Content from the BioVeL internal group

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

• Download

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)

• Download

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)

• Download

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)

• Download

Extracts confusion matrix data from a test result XML.

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

extract_roc_points (1)

• Download

Extracts the ROC points from a test result XML.

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

Credits: BioVeL

extract_auc (2)

• Download

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)

• Download

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)

• Download

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)

• Download

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

View Download

TRE file

Created: 2014-09-30 09:34:51

Credits: Antonio Velez-Espino Andres Araujo

Attributions: Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/csv

Comments: 0 | Viewed: 52 times | Downloaded: 31 times

View Download

TRE HR file

Created: 2014-09-30 09:32:41

Credits: Antonio Velez-Espino Andres Araujo

Attributions: Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/csv

Comments: 0 | Viewed: 58 times | Downloaded: 34 times

View Download

Term run file

Created: 2014-09-30 09:29:57 | Last updated: 2014-09-30 09:30:11

Credits: Antonio Velez-Espino Andres Araujo

Attributions: Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/csv

Comments: 0 | Viewed: 61 times | Downloaded: 32 times

View Download

ER_Indicators file

Created: 2014-09-30 09:27:47

Credits: Antonio Velez-Espino Andres Araujo

Attributions: Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: text/csv

Comments: 0 | Viewed: 56 times | Downloaded: 35 times

View Download

Killer whale demography documentation

Created: 2014-09-26 12:19:25

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Killer whale demography

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 65 times | Downloaded: 47 times

View Download

Resident killer whale-chinook salmon interactions an...

Created: 2014-09-26 12:09:28 | Last updated: 2014-09-26 12:11:12

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Exploration of fishing scenarios Resident killer whale-chinook salmon interactions

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 136 times | Downloaded: 53 times

Exploration of fishing scenarios (1)

• Download

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 Exploration of fishing scenario (post-processing) workflow. This workflow merges statistical inference derived from linkages between RKW vital rates (survival probability and fecundity rates) a...

Created: 2014-09-26

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Resident killer whale-chinook salmon interactions

Resident killer whale-chinook salmon inter... (1)

• Download

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 in demographic rates between killer whale (Orcinus orca) population that explain population growth; (ii) to determine the relative influence of vital rates and Chinook (Oncorhynchus tshawytsc...

Created: 2014-09-26

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

Attributions: Killer whale demography

Killer whale demography (1)

• Download

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 other killer whale populations or cetaceans counting with census data and life cycles that can be represented using the matrix models described in this document. This workflow perform the follow...

Created: 2014-09-24

Credits: Maria Paula Balcazar-Vargas Antonio Velez-Espino Andres Araujo Jon Giddy Francisco Quevedo

View Download

Sensitivity of resident killer whale population dyna...

Created: 2014-09-11 09:11:46 | Last updated: 2014-09-11 09:12:49

Credits: Antonio Velez-Espino Andres Araujo

License: Creative Commons Attribution-No Derivative Works 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 80 times | Downloaded: 51 times