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nested_echo (2)

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Just calls the echoer

Created: 2013-10-30 | Last updated: 2013-10-30

echoer (6)

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Renamed beanshell

Created: 2013-10-25 | Last updated: 2014-05-07

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Test components

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

8 items in this pack

Comments: 0 | Viewed: 110 times | Downloaded: 15 times

blast (1)

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This is a demo workflow to run BLAST program. It has multiple executionchoices: local execution, Map only, Map Reduce, Cross Reduce, and JobSubmission.NOTE: The Map only, Map Reduce and Cross Reduce choices only workwith the tabular output format (namely -m8). Also, Map Reduce andCross Reduce choices have scripts that only work on Mac and Linux.  bioKepler team (www.biokepler.org)Aug-24-2012 

Created: 2013-10-24

Credits: bioKepler

Find compounds pharmacology targets in Ope... (2)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTS API https://dev.openphacts.org/docs/1.5. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors. Until there is a Local worker to filter out...

Created: 2013-10-16 | Last updated: 2015-11-19

Credits: Stian Soiland-Reyes

Attributions: Find compounds pharmacology and align against target sequences

Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree

Fetch today's xkcd comic (1)

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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2013-10-15

Credits: Stian Soiland-Reyes

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2013-10-15

Credits: Stian Soiland-Reyes

Hello World (1)

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One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2013-10-15

Credits: Stian Soiland-Reyes

concatTwoStrings (1)

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for tests of TavernaServer

Created: 2013-10-10 | Last updated: 2013-10-10

Credits: mdabr

loadData (1)

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Permits loading data to Nencki Genomics Database.

Created: 2013-10-08

Credits: mdabr

showDatasetsGenomic (1)

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Shows all the datasets available in the Nencki Genomics Database (www.nencki-genomics.org). Click 'Use examples' to see all the datasets, separated into datasets of TFBS motifs, and all the remaining datasets (areas), the latter including data from Ensembl funcgen and (thus) Encode. Publication doi: 10.1093/database/bat069

Created: 2013-10-07

Credits: mdabr

plotGenomic (1)

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This workflow returns a graphical representation of selected Nencki Genomics Database (www.nencki-genomics.org) content in the ± 10 kb flank of the transcription start site of a chosen gene. More precisely, it returns instances of selected area types, and instances of selected motif types that intersect any of the returned area instances. The results are returned as three files: a pdf file with the plot, and two tab-separated files with the details of areas and motifs shown in the plot. P...

Created: 2013-10-07

Credits: mdabr

get promoter region + operate on genomic i... (5)

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This workflow computes a promoter region for each gene that we provide as input carrying the genomic information. Then it computes the overlap between the two datasets that contain genomic information plus some statistics. Returns rows of file_1 which overlap with the second file. A kolmogorov smirnov test is applied between the list that overlaps and the one that does not. Uses the R package GenomicRanges.

Created: 2013-10-04 | Last updated: 2013-11-04

Credits: Eleni

Crawl Web with filter words (1)

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Crawl Web with filter words

Created: 2013-09-30

WebCrawl with word filter (1)

WebCrawl with word filter

Created: 2013-09-23

Example of interoperability validation on ... (2)

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Workflow that exemplifies the use of PDL (parameter description language) descriptions for rest services. The web service provides a VOTable that is processed according to the PDL description. Some of the columns in the votable are provided as output in the artifacts (smartVORest config). To check interoperability we have to validatate the connections between outputs and inputs of the artifacts. In this case, there is an error in the connections. dec output is connected to dec input but d...

Created: 2013-09-20 | Last updated: 2013-10-31

Credits: Julian Garrido

Use of rest services described with PDL (1)

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Workflow that exemplifies the use of PDL (parameter description language) descriptions for rest services. There are two cases. - the artifact provides as output the response from the service (rest config). - the web service provides a VOTable that is processed according to the PDL description. Some of the columns in the votable are provided as output in the artifacts (smartVOrest config).

Created: 2013-09-20

Credits: Julian Garrido

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LR Software effort

Created: 2013-09-17 08:31:50

Credits: Miznokruge

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: JPEG image

Comments: 0 | Viewed: 18 times | Downloaded: 13 times

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Acquiring background knowledge on companie... (1)

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This workflow shows how to add background knowledge on companies (e.g., turnover, number of employees, branch) from DBpedia to a dataset.

Created: 2013-09-16

String upload (1)

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The component uploads the string within the InputBody to the File_name within the fixed WebDAV

Created: 2013-09-16 | Last updated: 2014-02-03

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WebDAV test

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

2 items in this pack

Comments: 0 | Viewed: 27 times | Downloaded: 15 times

Concatenated String of Hipsterisms (1)

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A workflow that gets a number of http://hipsteripsum.me/ through a REST call to http://hipsterjesus.com/ into a JSON string, then disassembles the record and concatenates into a paragraph.

Created: 2013-09-13

Credits: Scottschreckengaust tpacurtis Mutanthumb Chrisser Kayleigh Ayn Bohémier Atminer

Attributions: Concatenated String of Sentences Hello Hipster Hello Hipster Hello Hipster World

Example Workflow (1)

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This is an example workflow

Created: 2013-09-13

Using Linked Open Data from Eurostat as Ba... (2)

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This process shows how an existing data table containing data about countries can be enriched with background knowledge from Eurostat. The example takes tabular data about the alcohol consumption in European countries as input, adds more data about those countries from Eurostat, and finally learns a model based on the enriched data which explains high alcohol consumption.

