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1,069 results for “Data managment”
Supplementary material 2 from: Borghi J, Abrams S, Lowenberg D, Simms S, Chodacki J (2018) Support Your Data: A Research Data Management Guide for Researchers. Research Ideas and Outcomes 4: e26439. https://doi.org/10.3897/rio.4.e26439
A draft guide that corresponds with the "Planning your project" row of the RDM rubric. Suggested points of customization are highlighted in yellow (discipline-specific) and red (institution-specific).
Data from: Landscape configuration, organic management and within-field position drive functional diversity of spiders and carabids
<p>This repository contains functional diversity data of spiders and carabids. For details please see the original publication.</p>
Supplementary material 1 from: Van Tuyl S, Whitmire A (2018) Investigation of Non-Academic Data Management Practices to Inform Academic Research Data Management. Research Ideas and Outcomes 4: e30829. https://doi.org/10.3897/rio.4.e30829
Interview protocol used for the project, "Investigation of Non-Academic Data Management Practices to Inform Academic Research Data Management"
Why research data management: four videos
<p>See https://rdmpromotion.rbind.io, and doi: <a href="https://doi.org/10.5281/zenodo.1293375">10.5281/zenodo.1293375</a> </p> <p>The four videos are presented in their own folder, we have one version without sound, and the music and the voice over sound in three different files. Finally, the version with all 4 elements is also there. The videos were also pushed to figshare and got their own doi there (they are also on youtube at the moment).</p> <p>01_opendata, doi: https://doi.org/10.6084/m9.figshare.7379942<br> 02_retrievedata, doi: https://doi.org/10.6084/m9.figshare.7163396<br> 03_analysedata, doi: https://doi.org/10.6084/m9.figshare.7673543<br> 04_data_champions, doi: https://doi.org/10.6084/m9.figshare.7053797</p> <p>subtitles (including translations) can be found here and at https://github.com/open-science-promoters/RDM-promotion/tree/master/subtitlesvideo. You may want to check youtube for later translations. </p> <p>Note that timing of the voice over of the 3d movie had to be modified, and a second file with the modification is included.</p> <p><br> Source of videos:</p> <p>01_opendata:</p> <p>Superman, Secret Agent<br> Superman, Billion dollar limited<br> Superman, Superman (the mad scientist)<br> Superman, Japoteurs<br> Superman, the magnetic telescope (music only)</p> <p>source: toonamiarsenal.com (deprecated, see archive.org to get it)</p> <p>02_retrievedata:<br> Popeye, Parlez Vous Woo<br> Popeye, A date to skate<br> Popeye, A Haul in One</p> <p>source: archive.org</p> <p>03_analysedata:<br> The haunted house<br> One week</p> <p>source: archive.org</p> <p>04_data_champions:<br> classic TV commercial from the 50s,<br> ClassicT1948_7<br> ClassicT1948_8<br> Televisi1960</p> <p>source: prellinger collection, archive.org</p>
FAIRness of Repositories & Their Data: A Report from LIBER's Research Data Management Working Group
<p>Data repositories play a crucial role in the evolution of Open Science. The FAIR Data Principles establish how to make data Findable, Accessible, Interoperable and Reusable (Wilkinson et al., 2016). The FAIR principles are as follows: </p> <p><strong>To Be Findable</strong></p> <ul> <li>F1. (meta)data are assigned a globally unique and eternally persistent identifier.</li> <li>F2. data are described with rich metadata.</li> <li>F3. (meta)data are registered or indexed in a searchable resource.</li> <li>F4. metadata specify the data identifier.</li> </ul> <p><strong>To Be Accessible:</strong></p> <ul> <li>A1 (meta)data are retrievable by their identifier using a standardized communications protocol.</li> <li>A1.1 the protocol is open, free, and universally implementable.</li> <li>A1.2 the protocol allows for an authentication and authorization procedure, where necessary.</li> <li>A2 metadata are accessible, even when the data are no longer available.</li> </ul> <p><strong>To Be Interoperable</strong></p> <ul> <li>I1. (meta)data use a formal, accessible, shared, and broadly applicable language for knowledge representation.</li> <li>I2. (meta)data use vocabularies that follow FAIR principles.</li> <li>I3. (meta)data include qualified references to other (meta)data.</li> </ul> <p><strong>To Be Reusable</strong></p> <ul> <li>R1. meta(data) have a plurality of accurate and relevant attributes.</li> <li>R1.1. (meta)data are released with a clear and accessible data usage license.</li> <li>R1.2. (meta)data are associated with their provenance.</li> <li>R1.3. (meta)data meet domain-relevant community standards. </li> </ul> <p><strong>Methodology</strong></p> <p>Based on the FAIR Data Principles, two questionnaires were created. The first (hereafter #Q1 - see Appendix #1) targeted repository managers and/or librarians and consisted of 40 questions. The second (hereafter #Q2 - see Appendix #2) targeted technical staff responsible for repository development and maintenance and consisted of 25 questions. </p> <p>Members of LIBER’s <a href="https://libereurope.eu/strategy/research-infrastructures/rdm/">Research Data Management (RDM) Working Group</a> circulated the questionnaires between December 2018 and February 2019. Responses were collected from managers and/or librarians of 29 repositories for the first (#Q1) questionnaire. </p> <p>In addition, technical staff responsible for the development and maintenance of 14 repositories (Table 1) responded to the second (#Q2) questionnaire. In 11 cases, repositories filled out both #Q1 and #Q2. </p> <p>In this report, the responses for both questionnaires have been merged and analyzed to gain a comprehensive picture about FAIRness at the level of repositories and their data.<br> </p>
