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Selection: with tag check-list [41 articles] 


Do not publish

Science, Vol. 356, No. 6340. (25 May 2017), pp. 800-801,


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,


[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 ...


System of Systems - the meaning of of

System of Systems Engineering In 2006 IEEE/SMC International Conference on System of Systems Engineering, Vol. 0 (10 July 2006), pp. 118-123,


We present distinguishing characteristics (i.e. autonomy, belonging, connectivity, diversity, and emergence), that can help us to recognize or to realize a System of Systems (SoS). The principle differentiation that we make between a thing being either a 'system' or a SoS focuses on the nature of a system's composition. We will distinctly define this set of distinguishing characteristics which will include a set of cross references from our literature research where we believe others are articulating our chosen differentiating characteristics. We ...


Exploring transdisciplinary integration within a large research program: empirical lessons from four thematic synthesis processes

Research Policy, Vol. 46, No. 3. (April 2017), pp. 678-692,


[Highlights] [::] We adapt a framework to compare integration across four synthesis processes. [::] We identify challenges and derive recommendations for future synthesis processes. [::] We recommend initiating synthesis processes concurrently with research projects. [::] We consider professional competences and management skills crucial for integration. [::] We recommend the promotion of communities of practice to support integration. [Abstract] What challenges do researchers face when leading transdisciplinary integration? We address this question by analyzing transdisciplinary integration within four thematic synthesis processes of the Swiss National Research Programme (NRP 61) ...


Core trustworthy data repositories requirements



The Core Trustworthy Data Repository Requirements were developed by the DSA–WDS Partnership Working Group on Repository Audit and Certification, a Working Group (WG) of the Research Data Alliance . The goal of the effort was to create a set of harmonized common requirements for certification of repositories at the core level, drawing from criteria already put in place by the Data Seal of Approval (DSA: and the ICSU World Data System (ICSU-WDS: An additional goal of the project was ...


Regional variation in fire weather controls the reported occurrence of Scottish wildfires

PeerJ, Vol. 4 (02 November 2016), e2649,


Fire is widely used as a traditional habitat management tool in Scotland, but wildfires pose a significant and growing threat. The financial costs of fighting wildfires are significant and severe wildfires can have substantial environmental impacts. Due to the intermittent occurrence of severe fire seasons, Scotland, and the UK as a whole, remain somewhat unprepared. Scotland currently lacks any form of Fire Danger Rating system that could inform managers and the Fire and Rescue Services (FRS) of periods when there is ...


A data citation roadmap for scientific publishers

bioRxiv (19 January 2017), 100784,


This article presents a practical roadmap for scholarly publishers to implement data citation in accordance with the Joint Declaration of Data Citation Principles (JDDCP) [1], a synopsis and harmonization of the recommendations of major science policy bodies. It was developed by the Publishers Early Adopters Expert Group as part of the Data Citation Implementation Pilot (DCIP) project, an initiative of and the NIH BioCADDIE program. The structure of the roadmap presented here follows the “life of a paper” workflow and includes the categories Pre-submission, Submission, Production, ...


A manifesto for reproducible science

Nature Human Behaviour, Vol. 1, No. 1. (10 January 2017), 0021,


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 ...


INSPIRE data specification on geographical grid systems – Technical guidelines 3.1



[Excerpt] [:Interoperability of Spatial Data Sets and Services - General Executive Summary] The challenges regarding the lack of availability, quality, organisation, accessibility, and sharing of spatial information are common to a large number of policies and activities and are experienced across the various levels of public authority in Europe. In order to solve these problems it is necessary to take measures of coordination between the users and providers of spatial information. The Directive 2007/2/EC of the European Parliament and of the Council adopted on 14 March 2007 ...


Statistical analysis

In Science: editorial policies (2016)


[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 ...


Enhancing reproducibility for computational methods

Science, Vol. 354, No. 6317. (09 December 2016), pp. 1240-1241,


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 ...


