Ecology
Learn to analyse Ecological data through Galaxy.
You can view the tutorial materials in different languages by clicking the dropdown icon next to the slides (slides) and tutorial (tutorial) buttons below.Requirements
Before diving into this topic, we recommend you to have a look at:
Material
Data and Metadata Management
These tutorials are focusing on data and metadata management in Ecology.
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Creating FAIR Quality assessment reports and draft of Data Papers from EML metadata with MetaShRIMPS |
Data access
These lessons focus on ways to access data classicaly used in Ecology
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| QGIS Web Feature Services |
Data preprocessing
These lessons focus on manners to preprocess data used in Ecology
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Biodiversity data exploration | |||||
| Checking expected species and contamination in bacterial isolate | |||||
| Cleaning GBIF data for the use in Ecology |
Data analysis
These lessons focus on ways to analyse data in Ecology
Data visualization
These tutorials showcase data visualization in Ecology
| Lesson | Slides | Hands-on | Recordings | Input dataset | Workflows |
|---|---|---|---|---|---|
| Visualization of Climate Data using NetCDF xarray Map Plotting | |||||
| Visualize EBV cube data with Panoply netCDF viewer |
Galaxy instances
You can use a public Galaxy instance which has been tested for the availability of the used tools. They are listed along with the tutorials above.
You can also use the following Docker image for these tutorials:
docker run -p 8080:80 quay.io/galaxy/ecology-trainingNOTE: Use the -d flag at the end of the command if you want to automatically download all the data-libraries into the container.
It will launch a flavored Galaxy instance available on http://localhost:8080. This instance will contain all the tools and workflows to follow the tutorials in this topic. Login as admin with password password to access everything.
Frequently Asked Questions
Common questions regarding this topic have been collected on a dedicated FAQ page . Common questions related to specific tutorials can be accessed from the tutorials themselves.
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Editorial Board
This material is reviewed by our Editorial Board:
Yvan Le Bras
For any question related to this topic and the content, you can contact them or visit our Gitter channel.
Contributors
This material was contributed to by:
Soumya Jha
Yvan Le Bras
Frédéric Boyer
Elisa Michon
Olivier Norvez
Tanguy Genthon
Glinez Thibaud
Simon Benateau
Jean-Baptiste Mihoub
Pôle National de Données de Biodiversité
Bérénice Batut
Coline Royaux
Helena Rasche
Miguel Roncoroni
Dominique Pelletier
Clara Urfer
Clea Siguret
Eric Coissac
Marie Josse
Brigida Gallone
Anne Fouilloux
Funding
These individuals or organisations provided funding support for the development of this resource
References
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Reto Schmucki et al: A regionally informed abundance index for supporting integrative analyses across butterfly monitoring schemes
The rapid expansion of systematic monitoring schemes necessitates robust methods to reliably assess species' status and trends. Insect monitoring poses a challenge where there are strong seasonal patterns, requiring repeated counts to reliably assess abundance. Butterfly monitoring schemes (BMSs) operate in an increasing number of countries with broadly the same methodology, yet they differ in their observation frequency and in the methods used to compute annual abundance indices. Using simulated and observed data, we performed an extensive comparison of two approaches used to derive abundance indices from count data collected via BMS, under a range of sampling frequencies. Linear interpolation is most commonly used to estimate abundance indices from seasonal count series. A second method, hereafter the regional generalized additive model (GAM), fits a GAM to repeated counts within sites across a climatic region. For the two methods, we estimated bias in abundance indices and the statistical power for detecting trends, given different proportions of missing counts. We also compared the accuracy of trend estimates using systematically degraded observed counts of the Gatekeeper Pyronia tithonus (Linnaeus 1767). The regional GAM method generally outperforms the linear interpolation method. When the proportion of missing counts increased beyond 50%, indices derived via the linear interpolation method showed substantially higher estimation error as well as clear biases, in comparison to the regional GAM method. The regional GAM method also showed higher power to detect trends when the proportion of missing counts was substantial. Synthesis and applications. Monitoring offers invaluable data to support conservation policy and management, but requires robust analysis approaches and guidance for new and expanding schemes. Based on our findings, we recommend the regional generalized additive model approach when conducting integrative analyses across schemes, or when analysing scheme data with reduced sampling efforts. This method enables existing schemes to be expanded or new schemes to be developed with reduced within‐year sampling frequency, as well as affording options to adapt protocols to more efficiently assess species status and trends across large geographical scales. -
Vitor H. F. Gomes et al: Species Distribution Modelling: Contrasting presence-only models with plot abundance data
Species distribution models (SDMs) are widely used in ecology and conservation. Presence-only SDMs such as MaxEnt frequently use natural history collections (NHCs) as occurrence data, given their huge numbers and accessibility. NHCs are often spatially biased which may generate inaccuracies in SDMs. Here, we test how the distribution of NHCs and MaxEnt predictions relates to a spatial abundance model using inverse distance weighting (IDW)