myExperiment

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Alan Williams

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Taverna 1.7 starter pack

Created: 2008-07-17 21:06:12 | Last updated: 2018-01-28 19:42:32

Everything to get started with Taverna 1.7 - latest version is 1.7.2

19 items in this pack

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Alan Williams

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Taverna 2.2 starter pack

Created: 2010-06-11 13:40:05 | Last updated: 2012-01-03 15:46:09

The Taverna team are pleased to announce that Taverna 2.2.0 workbench and command line tool are now available for users to download. Taverna 2.2.0 includes improvements to the workbench user interface and gives users greater control over the workflow engine. Here are a few of the new features in the workbench: * Loading and sharing of service sets * Ability to load and edit workflows that contain services that are offline ...

20 items in this pack

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Alex Nenadic

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Taverna 2.5 Enterprise Starter Pack

Created: 2014-04-02 12:54:33 | Last updated: 2017-01-09 12:01:51

This is a Starter Pack for Taverna 2.5 Enterprise edition - it contains a number of example workflows to showcase various features of Taverna 2.5 Enterprise 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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Alan Williams

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Taverna 2.4 starter pack

Created: 2012-03-18 13:43:06 | Last updated: 2013-10-08 12:49:44

Taverna 2.4.0 Workbench and Command Line Tool released The Taverna team are pleased to announce that Taverna 2.4.0 Workbench and the Command Line Tool are now available for download. Here are a number of new features in the Workbench: Text Constant service allowing easier entry of large textual values Greater control over what is return from REST service Ability to use all the example values for a workflow run with one button Easier annotation of serv...

20 items in this pack

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Antoon Goderis

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Paul Fisher workflows for benchmarks PR and CA2

Created: 2008-07-12 20:26:49 | Last updated: 2008-07-13 09:21:55

Please note that the workflows in this pack are not being maintained. For updated workflows check out http://www.myexperiment.org/users/43

77 items in this pack

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benchmarks

Creator

Alan Williams

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Taverna localworker example pack

Created: 2008-09-27 17:57:39 | Last updated: 2012-03-05 11:33:29

A pack of examples of the calling of Taverna's localworkers. The example workflows make extensive use of the default value mechanism for associating a value with a port of a service. An alternative set of workflows that use string constants to make the values more explicit is under development.

103 items in this pack

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Hamish McWilliam

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EMBL-EBI Web Services (retired)

Created: 2008-07-11 01:24:33 | Last updated: 2013-03-28 12:39:25

The European Bioinformatics Institiute 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 the EMBL-EBI.NB: the Web Services used in this package have been decommissioned and are no longer available.

17 items in this pack

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ebi

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Alan Williams

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Taverna 2.1 starter pack

Created: 2009-12-10 16:04:54 | Last updated: 2009-12-18 11:15:36

The Taverna team are happy to announce that Taverna 2.1 is now available for download. It includes many new features and bug fixes based on extensive usability reviews and hours of testing. 2.1 truly is the next release up from the 1.7.x line. 2.1 features: * Copy/paste, shortcuts, undo/redo, drag and drop * An Animated workflow diagram * Remembers added/removed services * Secure Web services support * Up-to-da...

12 items in this pack

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example

Creator

Stian Soiland-Reyes

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Taverna 2.1 beta 2

Created: 2009-07-02 12:51:11 | Last updated: 2009-09-21 14:48:06

Taverna workbench 2.1 beta 2 Due to user response to Taverna 2 workbench, major improvements have been made to the user interface of Taverna 2.1 Beta 2 workbench. Many of these are described below. Installing Choose your download from the list of links in this pack depending on your operating system. Windows If you have administrator rights on your machine, you can download the Windows installer (taverna-workbench-2.1.b2-installer.exe). A wizard should guide you thro...

