myExperiment

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Azlinayati

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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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Maria Paula Balcazar-Vargas

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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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Maria Paula Balcazar-Vargas

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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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Maria Paula Balcazar-Vargas

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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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Maria Paula Balcazar-Vargas

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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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Jamie Wittenberg

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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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Maria Paula Balcazar-Vargas

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Log-log plots of variance vs. sensitivity and CV vs....

Created: 2014-08-13 10:27:13 | Last updated: 2014-08-21 09:16:30

This pack contains a workflow, a file and documentation (tutorial to run the workflow).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).

8 items in this pack

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biovel
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demography
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log-log plot cv vs. elasticity in matrix elements
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log-log plot of variance vs. sensitivity
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matrix
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matrix population models
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package ‘popbio’ in r
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stage matrix

Creator

Rekha Maryanne Louis

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usability test pack4

Created: 2014-08-07 10:43:42

for myExperiment usability testing exercise

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tested

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Biodiversity eLaboratory

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Application of Ecological Niche Modelling and Earth ...

Created: 2014-08-04 14:18:00 | Last updated: 2014-08-04 15:44:20

This pack contains some of the data, workflows and results that are described in the "MarCoast II - Marine and Coastal Environmental Information Services Ballast Water Option" report by:Kerstin Stelzer (Brockmann Consult GmbH)Karin HeyerDr. Sarah Bourlat (SeAnalytics AB)Dr. Matthias Obst (SeAnalytics AB)ScopeThis report describes the work that has been performed in the Ballast Water Option in the framework of the ESA GSE project Marcoast-2. The Option was dedicated to...

19 items in this pack

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Biodiversity eLaboratory

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Mapping present and future predicted distribution pa...

Created: 2014-08-04 09:48:54 | Last updated: 2014-08-05 10:28:43

This pack gathers together some of the data, results and workflows used in the "Mapping present and future predicted distribution patterns for a meso-grazer guild in the Baltic Sea" study byLeidenberger, Sonja; University of Gothenburg, Department of Biology and Environmental Sciences - KristinebergDe Giovanni, Renato; Centro de Referência em Informação Ambiental, Centro de Referência em InformaçãoKulawik, Robert; Fraunhofer IAI...

17 items in this pack

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Maria Paula Balcazar-Vargas

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Mean matrix pack

Created: 2014-07-31 13:34:16 | Last updated: 2014-08-14 17:52:30

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

8 items in this pack

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Maria Paula Balcazar-Vargas

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Calculate quasi-extinction threshold pack

Created: 2014-07-30 14:00:20 | Last updated: 2014-08-14 12:05:20

This pack contains a workflow, a file and documentation (tutorial to run the workflow).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 ...

8 items in this pack

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biovel
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cumulative distribution function (cdf)
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demography
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gentiana pneumonanthe
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matrix
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matrix population models
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morris and doak 2002.
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package ‘popbio’ in r
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population viability analysis (pva)
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probability of quasi-extinction threshold by time t
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simulating extinction probabilities
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stage matrix
|
stochastic environment

Creator

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...

3 items in this pack

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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).

3 items in this pack

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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...

8 items in this pack

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

Creator

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...

0 items in this pack

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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...

4 items in this pack

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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...

12 items in this pack

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Alan Williams

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openphacts

Created: 2014-07-06 15:46:09 | Last updated: 2014-07-06 15:47:27

Set of components corresponding to the OpenPHACTS API

2 items in this pack

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component family

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Maria Paula Balcazar-Vargas

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Net reproductive rate (Ro) pack

Created: 2014-07-04 13:59:07 | Last updated: 2014-07-25 11:25:32

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The . Net reproductive rate (Ro) Workflow provides an environment to calculate the net reproductive rate (Ro). Ro is the mean number of offspring by which a new-born individual will be replaced by the end of its life, and thus the rate by which the population increases from one generation to the next.

3 items in this pack

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Maria Paula Balcazar-Vargas

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Generation time (T) pack

Created: 2014-07-04 13:20:43 | Last updated: 2014-07-25 11:22:30

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Generation Time (T) Workflow provides an environment to calculate the generation time. Th generation time is the time T required for the population to increase by a factor of Ro (net reproductive rate). In other words, T calculates how much time takes to a plant/animal to replace itself by a factor of Ro.