Data for "Evaluation of Low Impact Development and Nature-Based Solutions for stormwater management: a fully distributed modelling approach"
<p>The data set corresponds the data used in the paper : “Evaluation of Low Impact Development and Nature-Based Solutions for stormwater management: a fully distributed modelling approach”, published in 2019 in the Journal “Hydrology and Earth System Sciences” (http://www.hydrol-earth-syst-sci.net/).</p> <p>More precisely it corresponds to the simulation input data that used in the Multi-Hydro model and the simulated discharge of the five scenarios investigated in the paper.</p>
Supplementary Data for risk management
<p>Data for reservoir inflows and lateral inflows are listed in the file "Inflows". Data for reservoir characteristcs and river flood routing parameters are listed in the file "characteristics of reservoirs and river flood routing parameters". Matlab codes for NSGA-III are listed in the file "nsga-iii".</p>
Demystifying Open Science and Research Data Management: A practical workshop for researchers
<p>Have you ever wondered why is everyone discussing about Open Science and Research Data Management (RDM) these days? Good Research Data Management (RDM) is crucial for reproducible and robust scientific research. Consequently, more and more funding bodies, governments, research institutions and other agencies have emphasised the value and importance of good data management and introduced policies on data management and sharing. However, it is easier said than done.<br> Like most researchers you might have more questions than answers about the topic. You are not alone! Come join us on the 24th at an interactive workshop where you can understand the why and how of open science and research data management in practical terms.</p> <p> </p> <p>This zenodo entry is a recording of the workshop described above. </p>
Galaxy Data Manager foor GTDB-Tk database - test database
<div>This tar.gz is just a dummy file that mimics the structure of the GTDB-tk releases as shown below and can be used as test case for <div>the data manager !</div> </div>
Soil and environmental data for "Interacting management effects on soil microbial alpha and beta diversity in Swiss agricultural grassland"
<p>This data shows the soil, environmental, and management data of 86 grassland sites that were sampled within the Canton of Solothurn, Switzerland. This data was used in the manuscript by F.J. Richter, R. Feola Conz, A. Lüscher, N. Buchmann, K.H. Valentin and M. Hartmann (2024): Interacting management effects on soil microbial alpha and beta diversity in Swiss agricultural grassland, which is published in the Journal of Applied Soil Ecology. </p>
Data Management Plan (DMP)v2
Open the record for dataset details and reuse information.
Data from: Resource-mediated indirect effects of grassland management on arthropod diversity
Intensive land use is a driving force for biodiversity decline in many ecosystems. In semi-natural grasslands, land-use activities such as mowing, grazing and fertilization affect the diversity of plants and arthropods, but the combined effects of different drivers and the chain of effects are largely unknown. In this study we used structural equation modelling to analyse how the arthropod communities in managed grasslands respond to land use and whether these responses are mediated through changes in resource diversity or resource quantity (biomass). Plants were considered resources for herbivores which themselves were considered resources for predators. Plant and arthropod (herbivores and predators) communities were sampled on 141 meadows, pastures and mown pastures within three regions in Germany in 2008 and 2009. Increasing land-use intensity generally increased plant biomass and decreased plant diversity, mainly through increasing fertilization. Herbivore diversity decreased together with plant diversity but showed no response to changes in plant biomass. Hence, landuse effects on herbivore diversity were mediated through resource diversity rather than quantity. Land-use effects on predator diversity were mediated by both herbivore diversity (resource diversity) and herbivore quantity (herbivore biomass), but indirect effects through resource quantity were stronger. Our findings highlight the importance of assessing both direct and indirect effects of land-use intensity and mode on different trophic levels. In addition to the overall effects, there were subtle differences between the different regions, pointing to the importance of regional land-use specificities. Our study underlines the commonly observed strong effect of grassland land use on biodiversity. It also highlights that mechanistic approaches help us to understand how different land-use modes affect biodiversity.