6 items in this pack

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Franck Tanoh

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Example workflow for KEGG web service

Created: 2008-09-29 13:28:02 | Last updated: 2008-10-08 16:37:49

The pack contains a number of test workflows for kegg web service (and operations)

14 items in this pack

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kegg

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James Eales

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Core text mining workflows

Created: 2010-02-19 10:12:33 | Last updated: 2011-12-13 16:03:17

This pack contains workflows we have created to support core text mining tasks. We currently provide workflows to do these tasks Loading documents (text or PDF) PDF to text conversion Sentence splitting Text cleaning (ASCII or XML-valid) Term recognition (using NaCTeM service TerMine)

7 items in this pack

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Katy Wolstencroft

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useful_for_sysmo

Created: 2008-12-17 12:31:48 | Last updated: 2009-06-10 09:43:20

These workflows have been collected as potentially useful protocols for the sysmo consortium

21 items in this pack

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Alan Williams

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Taverna 2.3 starter pack

Created: 2011-06-21 14:16:18 | Last updated: 2012-04-05 13:55:40

The Taverna team are pleased to announce that Taverna 2.3.0 Workbench and the Command Line Tool are now available for download. Taverna 2.3.0 includes new service types, integration with service catalogues and experimental export of provenance information. Here are a few of the new features in the Workbench: REST service allowing you to perform GET, POST, PUT and DELETE operations configured using a template XPath service where you can create an XPath expression from an example...

26 items in this pack

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starter

Creator

Jiten Bhagat

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Trident Example Workflows

Created: 2008-10-08 13:33:38 | Last updated: 2008-10-22 12:45:31

A set of example workflows for the Microsoft Trident workflow system

9 items in this pack

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Paul Fisher

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Open Data: Bilateral Perisylvian Polymicrogyria

Created: 2010-11-16 16:20:43 | Last updated: 2011-09-23 10:55:08

This pack contains freely accessible data for scientific researchers to try and identify key genes linked to Bilateral Perisylvian Polymicrogyria. For those who want more information about this condition before they download the data, please see this link, which describes the condition and traits: http://omim.org/entry/300388?search=bilateral%20perisylvian%20polymicrogyria The results conatined within this pack are the output from running a scientific workflow that identifies candidate genes...

7 items in this pack

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bilateral perisylvian polymicrogyria
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bioinformatics
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chromosome
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cosine vector space
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data-driven
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epilepsy
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genotype
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homo sapiens
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human
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Kegg Pathways
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phenotype
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text mining; term extraction; entity recognition
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trait

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Thomask...

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WikiPathways workflows

Created: 2008-09-16 11:43:57 | Last updated: 2009-02-03 12:47:00

A set of workflows that use the WikiPathways webservice.

5 items in this pack

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Biodiversity eLaboratory

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DEPRECATED - Matrix Population Models construction a...

Created: 2012-11-02 10:48:48 | Last updated: 2014-09-17 10:44:21

This pack is deprecated. To obtain a more recent version of this pack, please refer to: http://www.myexperiment.org/packs/483.html The Matrix Population Models Workflow provides an environment to create a stage-matrix with no density dependence and to perform several analyses on it:- Eigen analysis;- Age specific survival;- Generation time (T);- Net reproductive rate (Ro);- Transient Dynamics;- Bootstrap of observed census transitions (Confidence intervals of λ).This workflow has ...

4 items in this pack

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Simon Coles

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acetanilide comparison study (test)

Created: 2008-08-18 17:58:31 | Last updated: 2008-08-18 18:11:21

Links to repository records, data files and Blog discussions for infra-red, hot stage microscopy, differential scanning calorimetry and x-ray crystallography studies on a small family of simple acetanilides

7 items in this pack

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Paul Fisher

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Pathway to Phenotype using Text Mining

Created: 2009-08-10 13:01:47 | Last updated: 2009-08-11 14:51:31

This pack contains a list of workflows and result files obtained from the analysis of candidate pathways believed to play a role in resistance to African Trypanosomiasis in the mouse model organism.

