Group: BioVeL

Overview

This group is for sharing workflows relating to BioVeL - Biodiversity Virtual e-Laboratory - FP7-283359 BioVeL

 

The BioVeL group is curated. If you previously had membership or if you wish to share content with the group, please contact f.quevedo.fernandez@cs.cardiff.ac.uk  .


Please feel free to explore. You can find documentation on the BioVeL wiki. If you need assistance, you can get it by emailing to support@biovel.eu or by posting a question in our online forum.

 

For more information about the overall BioVeL project, please visit http://www.biovel.eu/.

 

 

Created at: Saturday 06 August 2011 15:38:58 (UTC)

Unique name: biovel

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  1. 4196?size=48x48
    Biodiversity eLaboratory shared Ecosystem modelling with Biome-BGC
    Brings together 5 workflows for ecosystem modelling and calculation of ecosystem service indicators. These workflows are developed around the Biome-BGC biogeochemical modelling software that simulates the storage and flux of water, carbon, and nitrogen between the ecosystem and the atmosphere, and wi …
    Tuesday 19 May 2015 09:00:27 (UTC)
  2. 1217?size=48x48
    Alan Williams shared Multiple selection
    An interaction page that allows multiple selections from a list of values. There is a single input port of depth one called selectionValues There is a single output port of depth one called answers
    Tuesday 31 March 2015 11:23:55 (UTC)
  3. 4196?size=48x48
    Biodiversity eLaboratory shared Alexandrium minutum potential distribution
    The potential distribution of Alexandrium minutum
    Monday 16 February 2015 11:53:00 (UTC)
  4. 4196?size=48x48
    Biodiversity eLaboratory shared Alexandrium minutum potential distribution in the Baltic Sea
    The potential distribution  of Alexandrium minutum in the Baltic Sea
    Monday 16 February 2015 11:52:32 (UTC)
  5. 4196?size=48x48
    Biodiversity eLaboratory shared Application of Ecological Niche Modelling and Earth Observation for the Risk Assessment and Monitoring of Invasive Species in the Baltic Sea
    This pack contains some of the data, workflows and results that are described in the "MarCoast II - Marine and Coastal Environmental Information Services Ballast Water Option" report by: Kerstin Stelzer (Brockmann Consult GmbH) Karin Heyer Dr. Sarah Bourlat (SeAnalytics AB) Dr. Matthia …
    Monday 16 February 2015 11:52:03 (UTC)
  6. 4196?size=48x48
    Biodiversity eLaboratory shared Fucus vesiculosus occurrences from GBIF
    This spreadsheet indicates the source of occurrences of Fucus vesiculosus retrieved from GBIF.
    Monday 16 February 2015 10:08:43 (UTC)
  7. 4196?size=48x48
    Biodiversity eLaboratory shared Fucus vesiculosus current and 2050 difference
    This PNG gives a low resolution image for the difference between the current and predicted 2050 niches for Fucus vesiculosus
    Monday 16 February 2015 10:08:19 (UTC)
  8. 4196?size=48x48
    Biodiversity eLaboratory shared Fucus vesiculosus current distribution
    This PNG gives a low-resolution picture of the predicted current niche of Fucus vesilosus
    Monday 16 February 2015 10:07:57 (UTC)
  9. 4196?size=48x48
    Biodiversity eLaboratory shared Fucus vesiculosus 2050 distribution
    This PNG gives a low resolution image of the niche predicted for Fucus vesiculosus in 2050
    Monday 16 February 2015 10:07:31 (UTC)
  10. 4196?size=48x48
    Biodiversity eLaboratory shared Mapping present and future predicted distribution patterns for a meso-grazer guild in the Baltic Sea
    This pack gathers together some of the data, results and workflows used in the "Mapping present and future predicted distribution patterns for a meso-grazer guild in the Baltic Sea" study by Leidenberger, Sonja; University of Gothenburg, Department of Biology and Environmental Sciences - Kr …
    Monday 16 February 2015 10:07:09 (UTC)
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    Monday 04 August 2014 11:35:16 (UTC)
  12. 4196?size=48x48
    Monday 04 August 2014 11:33:48 (UTC)

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75 shared items

This group has been credited 19 times

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Workflow

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Project Biovel

Workflow ENM resolution mix - multiple runs version (10)

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Multiple runs version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates ...

