Holcombe
Reproducibility problems afflict many sciences, including psychology. The problems are, to some extent, rooted in the criteria for and process of scientific publication. In response, many journals, funders and professional societies have begun incentivising change. For example, study preregistration, although traditionally used only by clinical trials researchers, is becoming more common. In this seminar, you will learn how it is now used even in basic experimental psychology, and how you can take advantage of preregistration and other new practices to smooth your path to publication and dissemination of your work. Bring your laptop (optional), walk with me through preregistering a study, and also learn how sites such as Open Science Framework facilitate project management and collaboration. One object of this seminar is to spark discussion of how we can all make our already wonderful system of science even better.
What is the future of scientific communication? Open Science (Claude Pirmez)http://bvsalud.org/
Apresentação da Profª Drª Claude Pirmez na Reunião de Editores Científicos do CRICS10, em 04/12/2018
http://crics10.org/eventos/pt/event/reuniao-de-editores-cientificos/
What is the reproducibility crisis in science and what can we do about it?Dorothy Bishop
Talk given to the Rhodes Biomedical Association, 4th May 2016.
For references see: http://www.slideshare.net/deevybishop/references-on-reproducibility-crisis-in-science-by-dvm-bishop
Reproducibility, preregistration, etc.: Making good science even betterAlex Holcombe
Reproducibility problems afflict many sciences, including psychology. The problems are, to some extent, rooted in the criteria for and process of scientific publication. In response, many journals, funders and professional societies have begun incentivising change. For example, study preregistration, although traditionally used only by clinical trials researchers, is becoming more common. In this seminar, you will learn how it is now used even in basic experimental psychology, and how you can take advantage of preregistration and other new practices to smooth your path to publication and dissemination of your work. Bring your laptop (optional), walk with me through preregistering a study, and also learn how sites such as Open Science Framework facilitate project management and collaboration. One object of this seminar is to spark discussion of how we can all make our already wonderful system of science even better.
What is the future of scientific communication? Open Science (Claude Pirmez)http://bvsalud.org/
Apresentação da Profª Drª Claude Pirmez na Reunião de Editores Científicos do CRICS10, em 04/12/2018
http://crics10.org/eventos/pt/event/reuniao-de-editores-cientificos/
What is the reproducibility crisis in science and what can we do about it?Dorothy Bishop
Talk given to the Rhodes Biomedical Association, 4th May 2016.
For references see: http://www.slideshare.net/deevybishop/references-on-reproducibility-crisis-in-science-by-dvm-bishop
Research misconduct: science's self-administered poisonLeonid Schneider
Microb&Co Workshop 7ICME, October 2016,
Catania October 2016 Talk 1
How research misconduct happens and how it can be prevented. The roles of universities, journals and funders
Talk 2 at Research Integrity workshop at Max Planck Institute for Plant Breeding Research in Cologne, April 6th 2018
http://www.mpipz.mpg.de/events/13302/4358571
Open Data and the Social Sciences - OpenCon Community WebcastRight to Research
These slides were created by Temina Madon.
Temina Madon, Executive Director of the Centre for Effective Global Action, outlines why Open Data is critical to the Social Sciences. She helped launch the Berkeley Initiative for Transparency in the Social Sciences (BITSS), which supports opportunities and tools for students and early career researchers to engage in more open, transparent, reproducible science. She will also discuss the Transparency and Openness Promotion Guidelines, a new set of standards for academic journals.
Research misconduct in plant science: infectious and toxic (Cologne 6.4.2018)Leonid Schneider
Talk 1 at Research Integrity workshop at Max Planck Institute for Plant Breeding Research in Cologne, April 6th 2018
http://www.mpipz.mpg.de/events/13302/4358571
What is salami slicing?
It refers to the practice of partitioning a large study that could have been reported in a single research article into smaller published articles.
In other words, it means breaking up a single research paper into their “least publishable units,” with each paper reporting different findings from the same study.
A set of papers are referred to as salami publications when more than one paper covers the same population, methods, and research question.
American Journal Experts presents "Five Myths About Open Access Publishing" to help address some of the misconceptions about this movement in international scholarly publishing. AJE supports open access as part of its mission of accelerating the process of global discovery.
Research misconduct: science's self-administered poisonLeonid Schneider
Microb&Co Workshop 7ICME, October 2016,
Catania October 2016 Talk 1
How research misconduct happens and how it can be prevented. The roles of universities, journals and funders
Talk 2 at Research Integrity workshop at Max Planck Institute for Plant Breeding Research in Cologne, April 6th 2018
http://www.mpipz.mpg.de/events/13302/4358571
Open Data and the Social Sciences - OpenCon Community WebcastRight to Research
These slides were created by Temina Madon.