Ethics among scholars in academic publishing

In 2012 Proceedings of the Information Systems Educators Conference (2012), 1948


This paper offers a survey of the contemporary and common-place ethical breaches concerning authorship, research, and publishing in today’s scholarly production, as juxtaposed with some of the predominant standards and guidelines that have been developed to direct academic publishing practices. While the paper may suggest the need for an updated and comprehensive set of guidelines for multiple discipline areas, the purpose here is to prepare the theoretical framework for a future computing discipline-specific study of ethical authorship and related concepts in ...


Ten steps to programming mastery



[Excerpt] Here are ten ways you can improve your coding. The overriding principle to improving your skill at coding, as well as almost endeavor, is open your mind and then fill it with better knowledge. Improvement necessarily implies change, yet it is human nature to fear and resist change. But overcoming that fear and embracing change as a way of life will enable you to reach new levels of achievement. [...] [::Big Rule 1: Break your own habits] When you began coding, you were much less experienced ...


The FAIR Guiding Principles for scientific data management and stewardship

Scientific Data, Vol. 3 (15 March 2016), 160018,


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, ...


How to review a paper



[Excerpt] As junior scientists develop their expertise and make names for themselves, they are increasingly likely to receive invitations to review research manuscripts. It’s an important skill and service to the scientific community, but the learning curve can be particularly steep. Writing a good review requires expertise in the field, an intimate knowledge of research methods, a critical mind, the ability to give fair and constructive feedback, and sensitivity to the feelings of authors on the receiving end. As a range ...


Stop ignoring misconduct

Nature, Vol. 537, No. 7618. (1 September 2016), pp. 29-30,


Efforts to reduce irreproducibility in research must also tackle the temptation to cheat, argue Donald S. Kornfeld and Sandra L. Titus. [Excerpt: Preventing misconduct] To diminish the threat that misconduct poses to science, scientists and society: [::] Authorities should acknowledge that deliberate misconduct is an important contributor to irreproducibility. [::] Mentors should be evaluated to assure quality; those who contribute to misconduct should be penalized. [::] Institutions and government agencies should have procedures to protect whistle-blowers from retaliation. [::] Senior faculty members who are found guilty of ...


Standards for reporting qualitative research

Academic Medicine, Vol. 89, No. 9. (September 2014), pp. 1245-1251,


[Purpose] Standards for reporting exist for many types of quantitative research, but currently none exist for the broad spectrum of qualitative research. The purpose of the present study was to formulate and define standards for reporting qualitative research while preserving the requisite flexibility to accommodate various paradigms, approaches, and methods. [Method] The authors identified guidelines, reporting standards, and critical appraisal criteria for qualitative research by searching PubMed, Web of Science, and Google through July 2013; reviewing the reference lists of retrieved sources; ...


A (partial) introduction to software engineering practices and methods



[Excerpt: Introduction] Software engineering is concerned with all aspects of software production from the early stages of system specification through to maintaining the system after it has gone into use. [...] [\n] [...] As a discipline, software engineering has progressed very far in a very short period of time, particularly when compared to classical engineering field (like civil or electrical engineering). In the early days of computing, not much more than 50 years ago, computerized systems were quite small. Most of the programming was done by scientists trying to ...


Raising the bar for reproducible science at the U.S. Environmental Protection Agency Office of Research and Development

Toxicological Sciences, Vol. 145, No. 1. (01 May 2015), pp. 16-22,


Considerable concern has been raised regarding research reproducibility both within and outside the scientific community. Several factors possibly contribute to a lack of reproducibility, including a failure to adequately employ statistical considerations during study design, bias in sample selection or subject recruitment, errors in developing data inclusion/exclusion criteria, and flawed statistical analysis. To address some of these issues, several publishers have developed checklists that authors must complete. Others have either enhanced statistical expertise on existing editorial boards, or formed distinct statistics ...


Top tips to make your research irreproducible

(8 Apr 2015)


It is an unfortunate convention of science that research should pretend to be reproducible; our top tips will help you mitigate this fussy conventionality, enabling you to enthusiastically showcase your irreproducible work. [Excerpt] [...] Irreproducibility is the default setting for all of science, and irreproducible research is particularly common across the computational sciences. [...] By following our starter tips, you can ensure that if your work is wrong, nobody will be able to check it; if it is correct, you will make everyone else do disproportionately ...