Created: 2014-11-13 | Last updated: 2015-05-12

Credits: User Renato De Giovanni Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow ENM resolution mix - single run version (6)

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Single run version of the workflow for comparing results of two kinds of ecological niche models: one using only low resolution layers and the other using a random mix of low and high resolution layers. Users select the study region and the environmental variables considered to be the main drivers of a virtual species niche. The workflow is all based on the ENM components, which use the openModeller Web Service (OMWS). After getting initial parameters from the user, the workflow generates a r...

Created: 2014-11-18 | Last updated: 2015-04-04

Credits: User Renato De Giovanni Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow define_frequently_used_constants (3)

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Defines constants that are frequently used as parameters for ENM Components. When building a new workflow with ENM Components, some constant values will likely be used multiple times as parameters. This component conveniently defines the most frequently used constants so that users can directly connnect them to the corresponding input ports without needing to manually create each constant.

Created: 2014-11-10 | Last updated: 2015-05-11

Credits: Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow extract_roc_points (1)

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Extracts the ROC points from a test result XML.

Created: 2014-10-13 | Last updated: 2014-12-04

Credits: Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow Ecological niche modelling workflow (28)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service. Algorithm, environmental layers and mask are selected during the workflow. The model is tested (internal test and optional cross validation external test) and then projected one or more times. All points from the input file are used to create a single model, even if there are differences in the scientific names. Cross validation calculates the mean AUC. Model projectio...

Created: 2013-01-07 | Last updated: 2015-06-11

Credits: User Renato De Giovanni User Alan Williams User Robert Kulawik User Francisco Quevedo User Vhernand Network-member BioVeL

Attributions:

Workflow

Uploader
Project Biovel

Workflow select_random_points_based_on_threshold (2)

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Selects random presence and/or absence points given a threshold and a set of points with the corresponding model values.

Created: 2014-11-13 | Last updated: 2015-05-11

Credits: Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow sample_points (11)

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Randomly samples a specified number of absence and/or presence points in a given environment (set of layers + mask).

Created: 2014-03-19 | Last updated: 2015-05-11

Credits: Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow extract_auc (2)

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Extracts the AUC value from a test result XML.

Created: 2014-10-09 | Last updated: 2014-10-13

Credits: Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow convert_points_xml_to_csv (4)

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Converts points in openModeller XML format into CSV format (header: occurrenceID,nameComplete,decimalLongitude,decimalLatitude). Most input/output ports related with presence or absence points expect/return data in openModeller XML format. This component can be used to simply convert such data back to a more human friendly format.

Created: 2014-11-05 | Last updated: 2015-05-11

Credits: Network-member BioVeL

Workflow

Workflow Microbial Metagenomic Trait Statistical An... (9)

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This workflow retrieves the following microbial metagenomic traits from the Microbial Metagenomic Trait Database: -GC content -Variance of GC content -Dinucleotides -Number of rRNA -Codon usage -Amino acid composition -Acidic to basic amino acids ratio -% of Transcriptional factors -% of classified reads -Functional content -Functional diversity -Taxonomic content -Taxonomic diversity After the retrieval performs the ecological analyses described in Barberan et al. 2012 (http://dx.doi.or...

