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

White, Ethan P.; Baldridge, Elita; Brym, Zachary; Locey, Kenneth J; McGlinn, Daniel J.; Supp, Sarah R.

doi:10.7287/peerj.preprints.7v1

Cited by 43 publications

(63 citation statements)

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“…The data and code for this study are archived in the repository figshare (Rupia et al 2015) following best practices (White et al 2013;Roche et al 2015).…”

Section: Data Accessibilitymentioning

confidence: 99%

Fight‐flight or freeze‐hide? Personality and metabolic phenotype mediate physiological defence responses in flatfish

Rupia

Binning

Roche

et al. 2016

Journal of Animal Ecology

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Survival depends on appropriate behavioural and physiological responses to danger. In addition to active 'fight-flight' defence responses, a passive 'freeze-hide' response is adaptive in some contexts. However, the physiological mechanisms determining which individuals choose a given defence response remain poorly understood. We examined the relationships among personality, metabolic performance and physiological stress responses across an environmental gradient in the olive flounder, Paralichthys olivaceus. We employed four behavioural assays to document the existence of two distinct behavioural types ('bold' and 'shy') in this species. We found consistent metabolic differences between individuals of a given behavioural type across an environmental gradient: shy individuals had overall lower aerobic scope, maximum metabolic rate and standard metabolic rate than bold individuals in both high (25 ppt) and low (3 ppt) salinity. These behavioural and metabolic differences translated into divergent physiological responses during acute stress: shy individuals adopted a passive 'freeze-hide' response by reducing their oxygen consumption rates (akin to shallow breathing) whereas bold individuals adopted an active 'fight-flight' response by increasing their rates of respiration. These distinct defence strategies were repeatable within individuals between salinity treatments. Although it has been suggested theoretically, this is the first empirical evidence that the metabolic response to stressful situations differs between bold and shy individuals. Our results emphasize the importance of incorporating physiological measures to understand the mechanisms driving persistent inter-individual differences in animals.

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“…The data and code for this study are archived in the repository figshare (Rupia et al 2015) following best practices (White et al 2013;Roche et al 2015).…”

Section: Data Accessibilitymentioning

confidence: 99%

Fight‐flight or freeze‐hide? Personality and metabolic phenotype mediate physiological defence responses in flatfish

Rupia

Binning

Roche

et al. 2016

Journal of Animal Ecology

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“…The old DZT =0 h is replaced by the new DZT =24 h , such that 0 h < DZT ≤ 24 h , while absence continues to be denoted as NotGiven . We think that this new approach has a robust Code2Brain interface (L oewe 2016) and provides a high-quality representation of Null for DZT values (see Table 2 and Discussion of Errors in Compilers below and elsewhere (W hite et al . 2013)).…”

Section: Modelsmentioning

confidence: 99%

“…We think that this new approach has a robust Code2Brain interface (L oewe et al . 2016b) and provides a high-quality representation of Null for DZT values (see Table 2 and Discussion of Errors in Compilers below and elsewhere (W hite et al . 2013)).…”

Section: Modelsmentioning

confidence: 99%

FlyClockbase: Importance of Biological Model Curation for Analyzing Variability in the Circadian Clock of Drosophila melanogaster by Integrating Time Series from 25 Years of Research

Scheuer

Hanlon

Dresel

et al. 2017

Preprint

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General Article SummarySubstantial biological model curation was essential for identifying differences in peak 23 time variance of the clock-proteins 'PERIOD' and 'TIMELESS', which probably stem 24 from differences in phosphorylation-network complexity. 25 We repeatedly encountered systemic limitations of contemporary data analysis 26 strategies in our work on circadian clocks. Thus, we used it as an opportunity for 27 composing a panoramic view of the broader challenges in biological model curation, 28 which are likely to increase as biologists aim to integrate all existing expertise in order to 29 address diverse grand challenges. We developed and tested a trans-disciplinary 30 research workflow, which enables biologists and compiler-architects to define biology-31 friendly compilers for efficiently constructing and maintaining Versioned Biological 32 Information Resources (VBIRs). We report insights gleaned from our practical clock 33 research that are essential for defining a VBIRs infrastructure, which improves the 34 efficiency of biological model curation to the point where it can be democratized. . CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It is made available under a was not peer-reviewed) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.The copyright holder for this preprint (which . http://dx.doi.org/10.1101/099192 doi: bioRxiv preprint first posted online Jan. 9, 2017;. CC-BY 4.0 International license It ...

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“…In order to share your data they have to be placed where they can be found and become accessible (see, for example, White et al, 2013). A number of such repository platforms are now being developed as part of both national research programmes as well as more subject-oriented initiatives; see, for example, CUASHI https://www.cuahsi.org/, TERN http://www.tern.org.…”

Section: The Fair and Square Of Data Handlingmentioning

confidence: 99%