How NOT to Review a Paper: The Tools and Techniques of the Adversarial Reviewer

SIGMOD Rec., Vol. 37, No. 4. (March 2009), pp. 100-104,


There are several useful guides available for how to review a paper in Computer Science [10, 6, 12, 7, 2]. These are soberly presented, carefully reasoned and sensibly argued. As a result, they are not much fun. So, as a contrast, this note is a checklist of how not to review a paper. It details techniques that are unethical, unfair, or just plain nasty. Since in Computer Science we often present arguments about how an adversary would approach a particular problem, ...


A tool for simulating and communicating uncertainty when modelling species distributions under future climates

Ecology and Evolution, Vol. 4, No. 24. (December 2014), pp. 4798-4811,


[::] Tools for exploring and communicating the impact of uncertainty on spatial prediction are urgently needed, particularly when projecting species distributions to future conditions. [::] We provide a tool for simulating uncertainty, focusing on uncertainty due to data quality. We illustrate the use of the tool using a Tasmanian endemic species as a case study. Our simulations provide probabilistic, spatially explicit illustrations of the impact of uncertainty on model projections. We also illustrate differences in model projections using six different global climate ...


What does it mean for your computer to be loyal?

GNU Operating System (2014)


We say that running free software on your computer means that its operation is under your control. Implicitly this presupposes that your computer will do what your programs tell it to do, and no more. In other words, that your computer will be loyal to you. [\n] In 1990 we took that for granted; nowadays, many computers are designed to be disloyal to their users. It has become necessary to spell out what it means for your computer to be a loyal ...


The Open Science Peer Review Oath

F1000Research (12 November 2014),


One of the foundations of the scientific method is to be able to reproduce experiments and corroborate the results of research that has been done before. However, with the increasing complexities of new technologies and techniques, coupled with the specialisation of experiments, reproducing research findings has become a growing challenge. Clearly, scientific methods must be conveyed succinctly, and with clarity and rigour, in order for research to be reproducible. Here, we propose steps to help increase the transparency of the scientific ...


  1. Ioannidis JP: Why most published research findings are false. PLoS Med. 2005; 2(8): e124.
  2. Ioannidis JP, Allison DB, Ball CA, et al.: Repeatability of published microarray gene expression analyses. Nat Genet. 2009; 41(2): 149–55.
  3. Prinz F, Schlange T, Asadullah K: Believe it or not: how much can we rely on published data on potential drug targets? Nat Rev Drug Discov. 2011; 10(9): 712.
  4. Hines WC,

Openness in science is key to keeping public trust

Nature, Vol. 515, No. 7527. (19 November 2014), pp. 313-313,


Silence stifles progress, says Mark Yarborough. The scientific enterprise needs a transparent culture that actively finds and fixes problems. [Excerpt] The Ebola crisis demonstrates once again that, despite all the posturing of politicians, it is scientists who the public looks to in times of crisis and concern. The public still trusts scientists. A UK survey this year found that they trust scientists even if they do not always trust scientific information itself. Still, the public’s trust is fragile. Given how much scientists ...


Managing the risks of organizational accidents



This is a practical book aimed at those whose daily task it is to think about and manage or regulate the risks of hazardous technologies. The book is not targeted at any one domain, but attempts to identify general tools and principles that are applicable to all organizations facing dangers of one sort or another. This could include banks and building societies just as much as nuclear power plants, oil exploration and production, chemical process plants, and air, sea and rail ...


Habitat suitability modelling and niche theory

Journal of Applied Ecology, Vol. 45, No. 5. (1 October 2008), pp. 1372-1381,


The concept of the ecological niche relates a set of environmental variables to the fitness of species, while habitat suitability models (HSMs) relate environmental variables to the likelihood of occurrence of the species. In spite of this relationship, the concepts are weakly linked in the literature, and there is a strong need for better integration. [\n] We selectively reviewed the literature for habitat suitability studies that directly addressed four common facets of niche theory: niche characteristics, niche interactions, community-wide processes and ...


