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Selection: with tag free-scientific-knowledge [115 articles] 

 

Do not publish

  
Science, Vol. 356, No. 6340. (25 May 2017), pp. 800-801, https://doi.org/10.1126/science.aan1362

Abstract

Biologists have long valued publishing detailed information on rare and endangered species. Until relatively recently, much of this information was accessible only through accessing specialized scientific journals in university libraries. However, much of these data have been transferred online with the advent of digital platforms and a rapid push to open-access publication. Information is increasingly also available online in public reports and wildlife atlases, and research published behind paywalls can often be found in the public domain. Increased data and information ...

 

Ten simple rules for making research software more robust

  
PLOS Computational Biology, Vol. 13, No. 4. (13 April 2017), e1005412, https://doi.org/10.1371/journal.pcbi.1005412

Abstract

[Abstract] Software produced for research, published and otherwise, suffers from a number of common problems that make it difficult or impossible to run outside the original institution or even off the primary developer’s computer. We present ten simple rules to make such software robust enough to be run by anyone, anywhere, and thereby delight your users and collaborators. [Author summary] Many researchers have found out the hard way that there’s a world of difference between “works for me on my machine” and “works for ...

 

How innovations thrive in GRASS GIS

  
In North Carolina GIS Conference, NCGIS2017 (2017)

Abstract

[Poster topic highlights] [::] Algorithms and models included in GRASS GIS remain available long term (Chemin et al., 2015). [::] Analytical tools are not limited to one domain but spread across many fields. [::] New tools can be built based on functionality or code of the existing ones regardless of the particular domain of problems they belong to. [::] Both the functionality and the code are evaluated by the community of users and developers in different fields and scales. [General GRASS GIS highlights] [::] The GRASS GIS development team ...

 

Corporate culture: protect idea factories

  
Nature, Vol. 543, No. 7646. (22 March 2017), pp. 491-491, https://doi.org/10.1038/543491a

Abstract

[Excerpt] It is unsurprising that universities have adopted corporate culture (Nature 540, 315; 10.1038/540315a2016), but surprising that they select such archaic models. Universities corporatize because they must raise funds through teaching, research and commercialization. [...] Universities are the only social institutions set up specifically to produce ideas, and this is their most valuable societal role. [...] Many universities have copied the manufacturing models of the 1950s. Power has shifted from academics to administrators. Academics are treated as interchangeable and replaceable, and performance ...

 

Robust modelling of the impacts of climate change on the habitat suitability of forest tree species

  
Keywords: abies-alba   array-of-factors   artificial-neural-networks   bioclimatic-predictors   change-factor   climate-change   data-uncertainty   diversity   environmental-modelling   europe   extrapolation-uncertainty   featured-publication   forest-resources   free-scientific-knowledge   free-scientific-software   free-software   fuzzy   gdal   genetic-diversity   geospatial   geospatial-semantic-array-programming   gnu-bash   gnu-linux   gnu-octave   habitat-suitability   integration-techniques   mastrave-modelling-library   maximum-habitat-suitability   modelling-uncertainty   multiplicity   peseta-series   python   regional-climate-models   relative-distance-similarity   robust-modelling   semantic-array-programming   semantic-constraints   semantics   spatial-disaggregation   sres-a1b   supervised-training   unsupervised-training  

Abstract

[::] In Europe, forests play a strategic multifunctional role, serving economic, social and environmental purposes. However, their complex interaction with climate change is not yet well understood. [::] The JRC PESETA project series proposes a consistent multi-sectoral assessment of the impacts of climate change in Europe. [::] Within the PESETA II project, a robust methodology is introduced for modelling the habitat suitability of forest tree species (2071-2100 time horizon). [::] Abies alba (the silver fir) is selected as case study: a main European tree ...