3 items in this pack

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Maria Paula Balcazar-Vargas

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Transient dynamics pack

Created: 2014-07-04 10:59:17 | Last updated: 2014-07-25 12:17:07

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Transient dynamics or Calculate population growth rates by projection Workflow provides an environment to calculates the population growth rate and stable stage distribution by repeated projections of the equation n(t+1)=An(t) and to produce plots of the short-term dynamics and convergence to stable stage distribution using stage vector projections.Transient dynamic analysisPopulation projectionLambda o...

3 items in this pack

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Maria Paula Balcazar-Vargas

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Eigen analysis pack

Created: 2014-07-03 15:57:49 | Last updated: 2014-07-25 11:18:57

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Eigen analysis workflow provides an environment for the analysis of a stage-matrix and perform several analyses on it.The Eigen analysis results are a set of demographic statistics:Lambda or dominant eigenvalue (λ).The stable stage distribution (w).The sensitivity matrixThe Elasticity matrix.Reproductive value (v).The damping ratio (ρ).

3 items in this pack

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Maria Paula Balcazar-Vargas

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Damping ratio pack

Created: 2014-07-02 13:32:31 | Last updated: 2014-07-25 11:07:16

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Damping ratio pack contains a workflow that provides an environment to calculate the damping ratio of several matrices and plot them.The damping ratio can be considered as a measure of the intrinsic resilience of the population, describing how quickly transient dynamics decay following disturbance or perturbation regardless of population structure, the larger the p, the quicker the population converges ...

8 items in this pack

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Maria Paula Balcazar-Vargas

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Age specific survival analysis pack

Created: 2014-07-02 11:49:01 | Last updated: 2015-05-19 09:46:30

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The age-specific survival analysis pack has a workflow that analyse the basic information on the mean, variance and coefficient of variation (CV) of the time spent in each stage class and the mean and variance of the time to death.Analyses:Fundamental matrix (N)Variance (var)Coefficient of variation (CV)MeanetaVareta

3 items in this pack

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Yuliya Fetyukova

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usability test pack4

Created: 2014-06-30 12:23:23 | Last updated: 2014-06-30 12:24:21

test

1 item in this pack

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John Pybus

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Test Pack

Created: 2014-06-25 12:46:21 | Last updated: 2014-06-25 16:27:41

Testing Pack as RO

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Boltmwj1

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test

Created: 2014-06-21 17:59:54

test

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Maria Paula Balcazar-Vargas

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Matrix Population Model construction pack

Created: 2014-06-19 11:23:27 | Last updated: 2014-07-25 12:48:25

This pack contains a workflow, a file and documentation (tutorial to run the workflow).Creation of a stage matrix model from demographic monitoring of individuals in an animal or plant population Workflow for local executionThe Creation of a stage matrix model Workflow allows us to construct a stage o several stage matrices. This workflow create a stage matrix based on two years census data that contains transitions probabilities from each stage to the next, of tagged or mapped individuals of...

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Cynthia Gibas

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Assembly comparison workflow

Created: 2014-06-15 20:05:38 | Last updated: 2014-06-15 20:07:45

This pack contains workflows used in the paper "Impact of Analytic Provenance in Genome Analysis" by Shatavia Morrison et al. presented at ISBRA 2013 and other MSS currently in preparation.

3 items in this pack

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Rekha Maryanne Louis

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usability test pack

Created: 2014-06-10 12:40:58

This is a test pack created for usability study of myExperiment from May to August 2014

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Marco Roos

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BioSemantics Concept Profile Generation Workflows

Created: 2014-06-04 12:31:09 | Last updated: 2014-06-04 13:01:44

This pack compiles concept profile-generation workflows by the LUMC/EMC Biosemantics groups.This work is made possible by EU projects 'Workflow Forever' (www.wf4ever-project.org) and RD-Connect (www.rd-connect.eu), and contribution from bioinformatics students from the Hogeschool Leiden.

9 items in this pack

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Eleni

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Supporting material for Mina et al., Journal of Biom...