Announcement: reducing our irreproducibility

Nature, Vol. 496, No. 7446. (24 April 2013), pp. 398-398,


[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 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 ...


Publishing: credit where credit is due

Nature, Vol. 508, No. 7496. (16 April 2014), pp. 312-313,


[Excerpt] Research today is rarely a one-person job. Original research papers with a single author are — particularly in the life sciences — a vanishing breed. Partly, the inflation of author numbers on papers has been driven by national research-assessment exercises. Partly, it is the emergence of big and collaborative science, assisted by technology, that is changing the research landscape. [\n] What we cannot tell easily by reading a paper is who did what. That is difficult to decipher by consulting the ...


Climate policy: streamline IPCC reports

Nature, Vol. 508, No. 7495. (4 April 2014), pp. 171-173,


As the Intergovernmental Panel on Climate Change asks how its assessment process should evolve, Dave Griggs argues for decadal updates and eased workloads. [Excerpt] Although the Intergovernmental Panel on Climate Change (IPCC) has gained a justified reputation for producing the most up-to-date, comprehensive and authoritative statements of our knowledge of climate change, this has come at a cost to the scientific community. On 13 April, the IPCC releases the last part of its Fifth Assessment Report. Each report has become longer — ...


(INRMM-MiD internal record) List of keywords of the INRMM meta-information database - part 7

(February 2014)
Keywords: chamaerops-humilis   change   change-factor   channel-network   chaos   characteristics   charcoal   charcoal-analysis   check-list   chemical-analisys   chemical-composition   chemical-control   chemicals   chemosystematics   chenopodium-spp   chernobyl   chestnut-disease   chile   chilopsis-linearis   chimborazo   china   chionosphaera-cuniculicola   chionosphaera-spp   chloroplast-dna   chlorosis   cholera   chorisia-speciosa   choristoneura-conflictana   choristoneura-fumiferana   choristoneura-spp   chorology   chosenia-arbutifolia   chromium   chrysomela-populi   chrysomela-scripta   chrysomela-tremulae   chrysophyllum-albidum   chrysoptharta-bimaculata   chytridiopsis-typographi   cinchona-pubescens   cinnamomum-camphora   circular-economy   cistus-spp   citation-errors   citation-metrics   citeulike   citizen-science   citizen-sensor   citrus-aurantium   classification   classification-trees   clc   clear-cutting   clematis-alpina   clematis-vitalba   cliamte-change   cliffs   climate   climate-change   climate-change-impacts   climate-change-velocity   climate-engineering   climate-equity   climate-extremes   climate-growth-relations   climate-history   climate-models   climate-policy   climate-projections   climate-signal   climate-zones   climatic-conditions   climatic-gradient   climatic-niche   climatic-niche-shift   clostera-anachoreta   clostera-anastomosis   cloud-condensation   cloud-formation   cloudiness   clusia-rosea   clustering   co-evolution   co2   coal   coastal-settlement   coastline   coccoloba-uvifera   cocos-nucifera   codelet   coeloides-bostrichorum   coffea-arabica   coffea-canephora   cognitive-biases   cognitive-breakdown   cognitive-complexity   cognitive-load   cognitive-structure   cold-tolerance   inrmm-list-of-tags  


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 ( ). ...


Best Practices for Scientific Computing

PLOS Biology, Vol. 12, No. 1. (7 January 2014), e1001745,


We describe a set of best practices for scientific software development, based on research and experience, that will improve scientists' productivity and the reliability of their software. ...


Modeling, informatics, and the quest for reproducibility

Journal of Chemical Information and Modeling, Vol. 53, No. 7. (12 June 2013), pp. 1529-1530,


There is no doubt that papers published in the Journal of Chemical Information and Modeling, and related journals, provide valuable scientific information. However, it is often difficult to reproduce the work described in molecular modeling and cheminformatics papers. In many cases the software described in the paper is not readily available, in other cases the supporting information is not provided in an accessible format. To date, the major journals in the fields of molecular modeling and cheminformatics have not established guidelines ...


Promoting transparency in social science research

Science, Vol. 343, No. 6166. (03 January 2014), pp. 30-31,


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 ...