References

  1. European Commission, 2013. Communication from the Commission to the European Parliament, the Council, the European Economic and Social Committee and the Committee of the Regions - A new EU forest strategy: for forests and the forest based sector. No. COM(2013) 659 final. Communication from the Commission to the Council and the European Parliament. http://eur-lex.europa.eu/legal-content/EN/TXT/?uri=celex:52013DC0659 , INRMM-MiD:12642065 .
  2. European Commission, 2013. Commission staff working document accompanying the document: Communication from the commission to
 

The importance of free and open source software and open standards in modern scientific publishing

  
Publications, Vol. 1, No. 2. (26 June 2013), pp. 49-55, https://doi.org/10.3390/publications1020049

Abstract

In this paper we outline the reasons why we believe a reliance on the use of proprietary computer software and proprietary file formats in scientific publication have negative implications for the conduct and reporting of science. There is increasing awareness and interest in the scientific community about the benefits offered by free and open source software. We discuss the present state of scientific publishing and the merits of advocating for a wider adoption of open standards in science, particularly where it ...

 

Robots and free software

  
In A World with Robots, Vol. 84 (2017), pp. 63-76, https://doi.org/10.1007/978-3-319-46667-5_5

Abstract

This article examines whether the arguments put forward by Free Software advocates in the context of computers also apply for robots. It summarises their key arguments and explores whether or not they appear transferable to robot cases. Doing so, it comes to the conclusion that, in the majority of cases, the reasons that may make the use of Free Software over proprietary software preferable in other technologies, equally apply in the case of robots. ...

 

Communication: science censorship is a global issue

  
Nature, Vol. 542, No. 7640. (08 February 2017), pp. 165-165, https://doi.org/10.1038/542165b

Abstract

[Excerpt] [...] Regrettably, suppression of public scientific information is already the norm, or is being attempted, in many countries [...]. We fear that such gagging orders could encourage senior bureaucrats to use funding as a tool with which to rein in academic freedoms. [...] The response of scientists to this type of coercion has been to share scientific information widely and openly using such legal means as social media to defend facts and transparency [...] ...

 

BIOMOD - A platform for ensemble forecasting of species distributions

  
Ecography, Vol. 32, No. 3. (1 June 2009), pp. 369-373, https://doi.org/10.1111/j.1600-0587.2008.05742.x

Abstract

BIOMOD is a computer platform for ensemble forecasting of species distributions, enabling the treatment of a range of methodological uncertainties in models and the examination of species-environment relationships. BIOMOD includes the ability to model species distributions with several techniques, test models with a wide range of approaches, project species distributions into different environmental conditions (e.g. climate or land use change scenarios) and dispersal functions. It allows assessing species temporal turnover, plot species response curves, and test the strength of species interactions ...

 

A manifesto for reproducible science

  
Nature Human Behaviour, Vol. 1, No. 1. (10 January 2017), 0021, https://doi.org/10.1038/s41562-016-0021

Abstract

Improving the reliability and efficiency of scientific research will increase the credibility of the published scientific literature and accelerate discovery. Here we argue for the adoption of measures to optimize key elements of the scientific process: methods, reporting and dissemination, reproducibility, evaluation and incentives. There is some evidence from both simulations and empirical studies supporting the likely effectiveness of these measures, but their broad adoption by researchers, institutions, funders and journals will require iterative evaluation and improvement. We discuss the goals ...

 

Position paper for the endorsement of Free Software and Open Standards in Horizon 2020 and all publicly-funded research

  
In Free Software Foundation Europe (January 2017)

Abstract

The Free Software Foundation Europe (FSFE) is a charity that empowers users to control technology by advocating for Free Software. In a digital world, Free Software is the fundament of Open Knowledge, Open Innovation and Open Science. [\n] Software is an integral part of today’s society. Our daily interactions, transactions, education, communication channels, work and life environments rely heavily on software. "Free Software" refers to all programs distributed under terms and licences that allow users to run the software for any purpose, ...

 

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 ...

 

Enhancing reproducibility for computational methods

  
Science, Vol. 354, No. 6317. (09 December 2016), pp. 1240-1241, https://doi.org/10.1126/science.aah6168

Abstract

Over the past two decades, computational methods have radically changed the ability of researchers from all areas of scholarship to process and analyze data and to simulate complex systems. But with these advances come challenges that are contributing to broader concerns over irreproducibility in the scholarly literature, among them the lack of transparency in disclosure of computational methods. Current reporting methods are often uneven, incomplete, and still evolving. We present a novel set of Reproducibility Enhancement Principles (REP) targeting disclosure challenges ...

