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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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Creator
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Relative importance of Chinook salmon abundance on r...


Created: 2014-08-29 11:04:10 | Last updated: 2014-09-30 09:35:02

The pack contains three workflows, 13 files and 2 documentations (tutorials to run the workflows).Workflows:1) Demography of the killer whales.2) Resident killer whale-chinook salmon interactions.3) Exploration of fishing scenarios.These workflow uses input data of two different populations of Orcas in the northeastern Pacific Ocean of Canada and the U.S. But these workflows can also use input data from other populations of the Orcas in the world (see requirements for data entry in the docume...

19 items in this pack

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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

Comments: 0 | Viewed: 46 times | Downloaded: 57 times

This File has no tags!

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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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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Variance matrix (1)

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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 Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ================================================================================== Literature Caswell, H. 20...

Created: 2014-08-28

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

Uploader
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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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Calculate and Plot abundance over the years (1)

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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 Package ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ================================================================================== Literature Caswell, H. 20...

Created: 2014-08-28

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

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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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Creator
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Elasticity and Sensitivity of the vital rates pack


Created: 2014-08-28 08:56:24 | Last updated: 2014-08-29 14:50:26

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This workflow calculate the Elasticity and Sensitivity of the vital rates. The goal in both cases is to determine which vital rates have the most influence on population growth or λ.

3 items in this pack

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

Created: 2014-08-27 13:43:56 | Last updated: 2014-09-02 07:59:09

Credits: User Christian

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a small list of Fasta IDs for testing workflows and tutorials.  

File type: Plain text

Comments: 0 | Viewed: 30 times | Downloaded: 26 times

This File has no tags!

Taverna 2
Uploader
1780?size=60x60 Gb Donal Fellows

Workflow myExperiment Group Activity Report (1)

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Prepares a report (three CSV files) on the activity of a group on myExperiment.

Created: 2014-08-26

Credits: User Donal Fellows

Bioclipse Scripting Language
Uploader
4506?size=60x60 Nl Egon Willighagen

Workflow Finding nodes in Anopheles gambiae pathway... (1)

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Groovy script to find Anopheles g. metabolites encoded as GPML <Label> with OPSIN and provide ChemSpider identifiers.

Created: 2014-08-24

Credits: User Egon Willighagen

Attributions: Workflow Extracts metabolites from GPML pathway files downloaded from WikiPathways

Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Demographic data Gentiana pneumonanthe 1987-1993

Created: 2014-08-22 12:01:38

Credits: User Maria Paula Balcazar-Vargas User Gerard Oostermeijer

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a .txt file of demographic data of the species: Gentiana pneumonanthe, collected and published by Gerard Oostermeijer (Instituut voor Biodiversiteit en Ecosysteem Dynamica (IBED), Universiteit van Amsterdam).This file allow users to run the workflow Calculate and Plot abundance over the years (http://www.myexperiment.org/packs/664.html)This table containing the demographic data on a series of individuals during 7 years, from 1987 to 1993 (6 periods: 1987-1988, 1988-1989 etc....

File type: Excel workbook

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Creator
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Calculate and Plot abundance over the years pack


Created: 2014-08-22 07:50:23 | Last updated: 2014-08-28 13:17:48

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This workflow calculates and plots the abundance per stage per year from a list of matrices.

3 items in this pack

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Creator
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Pack Variance matrix pack


Created: 2014-08-21 13:07:20 | Last updated: 2014-08-28 13:53:33

This pack contains a workflow, a file and documentation (tutorial to run the workflow).This workflow estimates the variance matrix from a list of matrices.

8 items in this pack

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Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Log-log plots of variance vs. sensitivity and CV vs....

Created: 2014-08-21 09:16:10

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

Attributions: Workflow Log-log plots of variance vs. sensitivity and CV vs. elasticity in matrix elements

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 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).

File type: Adobe PDF

Comments: 0 | Viewed: 69 times | Downloaded: 40 times

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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Log-log plots of variance vs. sensitivity ... (1)

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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. Please if you want to know more about this analyses please refer to: Pfister, C.A. 1998. Patterns of variance in stage-structured populations: Evolutionary predictions and ecological implica...

Created: 2014-08-21

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

Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Life Table Response Experiments Fixed design year ef...

Created: 2014-08-21 08:05:38

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

Attributions: Workflow Life Table Response Experiment year effect for multiple places

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.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 research years (2 or more) on λ. This workflow performs a fixed LTRE, o...

