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Showing 4527 results. Use the filters on the left and the search box below to refine the results.
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1217?size=60x60 Gb Alan Williams
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Blob Checking Taverna installation

Created: 2014-10-03 15:21:35

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file containing a presentation on how to check your Taverna installation

File type: Adobe PDF

Comments: 0 | Viewed: 11 times | Downloaded: 18 times

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1217?size=60x60 Gb Alan Williams
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Blob Advanced Taverna

Created: 2014-10-03 15:20:26

Credits: Network-member myGrid

License: Creative Commons Attribution-Share Alike 3.0 Unported License

A PDF file that contains a presentation about Advanced Taverna features

File type: Adobe PDF

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1217?size=60x60 Gb Alan Williams
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Blob forester_1037.jar

Created: 2014-10-03 11:27:41 | Last updated: 2014-10-03 12:33:14

License: GNU Lesser General Public License (LGPL) 2.1

forester is a collection of open source libraries of Java software for phylogenomics and evolutionary biology research. For example, the tree viewer Archaeopteryx is based on forester. The forester website is at https://sites.google.com/site/cmzmasek/home/software/foresterThe current developer version is available through Google code at: http://code.google.com/p/forester/Author: Christian Zmasek, Sanford-Burnham Medical Research Instituteforester is Cop...

File type: Trident (Package)

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Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Increment an integer (1)

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This workflow uses R to increment the input integer

Created: 2014-10-03

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Species chooser (1)

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In your browser, choose between marmots and horseshoe crabs

Created: 2014-10-03

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Get weather information (1)

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Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure.

Created: 2014-10-03

Credits: User Alan Williams User Franck Tanoh

Attributions: Workflow Get weather information

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Species Occurrence (1)

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Retrieve the first 100 occurrences of a species in Darwin format

Created: 2014-10-03

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Construct viewparams (1)

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Construct the viewparams parameter to OBIS services

Created: 2014-10-02

Credits: User Alan Williams

Taverna 2
Uploader
3850?size=60x60 Peter Ittzes
Project Biovel

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: User Peter Ittzes User Ferenc HORVATH User Dora Krasser User Zoltan BARCZA User Doborl Network-member BioVeL

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow xcorrSound_waveform-compare_alt (1)

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xcorrSound waveform-compare Wav File Comparison. "Alt" version uses the xcorrSound Project debian package installation rather than the scape toolwrapper debian package installation.

Created: 2014-09-30 | Last updated: 2014-09-30

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

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

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 equivalents (TREs) of all ER indicator stocks.

File type: text/csv

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

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

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 equivalent (TRE) ocean harvest rates of ER indicator stocks.

File type: text/csv

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Uploader
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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Uploader
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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KNIME
Uploader
Avatar Ch Christine Chichester

Workflow Q5: For molecules that contain substructur... (1)

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This workflow requires the input of a substructure of a chemical as represented as a SMILES string and a class of targets from either the ENZYME or Chembl target classification. It answers one of the scientific use cases (Question 5 see K. Azzaoui et al. Scientific competency questions as the basis for semantically enriched open pharmacological space development. Drug Discov. Today 18 (2013), p. 843-852) that was used as the basis for the development of the Open PHACTS Dis...

Created: 2014-09-29 | Last updated: 2014-09-29

Credits: User Christine Chichester User Daniela Digles Network-member Open PHACTS

Uploader
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...

File type: Adobe PDF

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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

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

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

Workflow Exploration of fishing scenarios (1)

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

Attributions: Workflow Resident killer whale-chinook salmon interactions

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

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

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

Attributions: Workflow Killer whale demography

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow Characterise_Audio_using_FFprobe (1)

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The workflow takes an inputfilepath as input parameter. It relies on FFprobe being installed locally, when it is run. It has been tested with ffprobe version 0.10.3. It outputs bitrate, bitsPerSample, channels, duration and audio sampling frequency (hz) as well as an activity report (raw FFprobe STDOUT+STDERR).