 

Trusting others to ‘do the math’

  
Interdisciplinary Science Reviews, Vol. 40, No. 4. (2 October 2015), pp. 376-392, https://doi.org/10.1080/03080188.2016.1165454

Abstract

Researchers effectively trust the work of others anytime they use software tools or custom software. In this article I explore this notion of trusting others, using Digital Humanities as a focus, and drawing on my own experience. Software is inherently flawed and limited, so when its use in scholarship demands better practices and terminology, to review research software and describe development processes. It is also important to make research software engineers and their work more visible, both for the purposes of ...

 

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." ...

 

Why linked data is not enough for scientists

  
Future Generation Computer Systems, Vol. 29, No. 2. (February 2013), pp. 599-611, https://doi.org/10.1016/j.future.2011.08.004

Abstract

[Abstract] Scientific data represents a significant portion of the linked open data cloud and scientists stand to benefit from the data fusion capability this will afford. Publishing linked data into the cloud, however, does not ensure the required reusability. Publishing has requirements of provenance, quality, credit, attribution and methods to provide the reproducibility that enables validation of results. In this paper we make the case for a scientific data publication model on top of linked data and introduce the notion of Research ...

 

Scientists behaving badly

  
Nature, Vol. 435, No. 7043. (9 June 2005), pp. 737-738, https://doi.org/10.1038/435737a

Abstract

To protect the integrity of science, we must look beyond falsification, fabrication and plagiarism, to a wider range of questionable research practices, argue Brian C. Martinson, Melissa S. Anderson and Raymond de Vries. [\n] Serious misbehaviour in research is important for many reasons, not least because it damages the reputation of, and undermines public support for, science. Historically, professionals and the public have focused on headline-grabbing cases of scientific misconduct, but we believe that researchers can no longer afford to ignore ...

 

Why policy needs philosophers as much as it needs science

  
The Guardian, Vol. 2016, No. October, 13. (2016), 57b3q

Abstract

[Excerpt] In a widely-discussed recent essay for the New Atlantis, the policy scholar Daniel Sarewitz argues that science is in deep trouble. While modern research remains wondrously productive, its results are more ambiguous, contestable and dubious than ever before. This problem isn’t caused by a lack of funding or of scientific rigour. Rather, Sarewitz argues that we need to let go of a longstanding and cherished cultural belief – that science consists of uniquely objective knowledge that can put an end to ...

 

ePiX tutorial and reference manual

  
(2008)

Abstract

[Excerpt: Introduction] ePiX, a collection of batch utilities, creates mathematically accurate figures, plots, and animations containing LATEX typography. The input syntax is easy to learn, and the user interface resembles that of LATEX itself: You prepare a scene description in a text editor, then “compile” the input file into a picture. LATEX- and web-compatible output types include a LATEX picture-like environment written with PSTricks, tikz, or eepic macros; vector images (eps, ps, and pdf); and bitmapped images and movies (png, mng, and gif). [\n] ePiX’s strengths include: [::] Quality of ...

 

The FAIR Guiding Principles for scientific data management and stewardship

  
Scientific Data, Vol. 3 (15 March 2016), 160018, https://doi.org/10.1038/sdata.2016.18

Abstract

There is an urgent need to improve the infrastructure supporting the reuse of scholarly data. A diverse set of stakeholders—representing academia, industry, funding agencies, and scholarly publishers—have come together to design and jointly endorse a concise and measureable set of principles that we refer to as the FAIR Data Principles. The intent is that these may act as a guideline for those wishing to enhance the reusability of their data holdings. Distinct from peer initiatives that focus on the human scholar, ...

 

Why scientists must share their research code

  
Nature (13 September 2016), https://doi.org/10.1038/nature.2016.20504

Abstract

'Reproducibility editor' Victoria Stodden explains the growing movement to make code and data available to others. [Excerpt] [...] [::What does computational reproducibility mean?] It means that all details of computation — code and data — are made routinely available to others. If I can run your code on your data, then I can understand what you did. We need to expose all the steps that went into any discovery that relies on a computer. [::What’s the scientific value of running the same data with the ...

 

Fast computing for distance covariance

  
Technometrics (25 June 2015), pp. 0-0, https://doi.org/10.1080/00401706.2015.1054435

Abstract

Distance covariance and distance correlation have been widely adopted in measuring dependence of a pair of random variables or random vectors. If the computation of distance covariance and distance correlation is implemented directly accordingly to its definition then its computational complexity is O(n2) which is a disadvantage compared to other faster methods. In this paper we show that the computation of distance covariance and distance correlation of real valued random variables can be implemented by an O(n log n) algorithm and ...