Created: 2013-09-12 | Last updated: 2013-09-13

Using PDL description and PDL smart descri... (1)

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This workflow call the same service using two different PDL descriptions. In the first case, the PDL_service artifact is set up to work with a rest service. In the second case, the PDL_service artifact is set up to work with a rest service but a votable is expected and processed according to the PDL description. It allows providing columns from the votable as output ports.

Created: 2013-09-11

Credits: Julian Garrido

PDL workflow for a VAMDC collision service (2)

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Example to show how to use a PDL description file implementation of a VAMDC collision asynchronous service

Created: 2013-09-11 | Last updated: 2013-10-31

Credits: Julian Garrido

Plane cut on planetary models provided und... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the value of a plane for different variables for a particular planetary model.

Created: 2013-09-11

Credits: David PS

Analyzing Data from a Linked Open Data SPA... (1)

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This process reads a list of countries, their GDP and energy consumption from the Eurostat Linked Open Data SPARQL Endpoint (http://wifo5-03.informatik.uni-mannheim.de/eurostat/) and analyzes whether there is a correlation between GDP and energy consumption

Created: 2013-09-11 | Last updated: 2013-09-11

Refresh SPI after plugin installation (1)

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This workflow hacks into Taverna's plugin system to force update the net.sf.taverna.t2.workbench.views.results.saveactions.SaveAllResultsSPIRegistry SPI, which means it is possible to install/update the Taverna PROV plugin without restarting. This is needed to enable live update of this plugin, because there is a bug in Taverna 2.4 and below where the SPI registries are not updated correctly after installation of a plugin.

Created: 2013-09-10

Credits: Stian Soiland-Reyes

Get Particle trajectories from starting po... (1)

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This is a workflow that uses 2 different services from IMPEx to calculate different variables at a certain radius for a particular planetary model.

Created: 2013-09-10

Credits: David PS

Attributions: Sphere lan-lot random points Particle trajectories in the planetary models provided under IMPEx VOTable on the net maker for IMPEx Interpolate n-randon points in a sphere on a planetary models provided under IMPEx

Interpolate n-randon points in a sphere on... (1)

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This is a workflow that uses 2 different services from IMPEx to calculate different variables at a certain radius for a particular planetary model.

Created: 2013-09-10

Credits: David PS

Attributions: Interpolate values on planetary models provided under IMPEx VOTable on the net maker for IMPEx Sphere lan-lot random points

Sphere lan-lot random points (1)

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It gest n lat-lon coordinates pairs as comma separated values. It uses a a random generator from http://www.random.org

Created: 2013-09-10

Credits: David PS

Vector field lines in the planetary models... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the field lines for the vector field requested for the starting points provided for a particular planetary model.

Created: 2013-09-10

Credits: David PS

Particle trajectories in the planetary mod... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the particle trajectories for the defined particle (initial position, velocity, mass and charge) for a particular planetary model.

Created: 2013-09-10

Credits: David PS

Interpolate values on planetary models pro... (2)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the value of different variables, at the cordinates that a spacecraft pass through for the time range provided, for a particular planetary model. The orbital values of the spacecraft are obtained by AMDA.

Created: 2013-09-10 | Last updated: 2013-09-10

Credits: David PS

Interpolate values on planetary models pro... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the value of different variables, at the cordinates provided, for a particular planetary model.

Created: 2013-09-10

Credits: David PS

VOTable on the net maker for IMPEx (1)

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This simple workflow is a way to create a simple votable that uses the standards from IMPEx and provides an URL for the created VOTable enabling re-use of it through the IMPEx services

Created: 2013-09-10

Credits: David PS

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RCOMM 2013 Data Mining Challenge

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

2 items in this pack

Comments: 0 | Viewed: 62 times | Downloaded: 33 times

RCOMM 2013 Challenge: 2. Solution (Re-infe... (1)

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This process is the solution for one of the RCOMM 2013 data mining challenge tasks which participants had to solve within 10 minutes. The task was this: Given (1) a variant of the Golf data set (found in the //Samples/data folder) where the attribute Outlook is missing, (2) a decision tree model built on the complete Golf data set, and (3) a utility data set containing only the three distinct values of Golf, create an example set based on the incomplete data set from (1) containing all po...

Created: 2013-09-09

RCOMM 2013 Challenge: 1. Generate input data (1)

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This process generates the input for one of the RCOMM 2013 data mining challenge tasks. For a description, please refer to the solution process.

Created: 2013-09-09 | Last updated: 2013-09-09

BioCyc:Reaction Scheme (1)

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The purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps: 1. determine all the reactions that the given metabolite participates in 2. determine all the compounds that participate in these reactions 3. filter certain compounds like H2O, ATP etc to avoid non-specific connections 4. determine all the reactions that the compounds passing through step 3 participate...

Created: 2013-09-06

Credits: Harish Dharuri

BioCyc:Pathway Scheme (1)

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The purpose of the workflow is to determine all the genes operating in BioCyc pathways that the input metabolite participates in. The overall idea is to generate a set of genes that potentially influence the levels of a metabolite due to the common pathways that they share.

Created: 2013-09-06

Credits: Harish Dharuri

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Introduction to Taverna Online & Interaction

Created: 2013-09-06 09:04:41

Credits: Aleksandra Pawlik Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 48 times | Downloaded: 43 times

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Introduction to Taverna Components - Bonn 2013

Created: 2013-09-06 07:39:49

Credits: Aleksandra Pawlik Stian Soiland-Reyes Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint 2007 presentation

Comments: 0 | Viewed: 59 times | Downloaded: 59 times

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XPath service Tutorial

Created: 2013-09-05 12:26:15

Credits: Katy Wolstencroft Alan Williams

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: PowerPoint presentation

Comments: 0 | Viewed: 56 times | Downloaded: 45 times

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