Content from the BioVeL internal group

MSA-PAD Gene Mode: DNA Multiple Sequence A... (1)

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BioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains 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 Homepage: [http://www.biovel.eu][1] [1]: http://www.biovel.eu ## 1 Description This workflow is used to submit the multip...

Created: 2014-12-05

Credits: Bachirb Giacinto Donvito Pasquale Notarangelo Saverio Vicario Graziano Pesole Alfonso Monaco

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: Renato De Giovanni BioVeL

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: Renato De Giovanni BioVeL

extract_confusion_matrix (1)

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Extracts confusion matrix data from a test result XML.

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

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: BioVeL

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: BioVeL

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: Ferenc HORVATH Dora Krasser Peter Ittzes Zoltan BARCZA BioVeL

Microbial Metagenomic Trait Calculation an... (3)

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This workflow calculates the microbial traits of your metagenome and retrieves additional traits data from the Microbial Metagenomic Trait Database http://mb3is.megx.net/mg-traits. The list of traits: - 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 As ...

Created: 2014-10-03 | Last updated: 2015-06-12

Credits: Renzo Antonio Fernandez-Guerra

Attributions: Microbial Metagenomic Trait Statistical Analysis 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: Peter Ittzes Ferenc HORVATH Dora Krasser Zoltan BARCZA Doborl BioVeL