File type: Adobe PDF

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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Life Table Response Experiment year effect... (1)

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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 research years (2 or more) on ?. This workflow performs a fixed LTRE, one way design (Caswell 2001). LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on ?...

Created: 2014-08-21

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

Uploader
Avatar Jamie Wittenberg
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Blob southern md

Created: 2014-08-17 20:26:57

Credits: User Jamie Wittenberg

License: Creative Commons Attribution-Share Alike 3.0 Unported License

movie of southern md

File type: video/quicktime

Comments: 0 | Viewed: 15 times | Downloaded: 4 times

This File has no tags!

Uploader
Avatar Jamie Wittenberg
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Blob hobie

Created: 2014-08-17 20:26:30

Credits: User Jamie Wittenberg

License: Creative Commons Attribution-Share Alike 3.0 Unported License

picture of hobie

File type: PNG image

Comments: 0 | Viewed: 30 times | Downloaded: 18 times

This File has no tags!

Creator
Avatar Jamie Wittenberg
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Pack Research Object Workflow Test


Created: 2014-08-17 19:31:07 | Last updated: 2014-08-17 20:29:04

Sample pack to explore depositing packs into DataBank

2 items in this pack

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

Created: 2014-08-14 17:52:17 | Last updated: 2014-08-28 13:50:22

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

Attributions: Workflow Mean 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 mean matrix from a list of matrices.

File type: Adobe PDF

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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Mean matrix (1)

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This mean matrix 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 ‘popbio’ in R. (Stubben & Milligan 2007; Stubben, Milligan & Nantel 2011). ================================================================================== Literature Caswel...

Created: 2014-08-14

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

Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Calculate the quasi-extinction probability documenta...

Created: 2014-08-14 12:05:06

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

Attributions: Workflow Calculate quasi-extinction threshold.

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 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 threshold, Stubben, Milligan and Nantel, 2013) based on the MATLAB cod...

File type: Adobe PDF

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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Calculate quasi-extinction threshold. (1)

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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 threshold, Stubben, Milligan and Nantel, 2013) based on the The MATLAB code in Box 7.5 (Morris and Doak 2002). For more details of the analysis see: Calculating the probability of hitting a q...

Created: 2014-08-14

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

Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Life Table Response Experiments Fixed design years e...

Created: 2014-08-14 08:44:30 | Last updated: 2014-08-14 08:45:27

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

Attributions: Workflow Life Table Response Experiment Year Effect in One Location or Place

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.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 a fixed LTRE, one way design (Caswell 2001).LTRE is a retrospectiv...

File type: Adobe PDF

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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Life Table Response Experiment Year Effect... (1)

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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 ?. This workflow performs a fixed LTRE, one way design (Caswell 2001). LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on ? under two or more sets of environmental conditions...

Created: 2014-08-14

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

Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel
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Blob Life Table Response Experiments Fixed design Place e...

Created: 2014-08-14 08:03:58

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

Attributions: Workflow Life Table Response Experiment fixed design Place Effect

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.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) on λ. This workflow performs a fixed LTRE, one way design (Caswell ...

File type: Adobe PDF

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Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Life Table Response Experiment fixed desig... (1)

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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) on ?. This workflow performs a fixed LTRE, one way design (Caswell 2001). LTRE is a retrospective analysis (Caswell 1989), beginning with data on the vital rates and on ? under two or more set...

Created: 2014-08-13

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

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-video-menco... (1)

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Converts any Mencoder supported video format to MPEG2

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-video-handb... (1)

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Converts any HandBrake supported video format to MPEG4

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-video-ffmpe... (1)

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Converts any FFmpeg supported video format to MPEG2

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-video-ffmpe... (1)

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Converts any FFmpeg supported video format to FLV

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-video-avide... (1)

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Converts any WMV to MPEG2

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-video-avide... (1)

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Converts any FLV to AVI

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-pdfb... (1)

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Converts Text to PDF

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-pdfb... (1)

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Converts a PDF to a TXT

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

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Converts Excel to PDF

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

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Converts Excel to OpenDocument Spreadsheet

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint (.pptx) to Flash

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint (.pptx) to PDF

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint (.pptx) to OpenDocument Presentation

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

Thumb
Converts Powerpoint to Flash

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

Thumb
Converts Powerpoint to PDF

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

Thumb
Converts Powerpoint to OpenDocument Presentation

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Text to PDF

Created: 2014-08-13

Taverna 2
Uploader
3439?size=60x60 Pt Hélder Silva

Workflow digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Text to Word

Created: 2014-08-13

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