 

Disciplinary action

  
Nature, Vol. 495, No. 7442. (27 March 2013), pp. 409-410, https://doi.org/10.1038/495409b

Abstract

How scientists share and reuse information is driven by technology but shaped by discipline. [Excerpt] [\n] [...] The transformation of research publishing is less a revolution and more a war of attrition. Battle lines were drawn long ago and all sides are well dug-in. In 2001, this journal published a series of viewpoints on the future of ‘e-access to the primary literature’ (see go.nature.com/pezj84). Those attitudes seem strikingly familiar today. At the time, the founders of the Public Library of Science initiative (then PLS, ...

 

Promoting research resource identification at JCN

  
Journal of Comparative Neurology, Vol. 522, No. 8. (01 June 2014), pp. 1707-1707, https://doi.org/10.1002/cne.23585

Abstract

[Excerpt] [\n] [...] [\n] The attention of scientists, editors, and policymakers alike have all turned recently to the issue of reproducibility in scientific research, focusing on research spanning from the pharmaceutical industry (Begley and Ellis, 2012) to the highest levels of government (Collins and Tabak, 2014; see also McNutt, 2014). While these commentaries point out that scientific misconduct is quite rare, they do point to a confluence of factors that hinder the reproducibility of scientific findings, including the identification of key reagents, such ...

 

The Resource Identification Initiative: a cultural shift in publishing

  
Neuroinformatics, Vol. 14, No. 2. (2016), pp. 169-182, https://doi.org/10.1007/s12021-015-9284-3

Abstract

A central tenet in support of research reproducibility is the ability to uniquely identify research resources, i.e., reagents, tools, and materials that are used to perform experiments. However, current reporting practices for research resources are insufficient to identify the exact resources that are reported or to answer basic questions such as “How did other studies use resource X?” To address this issue, the Resource Identification Initiative was launched as a pilot project to improve the reporting standards for research resources in ...

 

(INRMM-MiD internal record) List of keywords of the INRMM meta-information database - part 14

  
(February 2014)
Keywords: forest-fires   forest-floor-low-light-availability   forest-focus   forest-focus-monitoring   forest-inventories   forest-land-reclamation   forest-loss   forest-management   forest-pathogens   forest-pests   forest-product   forest-regeneration   forest-reproductive-material   forest-resource-information   forest-resources   forest-species   forest-species-composition   forest-structure   forest-succession   forest-types   forest-watering   forestcommunities   forestry   forestry-statistics   fortran   fossil-energy   fossil-resources   fp7-european-research-project   fracking   fractal   fragmentation   fragmented-world   frainetto   france   frangula-alnus   frangula-spp   fraxinus   fraxinus-angustifolia   fraxinus-augustifolia   fraxinus-excelsior   fraxinus-mandshurica   fraxinus-ornus   fraxinus-pennsylvanica   fraxinus-spp   free-access   free-access-book   free-riders   free-science-metrics   free-scientific-knowledge   free-scientific-software   free-software   free-software-directory   free-software-license-definition   freedom   freemat   french-alps   frequency   frost-resistance   frost-sensitivity   fruticosa   fuel   fuel-moisture   fuelwood   functional-connectivity   functional-descriptors   functional-programming   functional-traits   fungal-decay   fungal-diseases   fungi   fusarium-circinatum   fusarium-lateritium   future   future-climatic-envelopes   future-earth   future-internet   future-trends   fuzzy   gaia   galanthus-plicatus   galicia   gall-attributes   game-theory   gardening   gargano   garrulus-glandarius   gbif   gc-ms   gcm   gdal   gemmae-populi   gender-biases   gene-bank   gene-conservation   general-relation   generalized-additive-model   generalized-additive-models   generalized-linear-model   inrmm-list-of-tags  

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 ). ...

