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Selection: with tag transparency [30 articles] 

 

Steps towards transparency in research publishing

  
Nature, Vol. 549, No. 7673. (26 September 2017), pp. 431-431, https://doi.org/10.1038/549431a

Abstract

As research and editorial processes become increasingly open, scientists and editors need to be proactive but also alert to risks. [Excerpt] [...] The examples given here relate to initiatives by the Nature Research journals, some of which follow pioneering work by other publishers. [...] One such initiative is the checklist introduced by Nature and the Nature journals in 2013 for life-sciences submissions. [...] Malcolm Macleod of the University of Edinburgh, UK, and his colleagues [..] looked at the completeness of reporting in journals ...

 

The tragedy of the commons

  
Science, Vol. 162, No. 3859. (13 December 1968), pp. 1243-1248, https://doi.org/10.1126/science.162.3859.1243

Abstract

The population problem has no technical solution; it requires a fundamental extension in morality. [Excerpt] [...] A technical solution may be defined as one that requires a change only in the techniques of the natural sciences, demanding little or nothing in the way of change in human values or ideas of morality. In our day (though not in earlier times) technical solutions are always welcome. Because of previous failures in prophecy, it takes courage to assert that a desired technical solution is ...

 

Running an open experiment: transparency and reproducibility in soil and ecosystem science

  
Environmental Research Letters, Vol. 11, No. 8. (01 August 2016), 084004, https://doi.org/10.1088/1748-9326/11/8/084004

Abstract

Researchers in soil and ecosystem science, and almost every other field, are being pushed—by funders, journals, governments, and their peers—to increase transparency and reproducibility of their work. A key part of this effort is a move towards open data as a way to fight post-publication data loss, improve data and code quality, enable powerful meta- and cross-disciplinary analyses, and increase trust in, and the efficiency of, publicly-funded research. Many scientists however lack experience in, and may be unsure of the benefits ...

 

Five selfish reasons to work reproducibly

  
Genome Biology, Vol. 16, No. 1. (8 December 2015), 274, https://doi.org/10.1186/s13059-015-0850-7

Abstract

And so, my fellow scientists: ask not what you can do for reproducibility; ask what reproducibility can do for you! Here, I present five reasons why working reproducibly pays off in the long run and is in the self-interest of every ambitious, career-oriented scientist. [Excerpt] [::Reproducibility: what's in it for me?] In this article, I present five reasons why working reproducibly pays off in the long run and is in the self-interest of every ambitious, career-oriented scientist. [::] Reason number 1: reproducibility helps to avoid ...

 

Statistical analysis

  
In Science: editorial policies (2016)

Abstract

[Excerpt: Statistical analysis] Generally, authors should describe statistical methods with enough detail to enable a knowledgeable reader with access to the original data to verify the results. [::] Data pre-processing steps such as transformations, re-coding, re-scaling, normalization, truncation, and handling of below detectable level readings and outliers should be fully described; any removal or modification of data values must be fully acknowledged and justified. [::] [...] [::] The number of sampled units, N, upon which each reported statistic is based must be stated. [::] For continuous ...

 

Social software

  
Nature Methods, Vol. 4, No. 3. (01 March 2007), pp. 189-189, https://doi.org/10.1038/nmeth0307-189

Abstract

Software that is custom-developed as part of novel methods is as important for the method's implementation as reagents and protocols. Such software, or the underlying algorithms, must be made available to readers upon publication. [Excerpt] "An inherent principle of publication is that others should be able to replicate and build upon the authors' published claims. Therefore, a condition of publication in a Nature journal is that authors are required to make materials, data and associated protocols available to readers promptly on request." ...

 

Transparency in ecology and evolution: real problems, real solutions

  
Trends in Ecology & Evolution, Vol. 31, No. 9. (September 2016), pp. 711-719, https://doi.org/10.1016/j.tree.2016.07.002

Abstract

To make progress scientists need to know what other researchers have found and how they found it. However, transparency is often insufficient across much of ecology and evolution. Researchers often fail to report results and methods in detail sufficient to permit interpretation and meta-analysis, and many results go entirely unreported. Further, these unreported results are often a biased subset. Thus the conclusions we can draw from the published literature are themselves often biased and sometimes might be entirely incorrect. Fortunately there ...

