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 Taxonomic Refinement
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ACI analysis and oscilo plot
Other
Workflow that calculates the Acoustic Complexity Index (ACI) of a section of an audio file (it takes the URL of the file, and the start and end points of the section to analyse as parameters). The workflow also plots the 2Dspectrogram, frequency spectrum and dominant frequency of the time wave
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Age specific analysis
Population Modelling
The age specific analysis workflow gives the basic information on agespecific survival, this includes the mean, variance and coefficient of variation (cv) of the time spent in each stage class and the mean and variance of the time to death.
Fundamental matrix (N): is the mean of the time spent in
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Bayesian Phylogenetic Inference: Select Model  Submission
Phylogenetics
BioVeL – Biodiversity Virtual eLaboratory
Workflow Documentation
Name:Perform Short Bayesian Phylogenetic Inference
Capacities Programme of Framework 7: EC eInfrastructure Programme –
eScience Environments  INFRA20111.2.1
Grant Agreement No: 283359
Project Coordinator: Mr Alex Hardisty
Project
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Bayesian Phylogenetic Inference: Select Model For Me  Submission
Phylogenetics
BioVeL – Biodiversity Virtual eLaboratory
Workflow Documentation
Name:Perform Short Bayesian Phylogenetic Inference
Capacities Programme of Framework 7: EC eInfrastructure Programme –
eScience Environments  INFRA20111.2.1
Grant Agreement No: 283359
Project Coordinator: Mr Alex Hardisty
Project
...
Bayesian Phylogenetic Infererence: Evaluate MrBayes Run
Phylogenetics
BioVeL – Biodiversity Virtual eLaboratory
Workflow Documentation
Name:Perform Short Bayesian Phylogenetic Inference
Capacities Programme of Framework 7: EC eInfrastructure Programme –
eScience Environments  INFRA20111.2.1
Grant Agreement No: 283359
Project Coordinator: Mr Alex Hardisty
Project
...
Bayesian Phylogenetic Infererence: Input Ready  Submission
Phylogenetics
BioVeL – Biodiversity Virtual eLaboratory
Workflow Documentation
Name:Perform Short Bayesian Phylogenetic Inference
Capacities Programme of Framework 7: EC eInfrastructure Programme –
eScience Environments  INFRA20111.2.1
Grant Agreement No: 283359
Project Coordinator: Mr Alex Hardisty
Project
...
Bioclim workflow
Ecological Niche Modelling
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
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BiomeBGC CARBON 1.2
Ecosystem Modelling
BiomeBGC is a processbased biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. A new version of the model, called BiomeBGC MuSo was developed to perform more realistic simulations in terms of soil hydrology, and improved ecosystem
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BiomeBGC ESI version 1.4.1
Ecosystem Modelling
BiomeBGC is a processbased 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
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BiomeBGC GLUE 1.3
Ecosystem Modelling
BiomeBGC 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.
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BiomeBGC MCE 1.4.1
Ecosystem Modelling
BiomeBGC is a processbased biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models were implemented: BiomeBGC 4.1.1 MPI (Trusilova et al. 2009) and BiomeBGC MuSo 3.0 (Hidy & Barcza 2014). Its has about 40 and 60 various
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BiomeBGC SA 1.3
Ecosystem Modelling
BiomeBGC is a processbased biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models have been implemented: the BiomeBGC v4.1.1 Max Planck Institute model, and the newly developed BiomeBGC MuSo 3.0 model. Performance, success
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BioVeL ESW DIFF  ENM Statistical Workflow with raster difference computation
Ecological Niche Modelling
The ENM Statistical Difference Workflow (ESW DIFF) allows the computation of the extent and intensity of change in species potential distribution through computation of the differences between two raster layers using the R statistical environment (R Core Team 2013). The difference file is computed
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BioVeL ESW STACK  ENM Statistical Workflow with raster stack computation
Ecological Niche Modelling
The ENM Statistical Stack Workflow (ESW STACK) allows the computation of the extent, intensity and a cummulated potential species distribution through computation of an average sum layer from the input raster layers using the R statistical environment (R Core Team 2013). The sum layer is computed
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Bootstrap of observed census transitions.
Population Modelling
This workflow calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stagefate data frame of observed transitions. The goal of a demographic analysis is very often to estimate lambda, because lambda
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Calculate and Plot abundance over the years
Population Modelling
This workflow calculates and plots the abundance per stage per year.