 

Brain and Behavior: we want you to share your data

  
Brain and Behavior, Vol. 4, No. 1. (January 2014), pp. 1-3, https://doi.org/10.1002/brb3.192

Abstract

We at Brain and Behavior are happy, for one, that data sharing is now here. [Excerpt] [...] Many reasons are given as to why we cannot, do not, or should not make data available (e.g., Strasser 2013; Wallis et al. 2013), but I think that the main reason we do not routinely share data is that, until recently, we could not. And because we could not, a system of scholarly communication grew where data were disposable. Literally. Eventually, the boxes piled upon ...

 

Changes in data sharing and data reuse practices and perceptions among scientists worldwide

  
PLoS ONE, Vol. 10, No. 8. (26 August 2015), e0134826, https://doi.org/10.1371/journal.pone.0134826

Abstract

The incorporation of data sharing into the research lifecycle is an important part of modern scholarly debate. In this study, the DataONE Usability and Assessment working group addresses two primary goals: To examine the current state of data sharing and reuse perceptions and practices among research scientists as they compare to the 2009/2010 baseline study, and to examine differences in practices and perceptions across age groups, geographic regions, and subject disciplines. We distributed surveys to a multinational sample of scientific researchers ...

 

Commission Notice - Guidelines on recommended standard licences, datasets and charging for the reuse of documents 2014/C 240/01

  
Official Journal of the European Union, Vol. 57, No. C 240. (24 July 2014), pp. 1-10

Abstract

[Excerpt] [:1. Purpose of the notice] Opening up public sector information (PSI) for re-use brings major socioeconomic benefits. Data generated by the public sector can be used as raw material for innovative value-added services and products which boost the economy by creating new jobs and encouraging investment in data-driven sectors. They also play a role in increasing government accountability and transparency. These benefits have recently been recognised by the G8 leaders and enshrined in an Open Data Charter (1). [\n] Yet, studies conducted on ...

 

Commission Decision of 12 December 2011 on the reuse of Commission documents (2011/833/EU)

  
Official Journal of the European Union, Vol. 54, No. L 330. (12 December 2011), pp. 39-42

Abstract

[Excerpt] [...] [:Article 1] [::Subject matter] This Decision determines the conditions for the reuse of documents held by the Commission or on its behalf by the Publications Office of the European Union (the Publications Office) with the aim of facilitating a wider reuse of information, enhancing the image of openness of the Commission, and avoiding unnecessary administrative burdens for reusers and the Commission services alike. [:Article 2] [::Scope] [::1] This Decision applies to public documents produced by the Commission or by public and private entities ...

 

The case for open preprints in biology

  
PLoS Biology, Vol. 11, No. 5. (14 May 2013), e1001563, https://doi.org/10.1371/journal.pbio.1001563

Abstract

Biologists should submit their preprints to open servers, a practice common in mathematics and physics, to open and accelerate the scientific process. [Excerpt: Introduction] Public preprint servers allow authors to make manuscripts publicly available before, or in parallel to, submitting them to journals for traditional peer review. The rationale for preprint servers is fundamentally simple: to make the results of research available to the scientific community as soon as possible, instead of waiting until the peer-review process is fully completed. Sharing manuscripts using ...

 

Funders must encourage scientists to share

  
Nature, Vol. 522, No. 7555. (11 June 2015), pp. 129-129, https://doi.org/10.1038/522129a

Abstract

To realize the full potential of large data sets, researchers must agree on better ways to pass data around, says Martin Bobrow. [Excerpt] How can we make best use of the vast amounts of data on genomics, epidemiology and population-level health being collected by researchers? Maximizing the benefits depends on how well we as a scientific community share information. [...] [\n] Both those who generate data and those who want to use them expressed frustration at the way that data-access processes are ...

 

Data reuse and the open data citation advantage

  
PeerJ, Vol. 1 (01 October 2013), e175, https://doi.org/10.7717/peerj.175

Abstract

[Background] Attribution to the original contributor upon reuse of published data is important both as a reward for data creators and to document the provenance of research findings. Previous studies have found that papers with publicly available datasets receive a higher number of citations than similar studies without available data. However, few previous analyses have had the statistical power to control for the many variables known to predict citation rate, which has led to uncertain estimates of the “citation benefit”. Furthermore, ...

