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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