12 items in this pack

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Paul Fisher

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Towards Genotype-Phenotype Correlations

Created: 2009-04-08 13:14:54 | Last updated: 2009-08-11 14:50:01

It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing large datasets, and represent a framework for the re-use and the explicit declaration of experimental methods. In this pack is a paper which describes the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes.&n...

20 items in this pack

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Marco Roos

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AIDA demo pack

Created: 2008-12-14 21:35:43 | Last updated: 2009-05-01 17:35:26

Pack with AIDA demo material

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Wassinki

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Package: mapping oligonucleotides to an assembly

Created: 2008-12-11 12:02:47 | Last updated: 2009-01-22 09:06:26

This package contains all elements required to run the RShell use case "Mapping oligonucleotides to an assembly"

5 items in this pack

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Jiten Bhagat

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Everything You Need To Know About myExperiment...

Created: 2008-07-02 22:31:12 | Last updated: 2008-07-02 23:12:37

... but were afraid to ask. This is the pack to go to for all information about myExperiment and the people involved in this project!

9 items in this pack

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Maria Paula Balcazar-Vargas

Project

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Matrix Population Model construction and analysis pack

Created: 2013-08-13 14:31:09 | Last updated: 2015-06-12 13:48:43

This pack contains a workflow, a file and documentation (tutorial to run the workflow).The Matrix Population Models Workflow provides an environment for create a stage-matrix with no density dependence and perform several analyses on it.Analyses:Eigen analysis.Age specific survival.Generation time (T).Net reproductive rate (Ro).Transient Dynamics.Bootstrap of observed census transitions (Confidence intervals of λ).Survival curveKeyfitz’s ΔCohen’s cumulative distanceTh...

4 items in this pack

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Kristina Hettne

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Functional annotation of SNPs using next-generation ...

Created: 2012-06-26 10:41:38 | Last updated: 2015-09-01 14:31:18

This pack implements the concept profile matching pipeline in the knowledge discovery tool Anni (http://biosemantics.org/anni), and adapts it to interpret the top SNPs from a GWAS. The underlying literature and concept profile databases are the same as the for the current version of Anni (2.1). The pack consists of three main workflows (http://www.myexperiment.org/workflows/2999, http://www.myexperiment.org/workflows/2973, http://www.myexperiment.org/workflows/2972). Workflow 2999 returns a ...

12 items in this pack

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concept
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ensembl
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evidence
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gene
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GO
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literature
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ontology
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profile
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snp

Creator

Simon Fischer

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Who Wants to be a Data Miner?

Created: 2011-11-02 17:54:07 | Last updated: 2013-09-09 16:22:11

One of the most fun events at the annual RapidMiner Community Meeting and Conference (RCOMM) is the live data mining process design competition "Who Wants to be a Data Miner?". In this competition, participants must design RapidMiner processes for a given goal within a few minutes. The tasks are related to data mining and data analysis, but are rather uncommon. In fact, most of the challenges ask for things RapidMiner was never supposed to do. This pack contains solutions for these...

12 items in this pack

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Peter Li

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Systematic integration of experimental data and mode...

Created: 2010-03-25 20:31:36 | Last updated: 2010-03-26 17:23:44

A pack of workflows for the construction, parameterisation, optimisation and simulation of SBML models.

5 items in this pack

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Paul Fisher

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Genotype to Pathway

Created: 2009-08-11 14:44:16 | Last updated: 2009-08-11 14:52:12

This pack is for investigating links between the genotype of an organisms to possible pathways. This constitutes half of the pathway-driven approach, genotype to pathway, and pathway to phenotype.

18 items in this pack

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Andrea Wiggins

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FLOSS Research Analyses

Created: 2009-06-05 13:58:56 | Last updated: 2009-06-05 13:59:52

Workflows for analysis of free/libre open source software development.

