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| 2. |
- Grüning, Björn, et al.
(författare)
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Bioconda: A sustainable and comprehensive software distribution for the life sciences
- 2017
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- We present Bioconda (https://bioconda.github.io), a distribution of bioinformatics software for the lightweight, multi-platform and language-agnostic package manager Conda. Currently, Bioconda offers a collection of over 3000 software packages, which is continuously maintained, updated, and extended by a growing global community of more than 200 contributors. Bioconda improves analysis reproducibility by allowing users to define isolated environments with defined software versions, all of which are easily installed and managed without administrative privileges.
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| 3. |
- Jonzén, Niclas, et al.
(författare)
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Rapid advance of spring arrival dates in long-distance migratory birds
- 2006
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 312:5782, s. 1959-1961
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Tidskriftsartikel (refereegranskat)abstract
- Several bird species have advanced the timing of their spring migration in response to recent climate change. European short-distance migrants, wintering in temperate areas, have been assumed to be more affected by change in the European climate than long-distance migrants wintering in the tropics. However, we show that tong-distance migrants have advanced their spring arrival in Scandinavia more than short-distance migrants. By analyzing a long-term data set from southern Italy, we show that long-distance migrants also pass through the Mediterranean region earlier. We argue that this may reflect a climate-driven evolutionary change in the timing of spring migration.
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| 4. |
- Jonzén, Niclas, et al.
(författare)
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Response to comment on "Rapid advance of spring arrival dates in long-distance migratory birds"
- 2007
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 315:5812, s. 598-598
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Tidskriftsartikel (övrigt vetenskapligt/konstnärligt)abstract
- Both's comment questions our suggestion that the advanced spring arrival time of long-distance migratory birds in Scandinavia and the Mediterranean may reflect a climate-driven evolutionary change. We present additional arguments to support our hypothesis but underscore the importance of additional studies involving direct tests of evolutionary change.
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| 5. |
- Knudsen, Endre, et al.
(författare)
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Challenging claims in the study of migratory birds and climate change.
- 2011
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Ingår i: Biological Reviews. - 1469-185X. ; 86, s. 928-946
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Tidskriftsartikel (refereegranskat)abstract
- Recent shifts in phenology in response to climate change are well established but often poorly understood. Many animals integrate climate change across a spatially and temporally dispersed annual life cycle, and effects are modulated by ecological interactions, evolutionary change and endogenous control mechanisms. Here we assess and discuss key statements emerging from the rapidly developing study of changing spring phenology in migratory birds. These well-studied organisms have been instrumental for understanding climate-change effects, but research is developing rapidly and there is a need to attack the big issues rather than risking affirmative science. Although we agree poorly on the support for most claims, agreement regarding the knowledge basis enables consensus regarding broad patterns and likely causes. Empirical data needed for disentangling mechanisms are still scarce, and consequences at a population level and on community composition remain unclear. With increasing knowledge, the overall support ('consensus view') for a claim increased and between-researcher variability in support ('expert opinions') decreased, indicating the importance of assessing and communicating the knowledge basis. A proper integration across biological disciplines seems essential for the field's transition from affirming patterns to understanding mechanisms and making robust predictions regarding future consequences of shifting phenologies.
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| 6. |
- Knudsen, Endre, et al.
(författare)
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Characterizing bird migration phenology using data from standardized monitoring at bird observatories
- 2007
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Ingår i: Climate Research. - : Inter-Research Science Center. - 1616-1572 .- 0936-577X. ; 35:1-2, s. 59-77
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Forskningsöversikt (refereegranskat)abstract
- Long-term data from standardized monitoring programmes at bird observatories are becoming increasingly available. These data are frequently used for detecting changes in the timing of bird migration that may relate to recent climate change. We present an overview of problematic issues in the analysis of these data, and review approaches to and methods for characterizing bird migration phenology and its change over time. Methods are illustrated and briefly compared using autumn data on garden warbler Sylvia borin from a standardized mist-netting programme at Lista bird observatory, southern Norway. Bird migration phenology is usually characterized rather coarsely using a small number of sample statistics such as mean, median and selected quantiles. We present 2 alternative approaches. Smoothing methods describe the within-season pattern in the data at an arbitrary level of detail, while fitting a parametric seasonal distribution curve offers a coarse description of migration phenology relatively robust to sampling effects. Various methods for analyzing linear trends in the timing of bird migration are reviewed and discussed. Exploratory studies using long-term data gathered at bird observatories can yield more detailed insight into the phenomenon of bird migration and how phenologies relate to climate. Methodological advances are needed, particularly in order to better characterize the shape of phenological distributions and separate between sampling effects and 'true' phenology.
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