Data from: Structural and compositional mismatch between captive and wild Atlantic salmon (Salmo salar) parrs gut microbiota highlights the relevance of integrating molecular ecology for management and conservation methods.
Stocking methods are used in the Province of Quebec to restore Salmo salar populations. However, Atlantic salmon stocked juveniles show higher mortality rates than wild ones when introduced into nature. Hatchery environment, which greatly differs from the natural environment, is identified as the main driver of the phenotypic mismatch between captive and wild parrs. The latter is also suspected to impact the gut microbiota composition, which can be associated with essential metabolic functions for their host. We hypothesized that hatchery raised parrs potentially recruit gut microbial communities that are different from those recruited in the wild. This study evaluated the impacts of artificial rearing on gut microbiota composition in 0+ parrs meant for stocking in two distinct Canadian rivers: Rimouski and Malbaie (Quebec, Canada). Striking differences between hatchery and wild born parrs' gut microbiota suggest that microbiota could be another factor that could impact their survival in the targeted river, since the microbiome is narrowly related to host physiology. For instance, major commensals belonging to Enterobacteriaceae and Clostridiacea from wild parrs' gut microbiota were substituted in captive parrs by lactic acid bacteria from the Lactobacillaceae family. Overall, captive parrs host a generalist bacterial community whereas wild parrs' microbiota is much more specialized. This is the very first study demonstrating extensive impact of captive rearing on intestinal microbiota composition in Atlantic salmon intended for wild population stocking. Our results strongly suggest the need to implement microbial ecology concepts into conservation management of endangered salmon stocks supplemented with hatchery reared parrs.
Data from: Failure to coordinate management in transboundary populations hinders the achievement of national management goals: the case of wolverines in Scandinavia
1. Large carnivores are expanding in Europe, and their return is associated with conflicts that often result in policies to regulate their population size through culling. Being wide-ranging species, their populations are often distributed across several jurisdictions, which may vary in the extent to which they use lethal control. This creates the conditions for the establishment of source-sink dynamics across borders, which may frustrate the ability of countries to reach their respective management objectives. 2. To explore the consequences of this issue, we constructed a vec-permutation projection model, applied to the case of wolverines in south-central Scandinavia, shared between Norway (where they are culled) and Sweden (where they are protected). We evaluated the effect of compensatory immigration on wolverine population growth rates, and if the effect was influenced by the distance to the national border. We assessed to what extent compensatory immigration had an influence on the number of removals needed to keep the population at a given growth rate. 3. In Norway the model estimated a stable trend, whereas in Sweden it produced a 10% annual increase. The effect of compensatory immigration corresponded to a 0.02 reduction in population growth rate in Sweden and to a similar increase in Norway. This effect was stronger closer to the Norwegian-Swedish border, but weak when moving away from it. An average of 33 wolverines were shot per year in the Norwegian part of the study area. If no compensatory immigration from Sweden had occurred, 28 wolverines shot per year would have been sufficient to achieve the same goal. About 15.5% of all the individuals harvested in Norway between 2005-2012 were compensated for by immigrants, causing a decrease in population growth rate in Sweden. 4. Synthesis and applications. When a population is transboundary, the consequences of management decisions are also transboundary, even though the political bodies in charge of those decisions, the stakeholders who influence them, and the taxpayers who finance them are not. It is important that managers and citizens be informed that a difference in management goals can reduce the efficiency, and increase the costs, of wildlife management.
Data from: Population genetic structure and connectivity of deep-sea stony corals (Order Scleractinia) in the New Zealand region: implications for the conservation and management of Vulnerable Marine Ecosystems
Deep-sea stony corals, which can be fragile, long-lived, late to mature and habitat-forming, are defined as vulnerable marine ecosystem indicator taxa. Under United Nations resolutions these corals require protection from human disturbance such as fishing. To better understand the vulnerability of stony corals (Goniocorella dumosa, Madrepora oculata, Solenosmilia variabilis) to disturbance within the New Zealand region, and to guide marine protected area design, genetic structure and connectivity were determined using microsatellite loci and DNA sequencing. Analyses compared population genetic differentiation between two biogeographic provinces, amongst three sub-regions (north-central-south), and amongst geomorphic features. Extensive population genetic differentiation was revealed by microsatellite variation, whilst DNA sequencing revealed very little differentiation. For G. dumosa, genetic differentiation existed amongst regions and geomorphic features, but not between provinces. For M. oculata, only a north-central-south regional structure was observed. For S. variabilis, genetic differentiation was observed between provinces, amongst regions and amongst geomorphic features. Populations on the Kermadec Ridge were genetically different from Chatham Rise populations in all three species. A significant isolation-by-depth pattern was observed for both marker types in G. dumosa, and also in ITS of M. oculata. An isolation-by-distance pattern was revealed for microsatellite variation in S. variabilis. Medium to high levels of self-recruitment were detected in all geomorphic populations, and rates and routes of genetic connectivity were species-specific. These patterns of population genetic structure and connectivity at a range of spatial scales indicate that flexible spatial management approaches are required for the conservation of deep-sea corals around New Zealand.