Created: 2014-05-31 12:25:42 | Last updated: 2017-04-19 10:38:13

This pack contains the link to the AllegroGraph triple store and the SPARQL endpoint for the nanopublications presented in this paper. The user can login with username: test and password: tester

2 items in this pack

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Ferenc HORVATH

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Preparatory working with Biome-BGC Projects database...

Created: 2014-05-26 06:10:06 | Last updated: 2014-05-27 15:23:06

Various meteorology, EPC (ecophysiology parameter) and observation files for Biome-BGC simulation runs.

9 items in this pack

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Ferenc HORVATH

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Understanding Basics of a Biome-BGC simulation run

Created: 2014-05-21 04:31:40 | Last updated: 2014-05-21 05:03:34

Biome-BGC is a biogeochemical model that simulates the storage and flux of water, carbon, and nitrogen between the ecosystem and the atmosphere, and within the components of the terrestrial ecosystems (Thornton, 2000). The Biome-BGC was developed by the Numerical Terradynamic Simulation Group (NTSG), University of Montana.The executable code of Biome-BGC are embedded in web services and workflows, while input and parameter files or datasets are managed with Biome-BGC Projects d...

3 items in this pack

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Saverio Vicario

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Phylogenetic Diversity

Created: 2014-05-19 12:29:08 | Last updated: 2014-05-19 13:13:10

Tools to study diversity across sample and environment taking account the phylogenetic structure of the observation

3 items in this pack

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component family

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pinarpink

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LabelFlow evaluation pack

Created: 2014-05-07 21:08:35

This pack contains the material used for the evaluation of LabelFlow and also XLS based result data from experiments

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Stian Soiland-Reyes

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Test pack

Created: 2014-04-29 13:16:38 | Last updated: 2014-04-29 13:17:26

Pack for blab lblahttp://example.com/

2 items in this pack

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Alan Williams

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GBIF

Created: 2014-04-03 13:11:49

A family of components that provide access to the Global Biodiversity Information Facility (GBIF) registry

1 item in this pack

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Maria Paula Balcazar-Vargas

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Stage vectors, Survival and Growth rate curves (demo...

Created: 2014-04-03 08:11:33 | Last updated: 2014-07-25 12:41:24

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Stages vectors plots, Survival and Growth rate curves Workflow provides an environment to perform several analyses on a series of stage-matrices:Population projectionSurvival values calculations per stage per year and its respective plot;Growth rates (lambda) calculations per year and its respective plot;Stage Vectors calculations and their respective plots.

8 items in this pack

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Alex Nenadic

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Taverna 2.5 Bioinformatics Starter Pack

Created: 2014-04-02 12:44:47 | Last updated: 2017-01-09 13:08:53

This is a Starter Pack for Taverna 2.5 Bioinformatics edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Bioinformatics and help you get started using it.Workflows from this Starter pack can also be found in the myExperiment perspective of the Taverna Workbench.Tutorials for Taverna are available under the Taverna 2.x documentation on the Taverna Web site.Also check out the Taverna User Manual.

18 items in this pack

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Alex Nenadic

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Taverna 2.5 Biodiversity Starter Pack

Created: 2014-04-02 12:40:42 | Last updated: 2017-01-09 13:09:17

This is a Starter Pack for Taverna 2.5 Biodiversity edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Biodiversity and help you get started using it.Workflows from this Starter pack can also be found in the myExperiment perspective of the Taverna Workbench.Tutorials for Taverna are available under the Taverna 2.x documentation on the Taverna Web site.Also check out the Taverna User Manual.

14 items in this pack

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Julian Garrido

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Astronomy Taverna 2.5 starter pack

Created: 2014-03-03 17:02:08 | Last updated: 2014-03-03 17:16:57

This is a set of small snippets using Astronomy Taverna. The purpose of this pack is to make the design and development of astronomy Virtual Observatory workflows easier, learning by the example. Additionally, you can find other Astronomy related workflows and snippets related to general functionalities of Taverna.

45 items in this pack

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Donal Fellows

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Webpage Quality Assurance

Created: 2014-02-27 14:39:10 | Last updated: 2014-04-01 08:52:19

This family of digital preservation components is for actions that are used to compare webpages and their archives.

1 item in this pack

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component family

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Donal Fellows

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Webpage Characterisation

Created: 2014-02-27 14:38:33 | Last updated: 2014-02-27 14:39:52

This family of digital preservation components is for actions that are used to characterise webpages and their archives.

