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Taverna_logo ACI analysis and oscilo plot
Other

Scratchpads avatar

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 2D-spectrogram, frequency spectrum and dominant frequency of the time wave
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Uploaded 4 Dec 2014 18:41:28 UTC

Taverna_logo Age specific analysis
Population Modelling

BioVeL avatar

The age specific analysis workflow gives the basic information on age-specific 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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Uploaded 14 Aug 2014 18:13:08 UTC

Taverna_logo Bayesian Phylogenetic Inference: Select Model - Submission
Phylogenetics

BioVeL avatar

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform Short Bayesian Phylogenetic Inference

Capacities Programme of Framework 7: EC e-Infrastructure Programme –
e-Science Environments - INFRA-2011-1.2.1
Grant Agreement No: 283359
Project Co-ordinator: Mr Alex Hardisty
Project
...

Uploaded 4 Jul 2014 09:53:37 UTC

Taverna_logo Bayesian Phylogenetic Inference: Select Model For Me - Submission
Phylogenetics

BioVeL avatar

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform Short Bayesian Phylogenetic Inference

Capacities Programme of Framework 7: EC e-Infrastructure Programme –
e-Science Environments - INFRA-2011-1.2.1
Grant Agreement No: 283359
Project Co-ordinator: Mr Alex Hardisty
Project
...

Uploaded 4 Jul 2014 09:58:26 UTC

Taverna_logo Bayesian Phylogenetic Infererence: Evaluate MrBayes Run
Phylogenetics

BioVeL avatar

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform Short Bayesian Phylogenetic Inference

Capacities Programme of Framework 7: EC e-Infrastructure Programme –
e-Science Environments - INFRA-2011-1.2.1
Grant Agreement No: 283359
Project Co-ordinator: Mr Alex Hardisty
Project
...

Uploaded 24 Jun 2014 10:36:45 UTC

Taverna_logo Bayesian Phylogenetic Infererence: Input Ready - Submission
Phylogenetics

BioVeL avatar

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform Short Bayesian Phylogenetic Inference

Capacities Programme of Framework 7: EC e-Infrastructure Programme –
e-Science Environments - INFRA-2011-1.2.1
Grant Agreement No: 283359
Project Co-ordinator: Mr Alex Hardisty
Project
...

Uploaded 13 Apr 2014 19:13:10 UTC

Taverna_logo Bioclim workflow
Ecological Niche Modelling

BioVeL avatar

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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Uploaded 25 Mar 2014 14:34:43 UTC

Taverna_logo Biome-BGC CARBON 1.2
Ecosystem Modelling

BioVeL avatar

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
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Uploaded 12 Feb 2014 03:17:05 UTC

Taverna_logo Biome-BGC ESI version 1.4.1
Ecosystem Modelling

BioVeL avatar

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
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Uploaded 23 Feb 2014 07:49:59 UTC

Taverna_logo Biome-BGC GLUE 1.3
Ecosystem Modelling

BioVeL avatar

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.
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Uploaded 26 May 2014 09:48:21 UTC

Taverna_logo Biome-BGC MCE 1.4.1
Ecosystem Modelling

BioVeL avatar

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
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Uploaded 3 Feb 2014 09:23:58 UTC

Taverna_logo Biome-BGC SA 1.3
Ecosystem Modelling

BioVeL avatar

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
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Uploaded 24 Feb 2014 09:38:17 UTC

Taverna_logo BioVeL ESW DIFF - ENM Statistical Workflow with raster difference computation
Ecological Niche Modelling

BioVeL avatar

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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Uploaded 25 Mar 2014 14:27:29 UTC

Taverna_logo BioVeL ESW STACK - ENM Statistical Workflow with raster stack computation
Ecological Niche Modelling

BioVeL avatar

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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Uploaded 5 Feb 2014 10:41:59 UTC

Taverna_logo Bootstrap of observed census transitions.
Population Modelling

BioVeL avatar

This workflow calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to estimate lambda, because lambda
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Uploaded 21 Aug 2014 15:11:10 UTC

Taverna_logo Calculate and Plot abundance over the years
Population Modelling

BioVeL avatar

This workflow calculates and plots the abundance per stage per year.

This workflow has been created by the Biodiversity Virtual e-Laboratory (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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Uploaded 28 Aug 2014 16:58:06 UTC

Taverna_logo Calculate quasi-extinction threshold.
Population Modelling

BioVeL avatar

This workflow estimates by simulation the quasi-extinction 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 quasi-extinction
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Uploaded 21 Aug 2014 17:56:34 UTC

Taverna_logo Cohen’s cumulative distance
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 18:13:35 UTC

Taverna_logo Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:15:49 UTC

Taverna_logo Damping ratio
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:29:57 UTC

Taverna_logo Data Refinement Workflow v17
Taxonomic Refinement

BioVeL avatar

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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Uploaded 2 Sep 2014 09:08:26 UTC

Taverna_logo Ecological niche modelling workflow
Ecological Niche Modelling

BioVeL avatar

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
...

Uploaded 25 Mar 2014 08:23:17 UTC

Taverna_logo Ecological niche modelling workflow with remote data input
Ecological Niche Modelling

Swedish LifeWatch avatar

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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Uploaded 13 May 2014 18:03:43 UTC

Taverna_logo Eigen analysis
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:37:15 UTC

Taverna_logo Elasticity and Sensitivity of the Vital rates
Population Modelling

BioVeL avatar

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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Uploaded 29 Aug 2014 14:56:26 UTC

Taverna_logo Evaluate MrBayes Run on convergence, model fit and produce final consensus and visualization
Phylogenetics

BioVeL avatar

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform Short Bayesian Phylogenetic Inference

Capacities Programme of Framework 7: EC e-Infrastructure Programme –
e-Science Environments - INFRA-2011-1.2.1
Grant Agreement No: 283359
Project Co-ordinator: Mr Alex Hardisty
Project
...