This workflow has been created by the Biodiversity Virtual eLaboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.
This workflow was created using and based on
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Calculate quasiextinction threshold.
Population Modelling
This workflow estimates by simulation the quasiextinction probability time cumulative distribution function for a structured population in an independently and identically distributed (iid) stochastic environment. This workflow is based on the popbio package (stoch.quasi.ext  Calculate quasiextinction
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Cohen’s cumulative distance
Population Modelling
The Cohen’s cumulative distance Workflow provides an environment to calculate the Cohen’s cumulative distance. The Cohen’s cumulative distance measures the difference between observed and expected vectors along the matrix path that the population would take to reach the expected population vector.
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Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population
Population Modelling
This workflow create a stage matrix model based on two years census data of tagged or mapped individuals of an animal or plant population. Each annual census describes for each individual its life stage, reproductive output (estimated number offprings) and whether or not it is a new recruit. The
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Damping ratio
Population Modelling
The Damping ratio Workflow provides an environment to calculate the damping ratio of several matrices and plot them.
The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation
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Data Refinement Workflow v17
Taxonomic Refinement
The aim of the (Taxonomic) Data Refinement Workflow is to provide a streamlined workflow environment for preparing observational and specimen data sets for use in scientific analysis on the Taverna platform. The workflow has been designed in a way that,
• accepts input data in a recognized format,
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Ecological niche modelling workflow
Ecological Niche Modelling
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
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Ecological niche modelling workflow with remote data input
Ecological Niche Modelling
This workflow takes as input a URI that points to CSV data 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
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Eigen analysis
Population Modelling
The Eigen analysis results are a set of demographic statistics:
1) Lambda or dominant eigenvalue: The population will be stable, grow or decrease at a rate given by lambda: eg: λ = 1 (population is stable), λ > 1 (population is growing) and finally λ < 1 (populatiopn is decreasing) .
2) The stable
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Elasticity and Sensitivity of the Vital rates
Population Modelling
This workflow calculates the Elasticity and Sensitivity of population growth rate with respect to various vital rates. The goal in both cases is to determine which vital rates has/ve the most influence on population growth rate (λ).
Elasticity and Sensitivity: Sensitivity and elasticity analyses are
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Evaluate MrBayes Run on convergence, model fit and produce final consensus and visualization
Phylogenetics
BioVeL – Biodiversity Virtual eLaboratory
Workflow Documentation
Name:Perform Short Bayesian Phylogenetic Inference
Capacities Programme of Framework 7: EC eInfrastructure Programme –
eScience Environments  INFRA20111.2.1
Grant Agreement No: 283359
Project Coordinator: Mr Alex Hardisty
Project
...
Exploration of fishing scenarios
Population Modelling
This workflow must run after the workflow: Resident killer whalechinook salmon interactions. The interaction workflows generates a PostWorkspace file, this is a zip file and it is an R Workspace that transfers values from the Resident killer whalechinook salmon interactions (main) workflow to the
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Generation time (T)
Population Modelling
The time T required for the population to increase by a factor of Ro (net reproductive rate)
e.g.: If Ro (net reproductive rate) = 5.56 and T (generation time) = 8.055
The average plant of the species Gentiana pneumonanthe in Terschelling in the year 1987 replaced itself with almost six new plants
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Integral Projection Model for Demographic Modelling v34
Population Modelling
This workflow constructs and analyses an IPM with only continuous stages and without ramet production based on the IPMpack (R).
Information about the Input file:
The data must be organized in a table (in .csv format), where each row represents one observation of an organism in the population at one
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Keyfitz delta
Population Modelling
The Keyfit delta Workflow provides an environment to calculate the Keyfit delta value. Keyfitz’s delta is a measure of the distance between any two probability vectors (Keyfitz 1968). In this case is a measure of the distance between n (Observed Stage Distribution) and w (Stable Stage Distribution).