Data from: Description and preliminary results from a structured specialist behavioural weight management group intervention: Specialist Lifestyle Management (SLiM) Programme
Background: Specialist Lifestyle Management (SLiM) is a structured patient education and self-management group weight management programme. Each session is run monthly over a 6-month period providing a less intensive long-term approach. The groups are patient-centred incorporating educational, motivational, behavioural and cognitive elements. The theoretical background, programme structure and preliminary results of SLiM are presented. Subjects/methods: The study was a pragmatic service evaluation of obese patients with a body mass index (BMI) ≥35 kg/m2 with comorbidity or ≥40 kg/m2 without comorbidity referred to a specialist weight management service in the West Midlands, UK. 828 patients were enrolled within SLiM over a 48-month period. Trained facilitators delivered the programme. Preliminary anonymised data were analysed using the intention-to-treat principle. The primary outcome measure was weight loss at 3 and 6 months with comparisons between completers and non-completers performed. The last observation carried forward was used for missing data. Results: Of the 828 enrolled within SLiM, 464 completed the programme (56%). The mean baseline weight was 135 kg (BMI=49.1 kg/m2) with 87.2% of patients having a BMI≥40 kg/m2 and 12.4% with BMI≥60 kg/m2. The mean weight change of all patients enrolled was −4.1 kg (95% CI −3.6 to −4.6 kg, p=0.0001) at the end of SLiM, with completers (n=464) achieving −5.5 kg (95% CI −4.2 to −6.2 kg, p=0.0001) and non-completers achieving −2.3 kg (p=0.0001). The majority (78.6%) who attended the 6-month programme achieved weight loss with 32.3% achieving a ≥5% weight loss. Conclusions: The SLiM programme is an effective group intervention for the management of severe and complex obesity.
Data from: Detection of outlier loci and their utility for fisheries management
Genetics-based approaches have informed fisheries management for decades, yet remain challenging to implement within systems involving recently diverged stocks or where gene flow persists. In such cases, genetic markers exhibiting locus-specific ("outlier") effects associated with divergent selection may provide promising alternatives to loci that reflect genome-wide ("neutral") effects for guiding fisheries management. Okanagan Lake kokanee (Oncorhynchus nerka), a fishery of conservation concern, exhibits two sympatric ecotypes adapted to different reproductive environments, however, previous research demonstrated the limited utility of neutral microsatellites for assigning individuals. Here, we investigated the efficacy of an outlier-based approach to fisheries management by screening >11,000 expressed sequence tags for linked microsatellites and conducting genomic scans for kokanee sampled across seven spawning sites. We identified eight outliers among 52 polymorphic loci that detected ecotype-level divergence, whereas there was no evidence of divergence at neutral loci. Outlier loci exhibited the highest self-assignment accuracy to ecotype (92.1%), substantially outperforming 44 neutral loci (71.8%). Results were robust among-sampling years, with assignment and mixed composition estimates for individuals sampled in 2010 mirroring baseline results. Overall, outlier loci constitute promising alternatives for informing fisheries management involving recently diverged stocks, with potential applications for designating management units across a broad range of taxa.