 

Software search is not a science, even among scientists

  
(8 May 2016)

Abstract

When they seek software for a task, how do people go about finding it? Past research found that searching the Web, asking colleagues, and reading papers have been the predominant approaches---but is it still true today, given the popularity of Facebook, Stack Overflow, GitHub, and similar sites? In addition, when users do look for software, what criteria do they use? And finally, if resources such as improved software catalogs were to be developed, what kind of information would people want in them? These questions motivated our cross-sectional survey ...

 

(INRMM-MiD internal record) List of keywords of the INRMM meta-information database - part 36

  
(February 2014)
Keywords: inrmm-list-of-tags   thaumetopoea-processionea   thaumetopoea-pytiocampa   thecodiplosis-japonensis   theobroma-cacao   theoretical-approach   theory-driven-bias   theory-vs-actual-implemetation   thermal-requirements   thermodynamics   thermophilous-forest   thermophilous-plants   thespesia-populnea   thinning   thomson-reuters   threat   threatened-species   three-gorges-dam   thresholds   thrinax-radiata   thuja-occidentalis   thuja-plicata   thuja-spp   tibet   tilia-americana   tilia-amurensis   tilia-argentea   tilia-cordata   tilia-dasystyla   tilia-platyphyllos   tilia-spp   tilia-tomentosa   tilio-acerion   tillage   timber-harvesting   timber-quality   timber-uses   timber-value   time-lags   time-series   tipovers   tipping-point   todo-replace-book-abstract-with-chapter-abstract   tolerance   tomicobia-seitneri   tomicus-spp   tool-driven   toona-ciliata   top-down   topographic-position-index   topographic-wetness-index   topography   topology   topsoil-grain-size   torcello   tornado   torreya-californica   torreya-spp   torreya-taxifolia   tortrix-viridana   tourism   toxicity   trade-offs   trade-regulations   traditional-remedy   training-course   trait-based-approach   transboundary-effects   transdiciplinary-scientific-communication   transdisciplinary-research   transect   transparency   transport-system   treculia-africana   tree-age   tree-breeding   tree-cancer   tree-defoliation   tree-density   tree-diseases   tree-diversity   tree-ecology   tree-fall   tree-fruits   tree-height   tree-limit   tree-line   tree-mortality   tree-rings   tree-sap   tree-seeds   tree-species   tree-virus   treefall   trichiocampus-viminalis   trinidad-island   tropical-areas   tropical-forest   tropical-mountain-forest   tropical-storms  

Abstract

List of indexed keywords within the transdisciplinary set of domains which relate to the Integrated Natural Resources Modelling and Management (INRMM). In particular, the list of keywords maps the semantic tags in the INRMM Meta-information Database (INRMM-MiD). [\n] The INRMM-MiD records providing this list are accessible by the special tag: inrmm-list-of-tags ( http://mfkp.org/INRMM/tag/inrmm-list-of-tags ). ...

 

Research integrity: don't let transparency damage science

  
Nature, Vol. 529, No. 7587. (25 January 2016), pp. 459-461, https://doi.org/10.1038/529459a

Abstract

Stephan Lewandowsky and Dorothy Bishop explain how the research community should protect its members from harassment, while encouraging the openness that has become essential to science. [Excerpt] Transparency has hit the headlines. In the wake of evidence that many research findings are not reproducible1, the scientific community has launched initiatives to increase data sharing, transparency and open critique. As with any new development, there are unintended consequences. Many measures that can improve science2 — shared data, post-publication peer review and public engagement ...