Created: 2012-12-19 | Last updated: 2014-11-12

Credits: User Antonio Fernandez-Guerra User Renzo User Peliny Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow Biome-BGC GLUE 1.3 (2)

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Biome-BGC is working with a lots of ‘a priori’ unknown and hard to obtain model parameters. Therefore the parameterization is a critical step of using the model. Parameteres can be estimated using inverse calibration techniques based on measurement data, which means that the model is being calibrated. Measurement data have to be collected with respect to the model in order to compare them. Comparison is based on misfit measure (e.g. a sort of likelihood value), which is the function of the di...

Created: 2014-10-02 | Last updated: 2014-10-09

Credits: User Peter Ittzes User Ferenc HORVATH User Dora Krasser User Zoltan BARCZA User Doborl Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow Biome-BGC ESI version 1.4.1 (3)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. The model can help us to quantify a broad range of ecosystem service indicators. These newly developed measures include: annual wood increment, yearly production of grasslands or croplands, total average carbon stock, annual evapotranspiration, damping of ecosystem daily water outflow, living and dead biomass protecting the soil against erosion,...

Created: 2013-08-12 | Last updated: 2014-10-04

Credits: User Ferenc HORVATH User Dora Krasser User Peter Ittzes Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow Biome-BGC CARBON 1.2 (4)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. A new version of the model, called Biome-BGC MuSo was developed to perform more realistic simulations in terms of soil hydrology, and improved ecosystem management options essentially (Hidy et al. 2012; Hidy & Barcza 2014). The Biome-BGC CARBON service executes a single simulation run at a given geographic location under that distinctive environ...

Created: 2013-06-04 | Last updated: 2015-06-12

Credits: User Ferenc HORVATH User Dora Krasser User Peter Ittzes User Zoltan BARCZA Network-member BioVeL

Attributions:

Workflow

Uploader
Project Biovel

Workflow Biome-BGC MCE 1.4.1 (4)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models were implemented: Biome-BGC 4.1.1 MPI (Trusilova et al. 2009) and Biome-BGC MuSo 3.0 (Hidy & Barcza 2014). Its has about 40 and 60 various parameters. The only way to estimate or set these parameters is "calibration" (data-model-harmonization or model-data-fusion), which demands a hugh amount of computational capacity. Monte Carlo Exp...

Created: 2013-06-04 | Last updated: 2014-10-04

Credits: User Ferenc HORVATH User Zoltan BARCZA User Dora Krasser User Peter Ittzes Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow Biome-BGC SA 1.3 (1)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models have been implemented: the Biome-BGC v4.1.1 Max Planck Institute model, and the newly developed Biome-BGC MuSo 3.0 model. Performance, success or failure of these models are highly dependent on parameter settings and variation. Due to the high number of parameters (around 40 and 60 for 4.1.1 MPI and MuSo respectively) and the non-line...

Created: 2014-10-04

Credits: User Ferenc HORVATH User Dora Krasser User Peter Ittzes User Zoltan BARCZA Network-member BioVeL

Workflow

Uploader

Workflow Convert Taverna list of RExpr to R list - v2 (2)

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This workflow accepts a Taverna list of arbitrary R expressions and returns a single R expression representing an R list containing the original expressions. This workflow relies on the current Taverna behaviour of an R expression being represented by a list of strings containing the deparsed expression. If this changes, this workflow will likely break. The first BeanShell converts each R expression (actually a list of strings) to a single string. This uses implicit iteration to do this for...

Created: 2013-09-04 | Last updated: 2013-10-14

Credits: User Jon Giddy Network-member BioVeL

Workflow

Uploader
Project Biovel

Workflow Bioclim workflow (6)

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This workflow takes as input a file containing species occurrence points to create a model with the openModeller Web Service using the Bioclim algorithm. Environmental layers and mask are selected during the workflow. Points are filtered so that only environmentally unique points are used to create the model. You can use this workflow to either filter a set of species occurrence points excluding redundant points with the same environmental conditions (you can get the result in the output "se...

Created: 2013-09-02 | Last updated: 2015-04-04

Credits: User Renato De Giovanni Network-member BioVeL


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