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Maria Paula Balcazar-Vargas

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Parametric Bootstrap or Resample a projection matrix...

Created: 2014-07-25 09:41:10

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Parametric Bootstrap or Resample a projection matrix Workflow

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 Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants surveyed. The projection matrix A is first split into separate transition and ...

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Maria Paula Balcazar-Vargas

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Age-specific survival documentation

Created: 2014-07-24 11:48:40

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Age specific analysis

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 the same name.The age-specific survival analysis workflow gives the basic information of the mean, variance and coefficient of variation (CV) of the time spent in each stage class and the mean and variance of the time of death.AnalysesFundamental matrix (N)Variance(var)Coefficient of variation (CV)MeanetaVareta

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Maria Paula Balcazar-Vargas

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Keyfitz’s delta documentation

Created: 2014-07-24 08:25:05

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Keyfitz delta

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is documentation (tutorial to run the workflow) explains how to run a workflow that belongs to the pack with the same name.The Keyfitz’s delta Workflow provides an environment to calculate the Keyfitz delta value. Keyfitz’s delta is a measure of the distance between any two probability vectors (Keyfitz 1968). In this case is a measure of the distance between n (Observed Stage Distribution) and w (Stable Stage Distribution). The maximum value is 1 and the minimum value is 0 (w...

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Maria Paula Balcazar-Vargas

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Cohen’s cumulative distance documentation

Created: 2014-07-24 08:20:42

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Cohen’s cumulative distance

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 Cohen’s cumulative distance Workflow provides an environment to calculate the Cohen’s cumulative distance. The Cohen’s cumulative distance measures the difference between observed and expected vectors along the matrix path that the population would take to reach the expected population vector. It is a function of both the observed stage distribution (n...

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Taverna 2

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Maria Paula Balcazar-Vargas

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Cohen’s cumulative distance (1)

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The Cohen’s cumulative distance Workflow provides an environment to calculate the Cohen’s cumulative distance. The Cohen’s cumulative distance measures the difference between observed and expected vectors along the matrix path that the population would take to reach the expected population vector. It is a function of both the observed stage distribution (n0) and the structure of the matrix (A) (Williams et al 2011). Cohen’s cumulative distance will not work for reducible matrices or imprimiti...

Created: 2014-07-23

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model analysis v12 Matrix Population Model construction and analysis v20

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Maria Paula Balcazar-Vargas

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Cohen cumulative distance pack

Created: 2014-07-23 13:43:22 | Last updated: 2014-07-24 08:21:00

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Cohen’s cumulative distance Workflow provides an environment to calculate the Cohen’s cumulative distance. The Cohen’s cumulative distance measures the difference between observed and expected vectors along the matrix path that the population would take to reach the expected population vector. It is a function of both the observed stage distribution (n0) and the structure of the matrix...

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Taverna 2

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Maria Paula Balcazar-Vargas

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Keyfitz delta (1)

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The Keyfit delta Workflow provides an environment to calculate the Keyfit delta value. Keyfitz’s delta is a measure of the distance between any two probability vectors (Keyfitz 1968). In this case is a measure of the distance between n (Observed Stage Distribution) and w (Stable Stage Distribution). The maximum value is 1 and the minimum value is 0 (when the vectors are identical). ============================================================ This workflow has been created by the Biodiversit...

Created: 2014-07-23

Credits: Maria Paula Balcazar-Vargas Jon Giddy Gerard Oostermeijer

Attributions: Matrix Population Model analysis v12 Matrix Population Model construction and analysis v20

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Maria Paula Balcazar-Vargas

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Keyfitz's delta pack

Created: 2014-07-23 11:19:37 | Last updated: 2014-07-24 08:25:22

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Keyfit delta Workflow provides an environment to calculate the Keyfit delta value. Keyfitz’s delta is a measure of the distance between any two probability vectors (Keyfitz 1968). In this case is a measure of the distance between n (Observed Stage Distribution) and w (Stable Stage Distribution). The maximum value is 1 and the minimum value is 0 (when the vectors are identical).

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Alan Williams

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XPath tutorial presentation

Created: 2014-07-16 12:16:48

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial introducing how to use Taverna's XPath capabilities

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tutorial exercise

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Alan Williams

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Taverna Workbench introduction presentation

Created: 2014-07-16 12:15:19

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial designed to introduce the basic features of Taverna Workbench

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Alan Williams

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Help presentation

Created: 2014-07-16 12:13:54

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a presentation of information on where to find help on myGrid tools

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Alan Williams

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Introduction to using components presentation

Created: 2014-07-16 12:12:13

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a quick tutorial on how to use components within a workflow

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tutorial exercise

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Alan Williams

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Advanced Taverna Features Presentation

Created: 2014-07-16 12:09:47 | Last updated: 2014-07-16 12:10:55

Credits: Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This is a tutorial on some of Taverna's advanced features.