 

The true loss caused by biodiversity offsets

  
Biological Conservation, Vol. 192 (December 2015), pp. 552-559, https://doi.org/10.1016/j.biocon.2015.08.016

Abstract

Biodiversity offsets aim to achieve a “no-net-loss” of biodiversity, ecosystem functions and services due to development. The “no-net-less” objective assumes that the multi-dimensional values of biodiversity in complex ecosystems can be isolated from their spatial, evolutionary, historical, social, and moral context. We examine the irreplaceability of ecosystems, the limits of restoration, and the environmental values that claim to be compensated through ecosystem restoration. We discuss multiple ecological, instrumental, and non-instrumental values of ecosystems that should be considered in offsetting calculations. Considering ...

 

Author sequence and credit for contributions in multiauthored publications

  
PLoS Biology, Vol. 5, No. 1. (16 January 2007), e18, https://doi.org/10.1371/journal.pbio.0050018

Abstract

A transparent, simple, and straightforward approach that is free from any arbitrary rank valuation is required to estimate the credit associated with the sequence of authors' names on multiauthored papers. [Excerpt] The increasing tendency across scientific disciplines to write multiauthored papers [1,2] makes the issue of the sequence of contributors' names a major topic both in terms of reflecting actual contributions and in a posteriori assessments by evaluation committees. Traditionally, the first author contributes most and also receives most of the credit, ...

 

Opinion: lay summaries needed to enhance science communication

  
Proceedings of the National Academy of Sciences, Vol. 112, No. 12. (24 March 2015), pp. 3585-3586, https://doi.org/10.1073/pnas.1500882112

Abstract

[Excerpt] At first blush, the notion of lay summaries seems a simple idea with admirable aims: Scientists write summaries of journal articles emphasizing the broad significance of research in accessible language. However, viewed from an ivory tower that has been besieged by an increasing amount of paperwork, scientists could easily regard lay summaries as just one more hurdle in peer-reviewed publishing, another administrative task to fit into an already busy agenda. [\n] But rather than an unrewarding burden, scientists (and journal publishers) ...

Visual summary

  • Figure:60%: http://www.pnas.org/content/112/12/3585/F1.large.jpg
  • Source: http://dx.doi.org/10.1073/pnas.1500882112
  • Caption: A conceptual map depicts the pathways available for communicating research results between scientists and end users via different mechanisms (depicted by black dotted lines). Lay summaries of published articles would serve to enhance potential communication pathways (depicted by red solid lines) between scientists and the lay public, increase decision makers' access to information, and improve interdisciplinary communication.
 

Biochemist questions peer review at UK funding agency

  

Abstract

[Excerpt] Many researchers do little more than grumble if a funding agency declines their grant applications. But when the UK Medical Research Council (MRC) turned down two proposals from biochemist Ian Eperon – despite high scores from peer reviewers — he decided to find out how closely the agency follows the evaluations it invites from experts. After much chasing and a freedom-of-information request, he has received figures that surprised him: in 2013–14, the scores given to grant proposals in his field ...

 

Reproducible Research: Moving toward Research the Public Can Really Trust

  
Annals of Internal Medicine, Vol. 146, No. 6. (20 March 2007), 450, https://doi.org/10.7326/0003-4819-146-6-200703200-00154

Abstract

A community of scientists arrives at the truth by independently verifying new observations. In this time-honored process, journals serve 2 principal functions: evaluative and editorial. In their evaluative function, they winnow out research that is unlikely to stand up to independent verification; this task is accomplished by peer review. In their editorial function, they try to ensure transparent (by which we mean clear, complete, and unambiguous) and objective descriptions of the research. Both the evaluative and editorial functions go largely unnoticed ...

 

Promoting transparency in social science research

  
Science, Vol. 343, No. 6166. (03 January 2014), pp. 30-31, https://doi.org/10.1126/science.1245317

Abstract

There is growing appreciation for the advantages of experimentation in the social sciences. Policy-relevant claims that in the past were backed by theoretical arguments and inconclusive correlations are now being investigated using more credible methods. Changes have been particularly pronounced in development economics, where hundreds of randomized trials have been carried out over the last decade. When experimentation is difficult or impossible, researchers are using quasi-experimental designs. Governments and advocacy groups display a growing appetite for evidence-based policy-making. In 2005, Mexico ...