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Killer whale demography
Population Modelling
This workflow analyzes the demography and population growth of resident killer whale populations. Originally created for comparative studies of Northeastern Pacific populations at risk, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW), the workflow can be used for
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Life Table Response Experiment fixed design Place Effect
Population Modelling
The Life Table Response Experiments place effect workflow provides an environment to analyse one or more matrices (e.g. matrices of different years from the same place) from two or more places. The objective of this workflow is to determine the effects of the research places or localities (2 or more)
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Life Table Response Experiment year effect for multiple places
Population Modelling
The Life Table Response Experiments Year Effect for Multiple Places workflow provides an environment to analyse two or more matrices (e.g., two or more matrices of different years from one place) at two or more different locations. The objective of this workflow is to determine the effects of the
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Life Table Response Experiment Year Effect in One Location or Place
Population Modelling
The Life Table Response Experiments Effect of Years in One Place workflow provides an environment to analyse two or more matrices from different years in one location. The objective of this workflow is to determine the effects of the research years (2 or more) in one place on λ. This workflow performs
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Loglog plots of variance vs. sensitivity and CV vs. elasticity in matrix elements
Population Modelling
This workflow creates loglog plots of both variance vs. sensitivity and CV vs. elasticity in matrix elements. Plots are based on Figure 2 in Pfister (1998). This workflow calculates as well the summary mean, variance, CV, sensitivities and elasticities of each matrix element of the submitted matrices.
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Matrix Population Model analysis v12
Population Modelling
The Matrix Population Models Workflow provides an environment to perform several analyses on a stagematrix with no density dependence:
 Eigen analysis;
 Age specific survival;
 Generation time (T);
 Net reproductive rate (Ro);
 Transient Dynamics;
 Bootstrap of observed census transitions
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Matrix Population Model construction and analysis v20
Population Modelling
The Matrix Population Models Workflow provides an environment to create stagematrices with no density dependence and to perform several analyses on them:
 Eigen analysis;
 Age specific survival;
 Generation time (T);
 Net reproductive rate (Ro);
 Transient Dynamics;
 Bootstrap of observed
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Mean matrix
Population Modelling
This workflow estimates the mean matrix from a list of matrices.
This workflow has been created by the Biodiversity Virtual eLaboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.
This workflow was created using and based on Package
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Microbial Metagenomic Trait Statistical Analysis Workflow
Metagenomics
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
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Net reproductive rate (Ro)
Population Modelling
This workflow calculates the net reproductive rate (Ro) that is mean number of offspring by which a newborn individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next (Caswell, 2001)
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Parametric Bootstrap or Resample a projection matrix Workflow
Population Modelling
The Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants
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Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH
Phylogenetics
Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH .
The WF need a tree in newick format, a samplefile that show the where the leaf of the tree are found in the different sample and how many time, and a grouping file where the different sample are
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Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH with parsing Qiime
Phylogenetics
Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH .
The WF need a tree in newick format, a samplefile that show the where the leaf of the tree are found in the different sample and how many time, and a grouping file where the different sample are
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Resident killer whalechinook salmon interactions
Population Modelling
The resident killer whalechinook salmon interactions workflow provides an environment to calculate a twosex stagestructured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences
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Select Model
Phylogenetics
BioVeL – Biodiversity Virtual eLaboratory
Workflow Documentation
Name:Perform Short Bayesian Phylogenetic Inference
Capacities Programme of Framework 7: EC eInfrastructure Programme –
eScience Environments  INFRA20111.2.1
Grant Agreement No: 283359
Project Coordinator: Mr Alex Hardisty
Project
...
Select Model For Me with components
Phylogenetics
BioVeL – Biodiversity Virtual eLaboratory
Workflow Documentation
Name:Perform Short Bayesian Phylogenetic Inference
Capacities Programme of Framework 7: EC eInfrastructure Programme –
eScience Environments  INFRA20111.2.1
Grant Agreement No: 283359
Project Coordinator: Mr Alex Hardisty
Project
...
Simulate stochastic growth from a sequence of matrices
Population Modelling
The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices.
This workflow
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Stages vectors plots, Survival and Growth rate curves
Population Modelling
The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stagematrices:
 Survival values calculations per stage per year and its respective plot;
 Growth rates (lambda) calculations per year and its respective plot;

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Transient Dynamics.
Population Modelling
This workflow produces plots of the shortterm dynamics and convergence to stable stage distribution using stage vector projections.
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This workflow has been created by the Biodiversity Virtual eLaboratory (BioVeL http://www.biovel.eu/)
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Variance matrix
Population Modelling
This workflow estimates the variance matrix from a list of matrices.
This workflow has been created by the Biodiversity Virtual eLaboratory (BioVeL http://www.biovel.eu/) project. BioVeL is funded by the EU’s Seventh Framework Program, grant no. 283359.
This workflow was created using and based on
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