 

Nine simple ways to make it easier to (re)use your data

  
Ideas in Ecology and Evolution, Vol. 6, No. 2. (2013), https://doi.org/10.4033/iee.2013.6b.6.f

Abstract

Sharing data is increasingly considered to be an important part of the scientific process. Making your data publicly available allows original results to be reproduced and new analyses to be conducted. While sharing your data is the first step in allowing reuse, it is also important that the data be easy to understand and use. We describe nine simple ways to make it easy to reuse the data that you share and also make it easier to work with it yourself. ...

 

Reproducible research can still be wrong: adopting a prevention approach

  
Proceedings of the National Academy of Sciences, Vol. 112, No. 6. (11 February 2015), pp. 1645-1646, https://doi.org/10.1073/pnas.1421412111

Abstract

[Excerpt] Reproducibility—the ability to recompute results—and replicability—the chances other experimenters will achieve a consistent result—are two foundational characteristics of successful scientific research. Consistent findings from independent investigators are the primary means by which scientific evidence accumulates for or against a hypothesis. Yet, of late, there has been a crisis of confidence among researchers worried about the rate at which studies are either reproducible or replicable. To maintain the integrity of science research and the public’s trust in science, the scientific community ...

Visual summary

 

Open code for open science?

  
Nature Geoscience, Vol. 7, No. 11. (30 October 2014), pp. 779-781, https://doi.org/10.1038/ngeo2283

Abstract

Open source software is often seen as a path to reproducibility in computational science. In practice there are many obstacles, even when the code is freely available, but open source policies should at least lead to better quality code. ...

 

Data archiving

  
The American Naturalist, Vol. 175, No. 2. (February 2010), pp. 145-146, https://doi.org/10.1086/650340

Abstract

[Excerpt] Science depends on good data. Data are central to our understanding of the natural world, yet most data in ecology and evolution are lost to science—except perhaps in summary form—very quickly after they are collected. Once the results of a study are published, the data on which those results are based are often stored unreliably, subject to loss by hard drive failure and (even more likely) by the researcher forgetting the specific details required to use the data (Michener et ...

 

Data, eternal

  
Science, Vol. 347, No. 6217. (02 January 2015), pp. 7-7, https://doi.org/10.1126/science.aaa5057

Abstract

[Excerpt] During 2014, Science worked with members of the research community, other publishers, and representatives of funding agencies on many initiatives to increase transparency and promote reproducibility in the published research literature. Those efforts will continue in 2015. Connected to that progress, and an essential element to its success, an additional focus will be on making data more open, easier to access, more discoverable, and more thoroughly documented. My own commitment to these goals is deeply held, for I learned early in ...

 

Minimal make - A minimal tutorial on make

  
(2014)

Abstract

[Excerpt] I would argue that the most important tool for reproducible research is not Sweave or knitr but GNU make. Consider, for example, all of the files associated with a manuscript. In the simplest case, I would have an R script for each figure plus a LaTeX file for the main text. And then a BibTeX file for the references. Compiling the final PDF is a bit of work: [::] Run each R script through R to produce the relevant figure. [::] Run latex and ...

 

microclim: Global estimates of hourly microclimate based on long-term monthly climate averages

  
Scientific Data, Vol. 1 (27 May 2014), https://doi.org/10.1038/sdata.2014.6

Abstract

The mechanistic links between climate and the environmental sensitivities of organisms occur through the microclimatic conditions that organisms experience. Here we present a dataset of gridded hourly estimates of typical microclimatic conditions (air temperature, wind speed, relative humidity, solar radiation, sky radiation and substrate temperatures from the surface to 1 m depth) at high resolution (~15 km) for the globe. The estimates are for the middle day of each month, based on long-term average macroclimates, and include six shade levels and three generic ...

Visual summary

 

Nature makes all articles free to view

  

Abstract

Publisher permits subscribers and media to share read-only versions of its papers. [Excerpt] All research papers from Nature will be made free to read in a proprietary screen-view format that can be annotated but not copied, printed or downloaded, the journal’s publisher Macmillan announced on 2 December. The content-sharing policy, which also applies to 48 other journals in Macmillan’s Nature Publishing Group (NPG) division, including Nature Genetics, Nature Medicine and Nature Physics, marks an attempt to let scientists freely read and share ...