5 items in this pack

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Alan Williams

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Taverna 2.1 beta 1 pack

Created: 2009-05-29 13:16:30 | Last updated: 2012-03-05 11:34:00

Introduction This is a pack for the first beta of Taverna 2.1 It includes a zip of Taverna 2.1 beta 1. The zip includes the executable of Taverna 2.1 beta 1, some example files, release notes and a list of known issues. If you have any comments or problems with the beta, then please post them as comments to this pack, or preferably to the taverna-hackers@lists.sourceforge.net Welcome to Taverna 2.1 Beta 1 workbench Due to user response to Taverna 2 workbench, major improveme...

2 items in this pack

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David De Roure

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myExperiment paper for Concurrency Practice and Expe...

Created: 2009-04-10 13:41:56 | Last updated: 2009-04-14 08:38:09

This pack contains the materials used in the paper De Roure, D., Goble, C., Aleksejevs, S., Bechhofer, S., Bhagat, J., Cruickshank, D., Fisher, P., Hull, D., Michaelides, D., Newman, D., Procter, R., Lin, Y. and Poschen, M. (2009) Towards Open Science: The myExperiment approach. Concurrency and Computation: Practice and Experience. which has been submitted to the special issue of CCPE based on the Micorosfot e-Science workshop in Indianaopolis, December 2008. The paper uses a pack by Pail ...

8 items in this pack

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David De Roure

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Carole's Keynotes

Created: 2008-09-27 19:52:17 | Last updated: 2010-05-08 20:24:47

Carole Goble's 2008 keynote talks that feature myExperiment, in PowerPoint 97-2003 format. All myExperiment presentation can be found on the wiki on http://wiki.myexperiment.org/index.php/Presentations

5 items in this pack

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Marco Roos

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AIDA toolbox

Created: 2008-08-01 11:33:03 | Last updated: 2010-02-14 16:04:25

Adaptive Information Disclosure Application toolbox: AIDA web services for automated knowledge extraction and knowledge management Documentation

9 items in this pack

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Thomas Duigou

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KNIME workflows and associated data from Koch et. al...

Created: 2017-06-29 17:26:00 | Last updated: 2017-12-19 10:19:21

The pack provides the KNIME workflows and associated data from:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9Please browse the linked packs below.

4 items in this pack

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Eleni

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Supporting material for paper: A putative role for g...

Created: 2013-11-06 10:34:47 | Last updated: 2017-04-19 11:22:27

This pack contains links that refer to the myExperiment packs and Research object links that describe our two sets of workflow implementation, for data analysis and for data interpretation.

5 items in this pack

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Creator

Jose Enrique Ruiz

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AstroTaverna Starter Pack

Created: 2013-04-12 16:10:31 | Last updated: 2013-11-27 16:54:39

This is a set of small snippets using AstroTaverna plugin, developed in the Wf4Ever project. The purpose of this pack is to make the design and development of astronomy Virtual Observatory workflows easier, learning by the example.AstroTaverna may be installed on Taverna 2.4 Workbenchhttp://wf4ever.github.io/astrotaverna/

29 items in this pack

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Stian Soiland-Reyes

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Visualize PAV provenance as SVG

Created: 2013-04-05 09:18:51 | Last updated: 2018-01-04 11:39:09

A workflow that converts PAV provenance to SVG by inferring PROV-O statements.VoID descriptions following the Open PHACTS Dataset descriptions specification are fetched as Turtle, cleaned up to be valid OWL2 ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance.Note that this workflow downloads CWM, Pellet and ProvToolbox on dema...

11 items in this pack

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Tags:

ontology
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owl
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pav
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pellet
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prov
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provenance
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provtoolbox
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rdf
|
svg

Creator

Matko BoÅ¡njak

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e-LICO recommender workflows

Created: 2011-03-15 15:33:48 | Last updated: 2012-01-28 19:39:06

This pack contains recommender system workflows created for the purpose of e-LICO project.

6 items in this pack

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Szypul

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projekt v2

Created: 2009-06-08 11:12:52 | Last updated: 2009-06-17 14:34:18

Example project. It takes geographical coordinates and search target(ex. "pubs") to find them near the capital city of a country containing these coordinates.