1 item in this pack

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Donal Fellows

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Webpage Migration

Created: 2014-02-27 14:37:57 | Last updated: 2014-02-27 14:39:32

This family of digital preservation components is for actions that are used to migrate webpages and their archives between various formats.

1 item in this pack

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Donal Fellows

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Document Quality Assurance

Created: 2014-02-27 14:35:38 | Last updated: 2014-04-01 08:50:17

This family of digital preservation components is for actions that are used to compare documents.

1 item in this pack

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Donal Fellows

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Document Characterisation

Created: 2014-02-27 14:35:03 | Last updated: 2014-02-27 14:35:57

This family of digital preservation components is for actions that are used to characterise documents.

1 item in this pack

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Donal Fellows

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Document Migration

Created: 2014-02-27 14:33:59 | Last updated: 2014-08-13 10:54:10

This family of digital preservation components is for actions that are used to migrate documents between various formats.

31 items in this pack

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Donal Fellows

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Scientific Data Quality Assurance

Created: 2014-02-27 14:31:55 | Last updated: 2014-04-01 08:51:59

This family of digital preservation components is for actions that are used to compare scientific data files.

1 item in this pack

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Donal Fellows

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Scientific Data Characterisation

Created: 2014-02-27 14:29:55 | Last updated: 2014-02-27 14:31:11

This family of digital preservation components is for actions that are used to characterise scientific data files.

1 item in this pack

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Donal Fellows

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Scientific Data Migration

Created: 2014-02-27 14:27:50 | Last updated: 2014-02-27 14:28:16

This family of digital preservation components is for actions that are used to migrate scientific data between various formats.

1 item in this pack

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Donal Fellows

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Audio Video Quality Assurance

Created: 2014-02-27 14:25:53 | Last updated: 2014-09-30 10:06:12

This family of digital preservation components is for actions that are used to compare audio or video.

5 items in this pack

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Donal Fellows

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Audio Video Characterisation

Created: 2014-02-27 14:24:31 | Last updated: 2014-09-26 10:56:38

This family of digital preservation components is for actions that are used to characterise audio and video.

3 items in this pack

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Donal Fellows

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Audio Video Migration

Created: 2014-02-27 14:22:42 | Last updated: 2014-08-13 10:54:45

This family of digital preservation components is for actions that are used to migrate audio and video between various formats.

16 items in this pack

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Donal Fellows

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Image Quality Assurance

Created: 2014-02-27 14:21:12 | Last updated: 2014-11-06 23:02:54

This family of digital preservation components is for actions that are used to compare images.

15 items in this pack

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Donal Fellows

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Image Characterisation

Created: 2014-02-27 14:19:14 | Last updated: 2014-11-06 23:03:48

This family of digital preservation components is for actions that are used to characterise images.

3 items in this pack

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Donal Fellows

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Image Migration

Created: 2014-02-27 14:16:51 | Last updated: 2014-11-06 17:13:58

This family of digital preservation components is for actions that are used to migrate images between various formats.

39 items in this pack

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Maria Paula Balcazar-Vargas

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Life Table Response Experiments Fixed design Year Ef...

Created: 2014-02-27 12:49:10 | Last updated: 2014-08-27 09:58:12

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Life Table Response Experiments Year Effect in One Location or 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 retrospective analysis (Caswell 1989),...

9 items in this pack

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Maria Paula Balcazar-Vargas

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Life Table Response Experiments Fixed design year ef...

Created: 2014-02-21 13:12:33 | Last updated: 2014-08-21 08:06:21

This pack contains a workflow, a file and documentation (tutorial to run the workflow).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 of one place) of 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, one way design (Caswell 2001).LTRE is...

13 items in this pack

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Norman Morrison

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Embedding an R Script in a Workflow Exercise

Created: 2014-02-13 17:47:42 | Last updated: 2014-02-13 17:52:17

This pack has all the files for the problem based learning exercise of embedding an R Script in a workflow

4 items in this pack

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Norman Morrison

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Taverna Tool Service

Created: 2014-02-13 17:40:54 | Last updated: 2014-02-13 17:42:58

Taverna Tool service tutorial pack

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Norman Morrison

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Supplementary material for "An Introduction to Desig...

