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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Term run file

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

Credits: User Antonio Velez-Espino User Andres Araujo

Attributions: Workflow Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the time series of terminal run for each of the ER indicator stocks.

File type: text/csv

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob ER_Indicators file

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

Credits: User Antonio Velez-Espino User Andres Araujo

Attributions: Workflow Exploration of fishing scenarios

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file shows the exploitation rate (ER) indicator stocks used to represent exploitation-rate time series with terminal-run time series of Chinook salmon aggregates.

File type: text/csv

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Killer whale demography documentation

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

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

Attributions: Workflow Killer whale demography

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation contains the tutorial to run the Killer whale demography workflows. This tutorial explains the type of input data needed to run the workflow. The corresponding analysis use data from two distinct O. orca populations in Canada, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW). The Killer whale demography workflow performs the following analyses: •      Vital rates estimation and probability dis...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Resident killer whale-chinook salmon interactions an...

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

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

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

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation contains the tutorial to run two related workflows. 1.    Resident killer whale-chinook salmon interactions workflow The Resident killer whale-chinook salmon interactions workflow provides an environment to create 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 be...

File type: Adobe PDF

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4144?size=60x60 De Alexey Mints
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Blob FITS header printer

Created: 2014-09-23 15:01:02 | Last updated: 2014-11-27 08:26:31

Credits: User Alexey Mints

License: Creative Commons Attribution-Share Alike 3.0 Unported License

usage: fitsheader.py [-h] [-f FILENAME] [-k KEYS] [-t TABLE] [--history]                     [--comments] [--data] [-o]optional arguments:  -h, --help            show this help message and exit  -f FILENAME, --filename FILENAME                        File to use  -k KEYS, --keys KEYS  Header keys to use (mask can be given)  -...

File type: text/x-python

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Sensitivity of resident killer whale population dyna...

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

Credits: User Antonio Velez-Espino User Andres Araujo

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

Sensitivity of resident killer whale population dynamics to Chinook salmon abundance.L. Antonio Vélez-Espino1,£, John K.B. Ford2, Charles K. Parken1, Graeme Ellis2, Eric Ward3, Larrie LaVoy4, Ken Balcomb5, M. Bradley Hanson3, Dawn P. Noren3, Tom Cooney4, Rishi Sharma6,7.(1) Salmon and Freshwater Ecosystems Division, Fisheries and Oceans Canada; (2) Marine Mammal Division, Fisheries and Oceans Canada; (3) Conservation Biology Division, Northwest Fisheries Science Center (NOAA); (4...

File type: Adobe PDF

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Comparative Demography and Viability of Northeastern...

Created: 2014-09-11 09:03:19

Credits: User Antonio Velez-Espino User Andres Araujo

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

Comparative Demography and Viability of Northeastern Pacific Resident Killer Whale Populations at Risk.L.A. Vélez-Espino, J.K.B. Ford, H.A. Araujo, G. Ellis, C.K. Parken, and K.C. BalcombFisheries and Oceans CanadaScience Branch, Pacific RegionPacific Biological StationNanaimo, BCV9T 6N72014Canadian Technical Report ofFisheries and Aquatic Sciences 3084 Two distinct populations of resident killer whales (Orcinus orca) in the northeastern Pacific Ocean have been identified in Canad...

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Avatar Azlinayati
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Blob OWL Ontology Survey Data

Created: 2014-09-06 15:16:41 | Last updated: 2014-09-12 17:57:10

Credits: User Azlinayati

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the survey data for OWL Ontology on the Web survey.

File type: text/csv

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1404?size=60x60 Gb Christian
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Blob Bonn 2014 Help links

Created: 2014-09-03 08:19:52 | Last updated: 2014-09-03 08:20:20

Credits: User Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Many useful links accurate Sept 2014

File type: Adobe PDF

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1404?size=60x60 Gb Christian
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Blob Bonn 2014 Example Fasta Ids Mac Format

Created: 2014-09-02 08:02:51

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Fasta files in MAC format. 

File type: Plain text

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1404?size=60x60 Gb Christian
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Blob Bonn 2014 Fasta Example Values UNIX format

Created: 2014-09-02 07:57:46

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is the Fasta Example IDs in UNIX Format

File type: Plain text

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9?size=60x60 Gb Stian Soiland-Reyes
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Blob Bonn 2014 Agenda

Created: 2014-09-01 09:08:17 | Last updated: 2014-09-03 08:10:40

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Agenda Bonn “in silico experimentation” course 2014-09-01 / 2014-09-03Please sign up and join the myExperiment group: Bonn Workshop Sep 2014For each tutorial and presentation, there is an accompanying slideset in this group. For your convenience, this Agenda PDF has links to each of these as [T-xxx.pdf].  

File type: Adobe PDF

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Elasticity and Sensitivity of the Vital rates docume...