Uploaded 4 Jul 2014 09:34:59 UTC

Taverna_logo Exploration of fishing scenarios
Population Modelling

BioVeL avatar

This workflow must run after the workflow: Resident killer whale-chinook 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 whale-chinook salmon interactions (main) workflow to the
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Uploaded 26 Sep 2014 08:29:47 UTC

Taverna_logo Generation time (T)
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:41:00 UTC

Taverna_logo Integral Projection Model for Demographic Modelling v34
Population Modelling

BioVeL avatar

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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Uploaded 14 Aug 2014 19:02:48 UTC

Taverna_logo Keyfitz delta
Population Modelling

BioVeL avatar

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).
...

Uploaded 21 Aug 2014 18:15:48 UTC

Taverna_logo Killer whale demography
Population Modelling

BioVeL avatar

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
...

Uploaded 24 Sep 2014 14:14:47 UTC

Taverna_logo Life Table Response Experiment fixed design Place Effect
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:44:18 UTC

Taverna_logo Life Table Response Experiment year effect for multiple places
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:46:46 UTC

Taverna_logo Life Table Response Experiment Year Effect in One Location or Place
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:48:42 UTC

Taverna_logo Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements
Population Modelling

BioVeL avatar

This workflow creates log-log 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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Uploaded 21 Aug 2014 18:10:49 UTC

Taverna_logo Matrix Population Model analysis v12
Population Modelling

BioVeL avatar

The Matrix Population Models Workflow provides an environment to perform several analyses on a stage-matrix with no density dependence:
- Eigen analysis;
- Age specific survival;
- Generation time (T);
- Net reproductive rate (Ro);
- Transient Dynamics;
- Bootstrap of observed census transitions
...

Uploaded 14 Aug 2014 18:48:32 UTC

Taverna_logo Matrix Population Model construction and analysis v20
Population Modelling

BioVeL avatar

The Matrix Population Models Workflow provides an environment to create stage-matrices 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
...

Uploaded 14 Aug 2014 18:23:11 UTC

Taverna_logo Mean matrix
Population Modelling

BioVeL avatar

This workflow estimates the mean matrix from a list of matrices.

This workflow has been created by the Biodiversity Virtual e-Laboratory (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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Uploaded 21 Aug 2014 18:09:14 UTC

Taverna_logo Microbial Metagenomic Trait Statistical Analysis Workflow
Metagenomics

BioVeL avatar

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
...

Uploaded 5 Dec 2014 11:46:58 UTC

Taverna_logo Net reproductive rate (Ro)
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:50:35 UTC

Taverna_logo Parametric Bootstrap or Resample a projection matrix Workflow
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 15:52:22 UTC

Taverna_logo Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH
Phylogenetics

BioVeL avatar

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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Uploaded 20 Mar 2014 14:42:25 UTC

Taverna_logo Partitioning environmental sequencing data using categorical and phylogenetic information using PhyloH with parsing Qiime
Phylogenetics

BioVeL avatar

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
...

Uploaded 5 Feb 2014 10:47:02 UTC

Taverna_logo Resident killer whale-chinook salmon interactions
Population Modelling

BioVeL avatar

The resident killer whale-chinook salmon interactions workflow provides an environment to calculate a two-sex stage-structured 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
...

Uploaded 26 Sep 2014 08:15:52 UTC

Taverna_logo Select Model
Phylogenetics

BioVeL avatar

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform Short Bayesian Phylogenetic Inference

Capacities Programme of Framework 7: EC e-Infrastructure Programme –
e-Science Environments - INFRA-2011-1.2.1
Grant Agreement No: 283359
Project Co-ordinator: Mr Alex Hardisty
Project
...

Uploaded 11 Apr 2014 13:17:07 UTC

Taverna_logo Select Model For Me with components
Phylogenetics

BioVeL avatar

BioVeL – Biodiversity Virtual e-Laboratory

Workflow Documentation

Name:Perform Short Bayesian Phylogenetic Inference

Capacities Programme of Framework 7: EC e-Infrastructure Programme –
e-Science Environments - INFRA-2011-1.2.1
Grant Agreement No: 283359
Project Co-ordinator: Mr Alex Hardisty
Project
...

Uploaded 4 Feb 2014 10:11:08 UTC

Taverna_logo Simulate stochastic growth from a sequence of matrices
Population Modelling

BioVeL avatar

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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Uploaded 21 Aug 2014 17:53:59 UTC

Taverna_logo Stages vectors plots, Survival and Growth rate curves
Population Modelling

BioVeL avatar

The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:
- Survival values calculations per stage per year and its respective plot;
- Growth rates (lambda) calculations per year and its respective plot;
-
...

Uploaded 21 Aug 2014 15:58:26 UTC

Taverna_logo Transient Dynamics.
Population Modelling

BioVeL avatar

This workflow produces plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.

============================================================

This workflow has been created by the Biodiversity Virtual e-Laboratory (BioVeL http://www.biovel.eu/)
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Uploaded 21 Aug 2014 15:55:12 UTC

Taverna_logo Variance matrix
Population Modelling

BioVeL avatar

This workflow estimates the variance matrix from a list of matrices.

This workflow has been created by the Biodiversity Virtual e-Laboratory (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
...

Uploaded 28 Aug 2014 16:53:22 UTC
Eu_logo
BioVeL has received funding from the European Union's Seventh Framework Programme for research, technological development and demonstration under grant agreement no. 283359.

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