Created: 2014-02-06 16:10:58 | Last updated: 2014-02-06 16:11:35

Supplementary material for "An Introduction to Designing and Executing Workflows with Taverna - Part 2".

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Maria Paula Balcazar-Vargas

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Life Table Response Experiments Fixed design Place e...

Created: 2014-01-29 10:42:06 | Last updated: 2014-08-14 08:04:25

This pack contains a workflow, a file and documentation (tutorial to run the workflow).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 2001). LTRE is a retrospectiv...

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Saverio Vicario

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BayesianPhylogeneticInference

Created: 2013-12-11 13:40:50 | Last updated: 2014-05-19 13:01:14

The family propose different steps to perform a bayesian phylogenetic inference

8 items in this pack

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Saverio Vicario

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JSTInteraction

Created: 2013-12-11 13:12:49 | Last updated: 2014-06-17 15:20:46

Allow to interact with JST web service and JST Webdav server to access service of biodiversity catalogue https://www.biodiversitycatalogue.org/services/31

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Renato De Giovanni

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ENM components

Created: 2013-12-06 17:57:57 | Last updated: 2014-11-17 19:06:40

ENM Components is a set of Taverna components (sub-workflows) specialized in ecological niche modelling (ENM) tasks. They simplify the creation of new workflows by encapsulating details that may not be trivial to implement and they can be reused across different workflows. To use ENM components on new workflows with the Taverna workbench, just click on “import new service” on the “service panel”, choose “component service”, select “myExperiment”...

25 items in this pack

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Alan Williams

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GBIF transforms

Created: 2013-12-01 11:11:19 | Last updated: 2013-12-12 19:14:24

A set of components to transform GBIF data

6 items in this pack

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Julian Garrido

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PDL tutorial

Created: 2013-10-31 10:20:59 | Last updated: 2013-10-31 10:34:30

This pack contains the resources to be used in a PDL tutorial: The workflows in the pack use the different options to set up a PDL service (rest, smart rest and PDL server). There is a workflow with an interoperability error and a workflow using an asynchronous VAMDC-PDL service.

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Donal Fellows

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SCAPE Utility Components

Created: 2013-10-28 15:28:32 | Last updated: 2013-11-14 11:20:52

These are utility components for SCAPE; they do miscellaneous things that are needed stereotypically, but which are outside the standard model of SCAPE data items (e.g., because they are not operating on Digital Objects at all).

3 items in this pack

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Alan Williams

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Test components

Created: 2013-10-25 13:44:34 | Last updated: 2015-12-04 14:10:22

A family for testing

8 items in this pack

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Alan Williams

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WebDAV test

Created: 2013-09-16 13:50:08 | Last updated: 2014-02-03 13:53:58

A test family for WebDAV

2 items in this pack

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Simon Fischer

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RCOMM 2013 Data Mining Challenge

Created: 2013-09-09 16:20:45 | Last updated: 2013-09-09 16:24:00

This pack contains the solution and the input data generator for one of the tasks of the RCOMM 2013 data mining challenge "Who Wants to be a Data Miner?". Participants had to solve the task within 10 minutes. The task was this: Givena variant of the Golf data set (found in the //Samples/data folder) where the attribute Outlook is missing,a decision tree model built on the complete Golf data set, anda utility data set containing only the three distinct values of Golf,create an exampl...

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Raul Palma

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myPack

Created: 2013-09-04 10:57:02 | Last updated: 2013-09-04 11:06:30

test pack

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Eleni

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HD data interpretation

Created: 2013-09-02 13:18:22 | Last updated: 2015-04-03 21:14:41

This workflow pack, was created in order to further analyse and interpret the results from workflow pack 485 (HD chromatin analysis). The workflows in this pack are using the anni web services, implemented by the Biosemantics group.

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Eleni

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HD chromatin analysis

Created: 2013-08-28 12:17:37 | Last updated: 2016-10-28 15:02:27

This pack is comprised by all workflows used for the integration and the analysis of Huntington's Disease (HD) gene expression data and epigenetic datasets in order to establish links between HD and epigenetic regulation in disease.