 

Better living through transparency: improving the reproducibility of fMRI results through comprehensive methods reporting

  
In Cognitive, Affective, & Behavioral Neuroscience (2013), pp. 1-7, https://doi.org/10.3758/s13415-013-0188-0

Abstract

Recent studies suggest that a greater proportion of published scientific findings than expected cannot be replicated. The field of functional neuroimaging research is no exception to this trend, with estimates of false positive results ranging from 10 % to 40 %. While false positive results in neuroimaging studies stem from a variety of causes, incomplete methodological reporting is perhaps the most obvious: Most published reports of neuroimaging studies provide ambiguous or incomplete descriptions of their methods and results. If neuroimaging researchers do not ...

 

Git can facilitate greater reproducibility and increased transparency in science

  
Source Code for Biology and Medicine, Vol. 8, No. 1. (28 February 2013), 7, https://doi.org/10.1186/1751-0473-8-7

Abstract

Reproducibility is the hallmark of good science. Maintaining a high degree of transparency in scientific reporting is essential not just for gaining trust and credibility within the scientific community but also for facilitating the development of new ideas. Sharing data and computer code associated with publications is becoming increasingly common, motivated partly in response to data deposition requirements from journals and mandates from funders. Despite this increase in transparency, it is still difficult to reproduce or build upon the findings of ...

 

Faculty appointments and the record of scholarship

  
eLife Sciences, Vol. 2 (01 January 2013), https://doi.org/10.7554/elife.00452

Abstract

Academic review committees would benefit from more details about the contributions made by individual researchers to papers with multiple authors, and also from more information about other types of scholarly communication. ...

 

When transparency and collaboration collide: The USA Open Data program

  
J. Am. Soc. Inf. Sci., Vol. 62, No. 11. (1 November 2011), pp. 2085-2094, https://doi.org/10.1002/asi.21622

Abstract

President Obama's inaugural flagship Open Data program emphasizes the values of transparency, participation, and collaboration in governmental work. The Open Data performance data analysis, published here for the first time, proposes that most federal agencies have adopted a passive–aggressive attitude toward this program by appearing to cooperate with the program while in fact effectively ignoring it. The analysis further suggests that a tiny group of agencies are the only “real players” in the Data.gov web arena. This research highlights the contradiction ...

 

A call for disruptive innovation in science publishing with a new open data-sharing platform for the life sciences

  
FigShare Digital Science (2012), https://doi.org/10.6084/m9.figshare.91541

Abstract

“A disruptive innovation is an innovation that helps create a new market and value network, and eventually goes on to disrupt an existing market and value network (over a few years or decades), displacing an earlier technology. The term is used in business and technology literature to describe innovations that improve a product or service in ways that the market does not expect.” -Wikipedia On April 3rd, 2012 Nature Precedings, Nature Publishing Group’s experiment in free pre-print publishing was shut down and ...

 

Methods for collaboratively identifying research priorities and emerging issues in science and policy

  
Methods in Ecology and Evolution, Vol. 2, No. 3. (02 June 2011), pp. 238-247, https://doi.org/10.1111/j.2041-210x.2010.00083.x

Abstract

[::1] There is a widely recognized gap between the data generated by researchers and the information required by policy makers. In an effort to bridge the gap between conservation policy and science, we have convened in several countries multiple groups of policy makers, practitioners and researchers to identify priority information needs that can be met by new research in the social and natural sciences. [::2] The exercises we have coordinated included identification of priority policy-relevant research questions in specific geographies (UK, USA, Canada); questions ...

 

Sustainable Capital? The Neoliberalization of Nature and Knowledge in the European “Knowledge-based Bio-economy”

  
Sustainability, Vol. 2, No. 9. (13 September 2010), pp. 2898-2918, https://doi.org/10.3390/su2092898

Abstract

As an EU policy agenda, the “knowledge-based bio-economy” (KBBE) emphasizes bio-technoscience as the means to reconcile environmental and economic sustainability. This frames the sustainability problem as an inefficiency to be overcome through a techno-knowledge fix. Here ecological sustainability means a benign eco-efficient productivity using resources which are renewable, reproducible and therefore sustainable. The KBBE narrative has been elaborated by European Technology Platforms in the agri-food-forestry-biofuels sectors, whose proposals shape research priorities. These inform policy agendas for the neoliberalization of both nature ...