Temina Madon, Executive Director of the Centre for Effective Global Action, outlines why Open Data is critical to the Social Sciences. She helped launch the Berkeley Initiative for Transparency in the Social Sciences (BITSS), which supports opportunities and tools for students and early career researchers to engage in more open, transparent, reproducible science. She will also discuss the Transparency and Openness Promotion Guidelines, a new set of standards for academic journals.
Research misconduct in plant science: infectious and toxic (Cologne 6.4.2018)Leonid Schneider
Talk 1 at Research Integrity workshop at Max Planck Institute for Plant Breeding Research in Cologne, April 6th 2018
http://www.mpipz.mpg.de/events/13302/4358571
What is salami slicing?
It refers to the practice of partitioning a large study that could have been reported in a single research article into smaller published articles.
In other words, it means breaking up a single research paper into their “least publishable units,” with each paper reporting different findings from the same study.
A set of papers are referred to as salami publications when more than one paper covers the same population, methods, and research question.
American Journal Experts presents "Five Myths About Open Access Publishing" to help address some of the misconceptions about this movement in international scholarly publishing. AJE supports open access as part of its mission of accelerating the process of global discovery.
Open Access in the biomedical field - the rise of PloS ONE by Nathalie DuchangeMyScienceWork
To celebrate the Open Access Week 2012, MyScienceWork in partnership with UNESCO and UPMC organize for the first time in Paris, two events dedicated to Open Access.
Discover here the presentation of Nathalie Duchange (INSERM)
In the race to publish more papers, some researchers indulge in unethical practices, one of which is salami slicing. Salami slicing means fragmenting one study and publishing it in multiple papers. This practice is considered improper and can affect your career, besides being damaging to science. This SlideShare explains in detail what salami slicing is and why it is considered unethical. It also includes opinions of journal editors on the issue.
Reproducibility of Published Scientific and Medical Findings in Top Journals in an Era of Big Data by Shannon Bohle, BA, MLIS, CDS (Cantab), FRAS, AHIP
Reproducibility, argument and data in translational medicineTim Clark
Failures in reproducibility and robustness of scientific findings are explored from statistical, historical, and argumentation theory perspectives. The impact of false positives in the literature is connected to failures in T1 and T2 biomedical translation, and is shown to have a significant impact on the costs of therapeutic development and availability of needed treatments to the public. Technological and social approaches to resolve these issues are presented. "Reproducibility" initiatives are critiqued as unsustainable and non-authoritative; improved requirements and methods for scientific communication of findings including data, methods and material are supported as the best approaches for improved reproducibility.
Presentation to the J. Craig Venter Institute, Dec. 2014Mark Wilkinson
This is largely a compilation of various other talks that I have posted here - a summary of the past 3+ years of work on SADI/SHARE. It includes the (now well-worn!!) slides about SHARE, as well as some of the more contemporary stuff about how we extended GALEN clinical classes with richer semantic descriptions, and then used them to do automated clinical phenotype analysis. Also includes the slide-deck related to automated Measurement Unit conversion (related to our work on semantically representing Framingham clinical risk assessment rules)
So... for anyone who regularly follows my uploads, there isn't much "new" in here, but at least it's all in one place now! :-)
Subscription costs versus open access costs, & Dissolving journals' boundariesAlex Holcombe
draft of talk for Reclaiming the Knowledge Commons http://www.eventbrite.com.au/e/reclaiming-the-knowledge-commons-the-ethics-of-academic-publishing-and-the-futures-of-research-tickets-17560178968
Our Scholarship System is Broke. Can Open Access Fix It?Alex Holcombe
Auckland talk24october openaccessweek.
"Broke" in the sense of ain't got no money because giving too much to publishers. And "Broke" in the sense of broken, e.g. not publishing replication studies.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
4. Rule among early-stage venture
capital firms that “at least 50% of
published studies, even those in top-
tier academic journals, can't be
repeated with the same conclusions
by an industrial lab” - Prinz,
Schlange, & Asadullah. Nature Rev.
Drug Discov. 10, 712 (2011)
Bayer HealthCare :only about 25% of published
preclinical studies could be validated to the point
at which projects could continue
Amgen Fifty-three papers were deemed ‘landmark’
studies (see ‘Reproducibility of research
findings’)... scientific findings were confirmed in
only 6 (11%) cases
5. Academic knowledge is boxed
in by expensive journals.
Scientist meets Publisher
http://www.youtube.com/watch?v=GMIY_4t-DR0
9. How open science wins
Cultural change
• Early adopters
• Researcher training
• Advocacy, lobbying
• Journals strengthen
sharing policies
Tech work at grassroots
• Altmetrics
• Streamlining repositories
• Software for
reproducible research
CC-BY Alex Holcombe
Research funders ramp
up requirement that
code, data be posted
http://aoasg.org.au/2015/08/31/going-beyond-the-published-article-how-open-access-is-just-a-start/