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Alan Williams

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a

Created: 2013-07-10 13:12:46 | Last updated: 2013-11-14 11:20:52

a

1 item in this pack

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pinarpink

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Big Data 2013 Paper Supplementary Material

Created: 2013-06-19 07:40:14 | Last updated: 2013-06-19 07:44:43

The zip file contains the datasets used for the evaluation of our BigData paper "Pinar Alper, Khalid Belhajjame, Carole Goble, and Pinar Karagoz. Small is beautiful: Summarizing scientific workflows using semantic an- notations. In Proceedings of the IEEE 2nd International Congress on Big Data (BigData 2013), Santa Clara, CA, USA, June 2013."

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Alan Williams

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Population Model Analysis Family

Created: 2013-05-28 09:39:37 | Last updated: 2013-11-14 11:20:52

A family of components that do analysis of population models.

3 items in this pack

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Dasands

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Collarborative and Interdisciplinary Research in Adu...

Created: 2013-05-16 18:07:20 | Last updated: 2013-05-16 19:24:33

Immediate Items to define:1 - Definition of Collaborative and Interdisciplinary Education; Adult Education2. Problems of Collaborative and Interdisciplinary Education3. Methods of Collaborative and Interdisciplinary Education4. Implementation of Collaborative and Interdisciplinary Education

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Saverio Vicario

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Analysis of environmental sequences

Created: 2013-05-07 09:07:57 | Last updated: 2013-05-07 12:14:57

The pack should allow to analysis the differentiation across groups of samples of biological sequence

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David R Newman

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Pack with versions and relationships

Created: 2013-05-02 08:35:29 | Last updated: 2013-05-02 08:40:06

This is a pack to demonstrate both versions (snapshots) and relationships between pack entries.

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Julian Garrido

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pack test

Created: 2013-04-22 10:02:18 | Last updated: 2013-07-04 15:01:56

this is a test

5 items in this pack

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Donal Fellows

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SCAPE Image Characterisation Component

Created: 2013-04-04 12:39:14 | Last updated: 2013-11-14 11:20:52

These components handle extraction of characteristics from an image.

5 items in this pack

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Donal Fellows

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SCAPE Image Migration Action

Created: 2013-04-04 10:45:50 | Last updated: 2013-11-14 11:20:52

These components handle the migration of images from one format to another.

3 items in this pack

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Donal Fellows

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ImageMagick: Convert JPG to TIFF

Created: 2013-04-04 08:53:33 | Last updated: 2013-04-04 09:08:21

Converts a JPG image to a TIFF image

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component

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Hamish McWilliam

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EMBL-EBI Web Services

Created: 2013-03-28 12:41:28 | Last updated: 2013-03-28 12:42:30

The European Bioinformatics Institute (EMBL-EBI) offers a wide range of services covering may biological and bioinformatics domains. This Pack collates a set of workflows that provide wrappers for Web Services developed, and maintained by EMBL-EBI.

6 items in this pack

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Saverio Vicario

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Perform Short Bayesian Phylogenetic Inference

Created: 2013-02-20 15:07:21 | Last updated: 2013-08-21 16:09:33

The Pack contain 3 workflows that perform and validate bayesian phylogenetic inference that differ from the kind of input. The pack is called short because the worlflow require that the user need to keep taverna engine always on for the the time of the analysis. This could be quite problematic for large analysis. In this case search help in the "Perform Long Bayesian Phylogenetic Inference" packIn this pack there are 3 workflows:1) User locally formatted input file (for details in n...

3 items in this pack

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Saverio Vicario

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Perform Long Bayesian Phylogenetic Inference

Created: 2013-02-20 14:59:31 | Last updated: 2015-06-12 13:48:46

Phylogenetic inference with mrbayes requires long calculation. So is not possible to keep the taverna engine on for the time required for the analysis. The solution is to break the Workflow in 2 part: before and after submission to mrbayes service.In this pack there are 3 workflows for submission:1) User locally formatted input file (for details in nexus format for mrbayes http://mrbayes.sourceforge.net/wiki/index.php/Manual_3.2)2) User is helped by a GUI (graphical user interface) to define ...

4 items in this pack

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Marco Roos

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Demo pack for wf4ever

Created: 2013-01-30 13:53:40 | Last updated: 2013-01-30 14:08:08

This pack is a mirror of the Demo pack for the wf4ever review Demo. You should not be using any of this for real work.