 

Knowledge Freedom in computational science: a two stage peer-review process with KF eligibility access review

  

Abstract

Wide scale transdisciplinary modelling (WSTM) growingly demands a focus on reproducible research and scientific knowledge freedom. Data and software freedom are essential aspects of knowledge freedom in computational science. Therefore, ideally published articles should also provide the readers with the data and source code of the described mathematical modelling. To maximise transparency, replicability, reproducibility and reusability, published data should be made available as open data while source code should be made available as free software. Here, a two-stage peer review process ...

Visual summary

 

Openness makes software better sooner : Nature News

  

Abstract

Sharing code for computer software is best way to rid it of bugs. [Excerpt] Computer software develops more effectively when its code is freely accessible to all, UK researchers have calculated. This will come as no surprise to the legions of supporters of open-access software, such as the operating systems and tools the Linux and Apache projects distribute. To them, the superiority of freely available code is an article of faith - as much an ideological position as a technological decision. The theoretical model ...

 

Code share

  
Nature, Vol. 514, No. 7524. (29 October 2014), pp. 536-536, https://doi.org/10.1038/514536a

Abstract

Papers in Nature journals should make computer code accessible where possible. [Excerpt] A theme in Nature’s ongoing campaign for the replicability and reproducibility of our research papers is that key components of publications should be available to peers who wish to validate the techniques and results. A core element of many papers is the computercode used by authors in models, simulations and data analysis. In an ideal world, this code would always be transportable and easily used by others. In such a ...

 

Free Software on the final frontier: GNU Radio controls the ISEE-3 Spacecraft

  
(2014)

Abstract

[Excerpt] Equipped with free GNU Radio software, a group of citizen scientists has contacted, controlled, and is attempting to recapture a 1970s-era satellite and bring it back into an orbit close to Earth. The International Sun-Earth Explorer-3, or ISEE-3, was launched in 1978 by NASA to monitor activity on the sun. After three years of observation, NASA repurposed the satellite, which soon became the first spacecraft to visit a comet. The mission ended in 1999, when NASA abandoned ISEE-3 to orbit ...

 

Announcement: reducing our irreproducibility

  
Nature, Vol. 496, No. 7446. (24 April 2013), pp. 398-398, https://doi.org/10.1038/496398a

Abstract

[Excerpt] Over the past year, Nature has published a string of articles that highlight failures in the reliability and reproducibility of published research (collected and freely available at go.nature.com/huhbyr). The problems arise in laboratories, but journals such as this one compound them when they fail to exert sufficient scrutiny over the results that they publish, and when they do not publish enough information for other researchers to assess results properly. From next month, Nature and the Nature research journals will introduce editorial ...

 

Interactive comment on "Perturbation experiments to investigate the impact of ocean acidification: approaches and software tools" by J.-P. Gattuso and H. Lavigne

  
Biogeosciences Discussions, Vol. 6 (2009), pp. C1071-C1073

Abstract

[Excerpt] The referee wonders whether this manuscript should be published as a technical note rather than as a scientific article […][and] feels that the functions described are “black boxes”. We cannot disagree more with this statement as [the software tool] is free software, the source code of which is available to anyone (one just needs to download the package). Further, [the software tool] can be redistributed and/or modified under the terms of the GNU General Public License as published by the ...

 

Reproducible research

  
Computing in Science & Engineering, Vol. 11, No. 1. (2009), pp. 0005-7, https://doi.org/10.1109/mcse.2009.14

Abstract

Reproducibility is a core principle of science. For computational experiments to become reproducible, one needs to develop a system for linking scientific publications with computational recipes. Articles in this special issue argue in favor of computational reproducibility and describe several practical approaches to reproducible research. ...

 

Software in reproducible research: advice and best practice collected from experiences at the collaborations workshop

  
In Proceedings of the 1st ACM SIGPLAN Workshop on Reproducible Research Methodologies and New Publication Models in Computer Engineering (2014), https://doi.org/10.1145/2618137.2618140

Abstract

The Collaborations Workshop 2014 (CW14) brought together representatives from across the research community to discuss the issues around software's role in reproducible research. In this paper we summarise the themes, practices and ideas raised at the workshop. We also consider how the "unconference" format of the CW14 helps in eliciting information and forming future collaborations around aspects of reproducible research. In particular, we describe three distinct areas of concern which emerged from the event: collaboration readiness, capability enhancement and advocacy. ...

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