Data from: A century of changing flows: forest management changed flow magnitudes and warming advanced the timing of flow in a southwestern US river
The continued provision of water from rivers in the southwestern United States to downstream cities, natural communities and species is at risk due to higher temperatures and drought conditions in recent decades. Snowpack and snowfall levels have declined, snowmelt and peak spring flows are arriving earlier, and summer flows have declined. Concurrent to climate change and variation, a century of fire suppression has resulted in dramatic changes to forest conditions, and yet, few studies have focused on determining the degree to which changing forests have altered flows. In this study, we evaluated changes in flow, climate, and forest conditions in the Salt River in central Arizona from 1914–2012 to compare and evaluate the effects of changing forest conditions and temperatures on flows. After using linear regression models to remove the influence of precipitation and temperature, we estimated that annual flows declined by 8–29% from 1914–1963, coincident with a 2-fold increase in basal area, a 2-3-fold increase in canopy cover, and at least a 10-fold increase in forest density within ponderosa pine forests. Streamflow volumes declined by 37–56% in summer and fall months during this period. Declines in climate-adjusted flows reversed at mid-century when spring and annual flows increased by 10–31% from 1964–2012, perhaps due to more winter rainfall. Additionally, peak spring flows occurred about 12 days earlier in this period than in the previous period, coincident with winter and spring temperatures that increased by 1–2°C. While uncertainties remain, this study adds to the knowledge gained in other regions that forest change has had effects on flow that were on par with climate variability and, in the case of mid-century declines, well before the influence of anthropogenic warming. Current large-scale forest restoration projects hold some promise of recovering seasonal flows.
Data from: A dynamical model for invasive round goby populations reveals efficient and effective management options
1. When prevention of invasive species' introductions fails, society faces the challenge to manage these invasive species in an effective and efficient way. The success of this depends on biological aspects and on cooperation between decision makers and scientists. Using the case of the round goby Neogobius melanostomus, one of Europe's worst invasive species, we propose an approach guiding scientists to co-produce effective and efficient population control measures in collaboration with decision makers. 2. We surveyed the effectiveness, urgency and simplicity perceived by decision makers as well as the support of two population control options: removal of eggs and/or adults. Using a field study and a dynamical population model, we investigated the effectiveness and efficiency for both options in different population contexts. 3. Decision makers initially seemed to lack a clear preference for either control option. After being presented with preliminary field and modelling results, decision makers mostly approved measures being developed to implement the two control options. 4. Starting population control early after detecting the species requires in total fewer years for eradication than controlling an established population: to reach an eradication success rate of 95%, 13 years for early start vs. 18 years for late start are needed when removing eggs and adults; when removing adults only, 20 vs. 29 years are needed. Removing eggs and adults combined results in a yearly effort of 5.01 h m-2, while removing adults only results in a yearly effort of 1.76 h m-2. Thus, removing adults only proved to be the most efficient option to eradicate the population. Nonetheless, considerable effort is needed: when removing less than 57% of the adult population, eradication is not feasible, even assuming low survival and fecundity rates for the population. Further, inflow of new propagules renders eradication efforts ineffective. 5. Synthesis and applications. Scientists who aim to support decision makers in finding an optimal control strategy for invasive species need to be able to provide scientific knowledge on effectiveness and efficiency of different options. For round goby and most non-native species, eradication is only feasible if started early in recently arrived populations and if inflow of new propagules can be prevented.
Data from: Forest management adaptation to climate change: a Cornelian dilemma between drought resistance and soil macro-detritivore functional diversity
1. Global warming induces new constraints on forest ecosystems and requires forest management adaptation. The reduction in stand density is currently debated as a potential tool to face increasing summer drought risk by improving forest resistance to climate change-induced tree mortality. However, few studies have yet assessed the impacts of this management change on soil biodiversity. 2. We conducted a large-scale, multi-site assessment of the response of soil macro-detritivore assemblages and soil functioning to experimental manipulations of stand density. A total of 33 stands were studied covering a wide gradient of stand density, that is stand basal area from 2·5 to 43·7 m2 ha−1, stand age, that is 18–171 years old, and local abiotic context. 3. We observed contrasting responses as a function of both taxonomic and functional groupings. Exploratory analysis using causal diagrams, that is path analysis, highlights that these changes were mainly related to alterations in understorey vegetation, microclimatic and soil pH conditions. The response of soil macro-detritivore assemblages to stand density manipulation was consistent over the gradient of stand ages. 4. Among the litter-dwelling macro-detritivores, millipede abundance and diversity decreased with stand density reduction, while woodlice and epigeic earthworms were unaffected. Further, a shift in soil-dwelling earthworm community composition was observed in mull stands. Endogeic earthworm abundance showed a sharp increase with stand density reduction, which translated into an increase in soil respiration. In contrast, anecic earthworm abundance decreased and was strongly associated with a decline of the rate of forest floor turnover. 5. Synthesis and applications. Our study provides strong evidence that reductions of stand density will have substantial impacts on soil macro-detritivore assemblages and cascading effects on soil functioning, particularly in mull stands. Managing stand density of oak forests at an intermediate level, that is 25 m2 ha−1, appears to be best to optimize the trade-off between improving forest resistance to climate change and ensuring the conservation of functional diversity to preserve forest ecosystem functioning and stability.
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These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.