6 items in this pack

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Andrea Wiggins

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Network Analysis

Created: 2009-06-05 14:01:31 | Last updated: 2009-06-05 14:01:56

Workflows that employ (social) network analysis.

3 items in this pack

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Andrea Wiggins

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Metadata Management

Created: 2009-06-05 13:54:55 | Last updated: 2009-06-05 13:55:34

Workflows dealing with creating and updating metadata records.

3 items in this pack

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Marco Roos

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Supporting material for Roos et al., BMC Bioinformat...

Created: 2009-05-15 15:45:32 | Last updated: 2011-08-11 10:01:23

Supporting material for BMC Bioinformatics, supplement for Semantic Web Applications and Tools for Life Science (2009) Structuring and extracting knowledge for the support of hypothesis generation in molecular biology Marco Roos, M. Scott Marshall, Andrew P. Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas, Pieter W. Adriaans Acknowledgements We thank the myGrid team and OMII-UK for their support in applying their e-Science tools, and M...

5 items in this pack

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FunCUT package

Created: 2008-10-03 16:47:15 | Last updated: 2008-10-03 16:48:55

Input example and FunCUT workflow

1 item in this pack

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David De Roure

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myExperiment Papers

Created: 2008-09-27 20:14:10 | Last updated: 2008-09-27 22:09:49

This pack contains all the myExperiment papers. They can also be found on the myExperiment Wiki on http://wiki.myexperiment.org/index.php/Papers and are stored in ECS EPrints where they can be retrieved with this query http://eprints.ecs.soton.ac.uk/cgi/search/advanced?projects=myexperiment

11 items in this pack

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Paul Fisher

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Newcastle NeuroScience

Created: 2008-08-04 17:35:59 | Last updated: 2008-09-01 17:00:14

This pack contains two PowerPoint presentations given at the 01/08/2008 Taverna and myExperiment tutorial.

3 items in this pack

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Marco Roos

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e-science tool pack

Created: 2008-08-01 10:52:42 | Last updated: 2008-08-01 12:06:07

Pack of tools and software components that can be used to enhance your research. 'e-science' characteristics: interoperabie with other tools free to use by academics components can be shared and reused, potentially for other means stimulating sharing and reusing components

1 item in this pack

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Antoon Goderis

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Peter Li workflows for benchmarks PR and CA2

Created: 2008-07-13 20:32:39 | Last updated: 2008-07-13 20:47:19

Please note that the workflows in this pack are not being maintained. For updated workflows check out http://www.myexperiment.org/users/221

66 items in this pack

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benchmarks

Creator

Antoon Goderis

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Workflow discovery benchmarks

Created: 2008-07-12 11:20:23 | Last updated: 2008-10-09 16:41:46

This pack contains benchmarks that measure how bioinformaticians discover Taverna workflows. Several subpacks are available: Collection of workflows by Paul Fisher, used in benchmarks PR2 and CA2 Collection of workflows by Peter Li, used in benchmarks PR2 and CA2

7 items in this pack

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benchmarks

Creator

Franck Tanoh

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web services info

Created: 2008-07-02 17:15:34 | Last updated: 2008-07-13 23:00:16

This pack contains useful info related to bio services.

6 items in this pack

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web services

Creator

Thomas Duigou

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Pack #4 - Metabolome completion and metabolomics

Created: 2017-06-30 16:36:44 | Last updated: 2017-12-19 10:22:42

This pack provides part of the supporting material for:Koch M, Duigou T, Carbonell P, Faulon JL. Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0. Journal of Cheminformatics, 9:64, 2017. https://doi.org/10.1186/s13321-017-0252-9The pack contains (i) the RetroPath2.0-Mods-metabolomics workflow as well as (ii) all the associated data for the metabolome completion use case (see the main text for details, section 2.4 Metabolome completion and metabolo...

2 items in this pack

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