 

The disclosure of climate data from the Climatic Research Unit at the University of East Anglia - Eighth Report of Session 2009–10

  
No. HC 387-I. (March 2010)

Abstract

Summary. The disclosure of climate data from the Climatic Research Unit (CRU) at the University of East Anglia (UEA) in November 2009 had the potential to damage the reputation of the climate science and the scientists involved. We believe that the focus on CRU and Professor Phil Jones, Director of CRU, in particular, has largely been misplaced. Whilst we are concerned that the disclosed e-mails suggest a blunt refusal to share scientific data and methodologies with others, we can sympathise with ...

 

Are environmental models transparent and reproducible enough?

  
In MODSIM2011, 19th International Congress on Modelling and Simulation (December 2011), pp. 2954-2961

Abstract

Environmental computer models are considered essential tools in supporting environmental decision making, but their main value is that they allow a better understanding of our complex environment. Environmental models are in fact applications of shared theories on how real-world systems are functioning. Just like the underlying scientific theories they need to be evaluated and discussed among peers. To allow proper assessment of the quality and suitability of environmental models peers should be able to trace their results and insights through the model structure to the ...

 

Climate change in the context of development cooperation

  
No. COM(2003) 85 final. (March 2003)
 

Devil in the details

  
Nature, Vol. 470, No. 7334. (16 February 2011), pp. 305-306, https://doi.org/10.1038/470305b

Abstract

To ensure their results are reproducible, analysts should show their workings ...

 

The Open Knowledge Foundation: open data means better science

  
PLoS Biology, Vol. 9, No. 12. (6 December 2011), e1001195, https://doi.org/10.1371/journal.pbio.1001195

Abstract

Open data leads to better science, but overcoming the barriers to widespread publication and availability of open scientific data requires a community effort. The Open Knowledge Foundation Open Data in Science Working Group describes their role in this movement. ...

 

Must try harder

  
Nature, Vol. 483, No. 7391. (28 March 2012), pp. 509-509, https://doi.org/10.1038/483509a
 

We must be open about our mistakes

  
Nature, Vol. 489, No. 7414. (5 September 2012), pp. 7-7, https://doi.org/10.1038/489007a

Abstract

Greater transparency about the scientific process and a closer focus on correcting defective data are the way forward, says  Jim Woodgett. ...

This page of the database may be cited as:
Integrated Natural Resources Modelling and Management - Meta-information Database. http://mfkp.org/INRMM/tag/transparency

Publication metadata

Bibtex, RIS, RSS/XML feed, Json, Dublin Core

Meta-information Database (INRMM-MiD).
This database integrates a dedicated meta-information database in CiteULike (the CiteULike INRMM Group) with the meta-information available in Google Scholar, CrossRef and DataCite. The Altmetric database with Article-Level Metrics is also harvested. Part of the provided semantic content (machine-readable) is made even human-readable thanks to the DCMI Dublin Core viewer. Digital preservation of the meta-information indexed within the INRMM-MiD publication records is implemented thanks to the Internet Archive.
The library of INRMM related pubblications may be quickly accessed with the following links.
Search within the whole INRMM meta-information database:
Search only within the INRMM-MiD publication records:
Full-text and abstracts of the publications indexed by the INRMM meta-information database are copyrighted by the respective publishers/authors. They are subject to all applicable copyright protection. The conditions of use of each indexed publication is defined by its copyright owner. Please, be aware that the indexed meta-information entirely relies on voluntary work and constitutes a quite incomplete and not homogeneous work-in-progress.
INRMM-MiD was experimentally established by the Maieutike Research Initiative in 2008 and then improved with the help of several volunteers (with a major technical upgrade in 2011). This new integrated interface is operational since 2014.