Technical assessment and evaluation of environmental models and software: Letter to the Editor

Environmental Modelling & Software, Vol. 26, No. 3. (24 March 2011), pp. 328-336,


This letter details the collective views of a number of independent researchers on the technical assessment and evaluation of environmental models and software. The purpose is to stimulate debate and initiate action that leads to an improved quality of model development and evaluation, so increasing the capacity for models to have positive outcomes from their use. As such, we emphasize the relationship between the model evaluation process and credibility with stakeholders (including funding agencies) with a view to ensure continued support ...


Ten simple rules for reproducible computational research

PLoS Computational Biology, Vol. 9, No. 10. (24 October 2013), e1003285,


[Excerpt] The importance of replication and reproducibility has recently been exemplified through studies showing that scientific papers commonly leave out experimental details essential for reproduction [5], studies showing difficulties with replicating published experimental results [6], an increase in retracted papers [7], and through a high number of failing clinical trials [8], [9]. This has led to discussions on how individual researchers, institutions, funding bodies, and journals can establish routines that increase transparency and reproducibility. In order to foster such aspects, it ...


Ten principles for a landscape approach to reconciling agriculture, conservation, and other competing land uses

Proceedings of the National Academy of Sciences, Vol. 110, No. 21. (21 May 2013), pp. 8349-8356,


“Landscape approaches” seek to provide tools and concepts for allocating and managing land to achieve social, economic, and environmental objectives in areas where agriculture, mining, and other productive land uses compete with environmental and biodiversity goals. Here we synthesize the current consensus on landscape approaches. This is based on published literature and a consensus-building process to define good practice and is validated by a survey of practitioners. We find the landscape approach has been refined in response to increasing societal concerns ...


Applying quality assurance procedures to environmental monitoring data: a case study

Journal of Environmental Monitoring, Vol. 11, No. 4. (2009), pp. 774-781,


Managing data in the context of environmental monitoring is associated with a number of particular difficulties. These can be broadly split into issues originating from the inherent heterogeneity of the parameters sampled, problems related to the long time scale of most monitoring programmes and situations that arise when attempting to maximise cost-effectiveness. The complexity of environmental systems is reflected in the considerable effort and cost required to collect good quality data describing the influencing factors that can improve our understanding of ...


False-positive psychology: undisclosed flexibility in data collection and analysis allows presenting anything as significant

Psychological Science, Vol. 22, No. 11. (01 November 2011), pp. 1359-1366,


In this article, we accomplish two things. First, we show that despite empirical psychologists’ nominal endorsement of a low rate of false-positive findings (≤ .05), flexibility in data collection, analysis, and reporting dramatically increases actual false-positive rates. In many cases, a researcher is more likely to falsely find evidence that an effect exists than to correctly find evidence that it does not. We present computer simulations and a pair of actual experiments that demonstrate how unacceptably easy it is to accumulate ...


Turning science into policy: challenges and experiences from the science–policy interface

Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 360, No. 1454. (28 February 2005), pp. 471-477,


This paper discusses key issues in the science–policy interface. It stresses the importance of linking the conservation and sustainable use of biodiversity to the Millennium Development Goals and to issues of immediate concern to policy-makers such as the economy, security and human health. It briefly discusses the process of decision-making and how the scientific and policy communities have successfully worked together on global environmental issues such as stratospheric ozone depletion and climate change, and the critical role of international assessments in ...


The role of social and decision sciences in communicating uncertain climate risks

Nature Climate Change, Vol. 1, No. 1. (29 March 2011), pp. 35-41,


A major challenge facing climate scientists is explaining to non-specialists the risks and uncertainties surrounding potential changes over the coming years, decades and centuries. Although there are many guidelines for climate communication, there is little empirical evidence of their efficacy, whether for dispassionately explaining the science or for persuading people to act in more sustainable ways. Moreover, climate communication faces new challenges as assessments of climate-related changes confront uncertainty more explicitly and adopt risk-based approaches to evaluating impacts. Given its critical ...

This page of the database may be cited as:
Integrated Natural Resources Modelling and Management - Meta-information Database.

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.