Created: 2014-08-29 14:49:44 | Last updated: 2014-08-29 14:50:15

Credits: User Maria Paula Balcazar-Vargas User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Elasticity and Sensitivity of the Vital rates

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.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 rate(s) has/have the most influence on population growth rate (λ).Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses.The sensitivity matrix: The sensitivity desc...

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Orcinus orca (Killer whale) demography and populatio...

Created: 2014-08-29 12:21:35 | Last updated: 2014-08-29 16:23:18

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Jon Giddy

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name Normal 0 false false false EN-US X-NONE X-NONE ...

File type: Adobe PDF

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob ChinookAbundance_FI_R file

Created: 2014-08-29 12:08:37

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table showing the time series of Fishery Impacts of all stocks by time lag used in the analysis.

File type: Excel workbook

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob ChinookAbundance_Data_R file

Created: 2014-08-29 12:04:46 | Last updated: 2014-08-29 16:24:00

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table showing the time series of abundance (TR or OA) of all stocks and stock aggregates by time lag used in the analysis.

File type: Excel workbook

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Chinook_Ab_Defs_FI_R file

Created: 2014-08-29 11:55:36

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table used to define fishery impacts (FI) on Chinook abundance by stock aggregate, time lag (5YA: 5-year running average), and hypothesis (SR: Southern Resident Killer Whale; NR: Northern Resident Killer Whale) and abundance ID. FI represent ocean catch of specific Chinook stocks or stock aggregates. See below information about hypothesis.

File type: Excel workbook

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Chinook_Ab_Definitions_R file

Created: 2014-08-29 11:53:56

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Table that contains Chinook abundance definitions by stock aggregate, abundance type (TR: Terminal Run; OA: Ocean Abundance), time lag (5YA: 5-year running average), and hypothesis (SR: Southern Resident Killer Whale; NR: Northern Resident Killer Whale) and abundance ID. See below information about hypothesis.

File type: Excel workbook

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Vital Rates_combined

Created: 2014-08-29 11:51:09

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The stage-structured life cycle of resident killer whales with seven life stages:(1) calves; (Calf)(2) juveniles; (Juv)(3) young reproductive females; (F1)(4) old reproductive females; (F2)(5) post-reproductive females; (F3)(6) young mature males; and (M1)(7) old mature males (M2).Fi represent fertility; Gi represent stage transition probabilities, with female and male juvenile-to-adult transitions indicated as G2f and G2m, respectively; and, Pi represent the probability of surviving and rema...

File type: Excel workbook

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Northern Resident Killer Whale (NRKW) demographic data

Created: 2014-08-29 11:46:14 | Last updated: 2014-08-29 16:25:25

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Northern Resident Killer Whale (NRKW) demographic data.The input data (a .csv-file) has to have the format of a table containing the Orcinus orca demographic data with the columns named: Year, Age, Count, Offspring and Cat1. Each year, the number of individuals per age and the number of offspring per age reproductive female category are counted (females ≥ 10 years old). IF A Female category does not have offspring equals to 0. For the called column, Cat1; Ages 1 to 9 belongs to Juv (Juveni...

File type: Excel workbook

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Southern Resident Killer Whale (SRKW) demographic data

Created: 2014-08-29 11:43:47

Credits: User Antonio Velez-Espino

Attributions:

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Southern Resident Killer Whale (SRKW) demographic dataThe input data (a .csv-file) has to have the format of a table containing the Orcinus orca demographic data with the columns named: Year, Age, Count, Offspring and Cat1. Each year, the number of individuals per age and the number of offspring per age reproductive female category are counted (females ≥ 10 years old). IF A Female category does not have offspring equals to 0. For the called column, Cat1; Ages 1 to 9 belongs to Juv (Juvenil...

File type: Excel workbook

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1404?size=60x60 Gb Christian
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Blob Example Fasta Ids CVS

Created: 2014-08-29 10:44:20

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a small csv file which has Fasta IDs in Column B rows 2 to 6

File type: Excel workbook

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Variance matrix documentation

Created: 2014-08-28 13:53:09

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Francisco Quevedo User Gerard Oostermeijer

Attributions: Workflow Variance matrix

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow estimates the variance matrix from a list of matrices.

File type: Adobe PDF

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Calculate and Plot abundance over the years document...

Created: 2014-08-28 13:17:28

Credits: User Maria Paula Balcazar-Vargas User Mikolaj Krzyzanowski User Jon Giddy User Gerard Oostermeijer

Attributions: Workflow Calculate and Plot abundance over the years

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with same name.This workflow calculate and plot the survival based on two or more years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of an animal or plant population.

File type: Adobe PDF

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4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Decomposed matrix of Gentiana pneumonanthe

Created: 2014-08-28 11:28:44

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file (decomposed matrix) is used in the documentation as example to run the Elsticity and Sensitivity of the Vital rates Workflow.

File type: Excel workbook

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