6 items in this pack

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wf4ever

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pinarpink

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Scientific Workflow Motifs - FGCS Special Issue Subm...

Created: 2013-01-28 10:16:31 | Last updated: 2013-01-28 10:19:29

Abstract of our paper describing motifs presented at eSci2012 "While workflow technology has gained momentum in the last decade as a means for specifying and enacting compu- tational experiments in modern science, reusing and repurposing existing workflows to build new scientific experiments is still a daunting task. This is partly due to the difficulty that scientists experience when attempting to understand existing workflows, which contain several data preparation and ada...

1 item in this pack

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Katy Wolstencroft

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Bioinformatics Workflow Examples

Created: 2013-01-28 08:45:33 | Last updated: 2013-01-28 10:09:41

This pack contains examples of workflows in the field of bioinformatics.

7 items in this pack

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Jose Enrique Ruiz

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Galaxies Sample Selection Research Object

Created: 2013-01-05 16:51:56 | Last updated: 2013-01-05 16:59:16

In order to understand the evolution of galaxies, detailed analysis of images plays a key role. During the last years telescopes working at different wavelengths have been imaging the whole sky. One example of this is the Sloan Digital Sky Survey. The generated images provides a wealth of information, publicly available, and hence allowing them to be used by any interested group in the study of their own samples of objects or generation of new samples. The two main processing of the ima...

4 items in this pack

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Jose Enrique Ruiz

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Luminosity Profiles Research Object

Created: 2013-01-05 16:34:46 | Last updated: 2013-01-05 16:58:18

In order to understand the evolution of galaxies, detailed analysis of images plays a key role. During the last years telescopes working at different wavelengths have been imaging the whole sky. One example of this is the Sloan Digital Sky Survey. The generated images provides a wealth of information, publicly available, and hence allowing them to be used by any interested group in the study of their own samples of objects or generation of new samples. The two main processing of the images ge...

7 items in this pack

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David De Roure

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Presentation - End-to-End Semantics

Created: 2012-11-12 15:28:38 | Last updated: 2012-11-13 00:35:30

Keynote talk by David De Roure at SSN workshop at ISWC 2012, Boston, 12 November 2012 In many respects the music industry has gone digital "end-to-end", with success stories in Semantic Web adoption. Science too is dealing with a "digital turn" and the R&D community is active with Semantic Web. Meanwhile the Semantic Sensor Network workshop series has demonstrated the applicability of Semantic Web approaches in the sensor network domain. Looking to the future,...

4 items in this pack

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David De Roure

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Presentation - Knowledge Infrastructure for Global S...

Created: 2012-11-10 07:47:48 | Last updated: 2012-11-10 09:04:05

Presentation at the First Open Global Systems Science Conference, Brussels, 8-10 November 2012 http://www.gsdp.eu/nc/news/news/date/2012/10/31/first-open-global-systems-science-conference/ Related blog post http://global-systems-science.eu/?p=272

3 items in this pack

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David De Roure

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Presentation - Introduction to Big Data and its Pote...

Created: 2012-10-25 01:09:14 | Last updated: 2012-10-25 01:09:46

Presentation at Dementia Conference (Evington Initiative) held at Wellcome Trust, 22-23 October 2012. Acknowledgements to McKinsey & Company, also Tim Clark (MGH) and Iain Buchan (University of Manchester), for input to slides.

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Azlinayati

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SKOS vocabularies repository

Created: 2012-10-15 10:11:26

A collection of SKOS vocabularies from the Web

0 items in this pack

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David De Roure

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Presentation - The Reality of Reproducibility of Com...

Created: 2012-10-12 19:48:14 | Last updated: 2012-10-12 20:14:01

Title: The Reality of Reproducibility of Computational Science Speaker: Carole Goble Event: IEEE e-Science 2012 Event URL: http://www.ci.uchicago.edu/escience2012/ Location: Chicago, US Date: Thursday, October 11, 2012 Formats: .ppt Abstract: Reproducibility in principle underpins the scientific method. For an experimental finding to be reproducible its materials must be available and its methods clear, accurate and transparent. In this talk I will explore the reality of rep...

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