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Alex Nenadic

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myGrid Tools for Scientists Presentation

Created: 2014-07-16 12:03:42 | Last updated: 2014-07-18 14:43:15

Credits: Alex Nenadic

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Introduction to myGrid tools for scientists

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Taverna 2

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Alan Williams

EBI_InterproScan (1)

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Perform EBI Interproscan

Created: 2014-07-16 | Last updated: 2014-07-16

Taverna 2

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Alan Williams

Experiments for gene (2)

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This workflow uses the Allen Brain REST API to fetch the experiements corresponding to a named gene

Created: 2014-07-15 | Last updated: 2014-07-15

Credits: Alan Williams

Taverna 2

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Alan Williams

Download images for gene (3)

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This workflow downloads the first few images corresponding to experiments for the specified gene

Created: 2014-07-13 | Last updated: 2014-07-15

Credits: Alan Williams

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Maria Paula Balcazar-Vargas

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Simulate stochastic growth from a sequence of matric...

Created: 2014-07-10 12:05:44 | Last updated: 2014-07-30 13:48:06

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Simulate stochastic growth from a sequence of matrices Workflow provides an environment to simulate stochastic growth by projection using whole matrix selection techniques in an independently and identically distributed (iid) environment from a set of 2 or more projection matrices.Outputs:Equal selection dataStochastic projectionUnequal selection dataTo know more details about the analysis, Morris and D...

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biovel
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demography
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gentiana pneumonanthe
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independently and identically distributed (iid)
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matrix population models
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model
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morris and doak 2002.
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package ‘popbio’ in r
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population
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population viability analysis (pva)
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stage matrix
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stochastic environment
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stochastic growth
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stochastic projection

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Sven

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ARC to WARC migration with quality assurance scripts

Created: 2014-07-10 08:39:49

These are the tool service scripts used in Taverna workflow available on myExperiment (http://www.myexperiment.org/workflows/4333). The Taverna workflow is configured by adapting the values of the constant values (light-blue boxes) which define the paths to configuration files, deployment files, and scripts in the processing environment. However, as Taverna is just used as an orchestration tool to build a sequence of bash script invocations, it is also possible to just use the individual scri...

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Taverna 2

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Sven

ARC to WARC Migration with CDX Index and w... (1)

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Workflow for migrating ARC to WARC and comparing the CDX index files (Linux). The workflow has an input port “input_directory” which is a local path to the directory containing the ARC files, and an input port “output_directory” which is the directory where the workflow outputs are created. The files in the input directory are migrated using the “arc2warc_migration_cli” tool service component to perform the migration. The “cdx_creator_arc” and “cdx_creator_warc” tool service components creat...

Created: 2014-07-09

Credits: Sven

Taverna 2

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Alan Williams

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2014-07-09

Credits: Alan Williams

Attributions: Demonstration of configurable iteration

Taverna 2

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Alan Williams

EBI_InterproScan_broken (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration. Note that this workflow is deliberately broken

Created: 2014-07-09

Credits: Alan Williams Katy Wolstencroft Hamish McWilliam

Attributions: EBI_InterproScan_NewServices

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Maria Paula Balcazar-Vargas

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Parametric Bootstrap or Resample a projection matrix...

Created: 2014-07-09 14:03:43 | Last updated: 2014-07-25 09:41:32

This pack contains a workflow, a file and documentation (tutorial to run the workflow). The Parametric Bootstrap or Resample a projection matrix Workflow provides an environment to resample a projection matrix using a multinomial distribution for transitions and a log normal distribution for fertilities (Stubben, Milligan, and Nantel. 2011). The resample is based on number of plants surveyed. The projection matrix A is first split into separate transition and fertility matrices. Dead fates ar...

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Maria Paula Balcazar-Vargas

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Bootstrap of observed census transitions pack

Created: 2014-07-09 12:56:51 | Last updated: 2014-07-25 10:37:19

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Bootstrap of observed census transitions (confidence intervals of λ) workflow for local execution calculates bootstrap distributions of population growth rates (λ), stage vectors, and projection matrix elements by randomly sampling with replacement from a stage-fate data frame of observed transitions. The goal of a demographic analysis is very often to estimate lambda, because lambda is es...

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Alex Nenadic

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Taverna - VPH-Share workshop 17-18 July 2014

Created: 2014-07-09 11:36:13 | Last updated: 2014-08-13 14:37:51

Taverna - VPH-Share workshop 17-18 July 2014Location: The Pam Liversidge Building, Sir Frederick Mappin Building – Sheffield S1 3JD, UKRegistration link: http://bit.ly/vph-share-trainingFormat: The workshop is a two-day hands-on training event about workflows in the biomedical arena, with a focus on VPH-Share and Taverna.Target community & qualifications: The target community is developers and research scientists working in all areas of biomedical/healthcare research within the...

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