Created: 2014-09-26 | Last updated: 2014-09-26

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow xcorrSound_sound-match_2.0.2 (1)

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This component uses xcorrSound sound-match to find occurrences of the first (small) input wav file in the second (larger) wav file and output the result in a txt output format.

Created: 2014-09-26 | Last updated: 2014-09-26

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow xcorrSound_overlap-analysis_2.0.2 (1)

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This component uses xcorrSound overlap-analsis to find the overlap between two input wav files and output an analysis report in a txt output format.

Created: 2014-09-26 | Last updated: 2014-09-26

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow Workflow_waveform-compare_2.0.2 (2)

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xcorrSound waveform-compare component - minor edits

Created: 2014-09-25 | Last updated: 2014-09-26

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

Workflow Killer whale demography (1)

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

Uploader
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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Uploader
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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Uploader
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...

File type: Adobe PDF

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Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow Photohawk PAE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk PAE.

Created: 2014-09-07

Credits: User Markus Plangg

Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow Photohawk MAE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk MAE.

Created: 2014-09-07

Credits: User Markus Plangg

Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow Photohawk AE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk AE.

Created: 2014-09-07

Credits: User Markus Plangg

Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow Photohawk MSE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk MSE.

Created: 2014-09-07

Credits: User Markus Plangg

Taverna 2
Uploader
3505?size=60x60 At Markus Plangg

Workflow Photohawk SSIM tiff/png/jpeg-jp2 (3)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk SSIM.

Created: 2014-09-07 | Last updated: 2014-09-07

Credits: User Markus Plangg

Uploader
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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Creator
Avatar Azlinayati
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Pack OWL Ontology Survey Data


Created: 2014-09-06 15:15:00 | Last updated: 2014-09-12 18:02:18

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

2 items in this pack

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This Pack has no tags!

Taverna 2
Uploader
71?size=60x60 Nl Katy Wolstencroft

Workflow entreztoKeggImage (1)

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This workflow accepts a list of Entrez Gene IDs. It dentifies which KEGG pathway each gene is involved with and displays the pathway diagrams

Created: 2014-09-05

Credits: User Katy Wolstencroft

Taverna 2
Uploader
71?size=60x60 Nl Katy Wolstencroft

Workflow ImportConvertEnsembl (1)

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This workflow accepts a spreadsheet file as input and extracts a list of ENSEMBL Gene IDs from column A. The hsapiens_gene_ensembl service converts these IDs to Entrez_geneIds

Created: 2014-09-05

Credits: User Katy Wolstencroft

Taverna 2
Uploader
71?size=60x60 Nl Katy Wolstencroft

Workflow FunctionalClusterDavid (1)

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This workflow takes a list of Entrez Gene IDs as input and submits them to the DAVID REST API for functional clustering using OG annotaiton, biological pathways and disease associations. Used for analysing a set of genes (i.e. those differentially expressed for a particular disease condition).

Created: 2014-09-05

Credits: User Katy Wolstencroft

Taverna 2
Uploader
9?size=60x60 Gb Stian Soiland-Reyes

Workflow Example dbfetch (2)

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Run EBI's dbfetch

Created: 2014-09-03 | Last updated: 2014-09-03

Credits: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions:

Uploader
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

Comments: 0 | Viewed: 37 times | Downloaded: 21 times

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

Workflow Finding nodes in Homo sapiens pathways wit... (1)

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Groovy script to find Homo sapiens metabolites encoded as GPML <Label> with OPSIN and provide ChemSpider identifiers. The results are stored in a report file.

Created: 2014-09-01

Credits: User Egon Willighagen

Attributions: Workflow Finding nodes in Anopheles gambiae pathways with IUPAC names

Uploader
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...

File type: Adobe PDF

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

Workflow Elasticity and Sensitivity of the Vital rates (1)

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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 (?). Elasticity and Sensitivity: Sensitivity and elasticity analyses are prospective analyses. a) The sensitivity matrix: The sensitivity describes the effect on ? of changes in vital rates of the matrix. The derivative tells what would happened to ? if aij was to c...

Created: 2014-08-29

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

Uploader
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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