Workflows

A Talend mashup to discover PARP proteins ... (3)

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A Talend workflow to answer this specific question :What is known about PARP family proteins involved in pathway according to Reactome ?by fetching RDF data from Bio2RDF`s HGNC, UniProt REST service and EBI Reactome SPARQL endpoint, all Semantic Web public resources.

Created: 2014-02-10 | Last updated: 2014-04-07

Credits: Francois Belleau

RTCalc Retention Time Prediction and Outli... (1)

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This workflow takes as input a pepXML file from PeptideProphet, applied RTCalc and outputs a filtered list of peptides based on the retention time Z-scores.

Created: 2014-02-06 | Last updated: 2014-02-06

Credits: Magnus Palmblad Sonja Holl

PhotoHawk - SSIM (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using SSIM metric (http://purl.org/DP/quality/measures#15).

Created: 2014-02-05

Credits: Artur Kulmukhametov

PhotoHawk - AE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using AE metric (http://purl.org/DP/quality/measures#4).

Created: 2014-02-05

Credits: Artur Kulmukhametov

PhotoHawk - MAE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using MAE metric (http://purl.org/DP/quality/measures#5).

Created: 2014-02-05

Credits: Artur Kulmukhametov

PhotoHawk - MSE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using MSE metric (http://purl.org/DP/quality/measures#6).

Created: 2014-02-05

Credits: Artur Kulmukhametov

PhotoHawk - PAE (1)

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This workflow provides a comparison result for 2 raw images based on PhotoHawk tool (http://datascience.github.io/photohawk/). The result is measured using PAE metric (http://purl.org/DP/quality/measures#7).

Created: 2014-02-05

Credits: Artur Kulmukhametov

Test interaction page in myExperiment (9)

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This workflow demonstrates the feasibility of storing interaction pages in myExperiment

Created: 2014-02-04 | Last updated: 2014-02-06

Credits: Jon Giddy

Entrez Gene to KEGG Pathway (1)

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This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Created: 2014-01-30

Credits: Alice Heliou

setp2 (1)

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Traduction test

Created: 2014-01-30 | Last updated: 2014-01-30

Credits: Alice Heliou

SimpleTest (1)

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This is a simple test workflow. It has only one node that takes an input (a string) and return a string of the form processed(input).

Created: 2014-01-28 | Last updated: 2014-01-28

Credits: Gab

Empty list output (1)

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Simply returns a single port, depth 1, with nothing in it.

Created: 2014-01-24

Credits: Robert Haines Alan Williams

Empty list output and a value (1)

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Simply returns a port, depth 1, with nothing in it and a port, depth 0, with a constant.

Created: 2014-01-24

Credits: Robert Haines Alan Williams

PDF Read (1)

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Read a PDF from a URL

Created: 2014-01-24

Credits: Robert Haines Alan Williams

P15409 (1)

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worflow to demostrate how to use Taverna with service anel or catalogue

Created: 2014-01-22

Credits: Lilly Hueber

Taverna Workflow -1 (1)

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P15409

Created: 2014-01-22

Credits: Zoe Ward

Test (1)

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A Simple work flow to gain experiance in using Tavern

Created: 2014-01-22

Credits: Gregory Prescott Anthony A Numan Uddin Joanne Stonehouse Cranfield Course - January 2014

simple fasta workflow (1)

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workflow using services

Created: 2014-01-22

Credits: Ruth Eberhardt Aleksandra Pawlik

Simple FASTA workflow (1)

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A simple Taverna workflo

Created: 2014-01-22

Credits: Aleksandra Pawlik Katy Wolstencroft Alan Williams

Test sharing 2 (1)

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bla,bla

Created: 2014-01-16

Credits: quevedo79 Francisco Quevedo

BiomartAndEMBOSSAnalysis (1)

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2014-01-14

Credits: al basyid basyid

Average solar wind speed at ACE (1)

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This routine returns the average solar wind speed from ACE data given an input time interval.

Created: 2014-01-13

Credits: Eoincar

CME froward propagation (1)

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Ballistic propagation of CME is the SHEBA propagation model. CME speed and speed error produces an estimated time of arrival at desired location.Constructed by David Perez Suarez.

Created: 2014-01-13

Credits: Eoincar

Produce time interval from single time (1)

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Produce a time interval from a single input time.

Created: 2014-01-13

Credits: Eoincar

Produce vo table from helio catalogue (Cat... (1)

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A simple query of the Helio Event Catalogue (http://msslkz.mssl.ucl.ac.uk/helio_hec/HelioTavernaService?wsdl). User can enter catalogue name, time start, time end, and an SQL condition on the query.

Created: 2014-01-13

Credits: Eoincar

Produce vo table from helio catalogue (Cat... (1)

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A simple query of the Helio Event Catalogue (http://msslkz.mssl.ucl.ac.uk/helio_hec/HelioTavernaService?wsdl). User can enter catalogue name, time start, time end, the desired parameter, parameter to order by, and limit on the search result.

Created: 2014-01-13

Credits: Eoincar

Produce vo table from helio catalogue (Cat... (1)

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A simple query of the Helio Event Catalogue (http://msslkz.mssl.ucl.ac.uk/helio_hec/HelioTavernaService?wsdl). User can enter catalogue name, time start, time end and desired paramter(s).

Created: 2014-01-13

Credits: Eoincar

Workflow of IFC data collection, crowd mod... (3)

Simulation workflow for crowd modeling in building. It combines all the components needed for crowd simulation (CAD/BIM data collection, crowd modeling, crowd simulation and 3D visualization). This version cannot be executed as is due to local tools dependancies (the components in yellow). The lattest version is available in http://www.myexperiment.org/workflows/4247.html.

Created: 2013-12-18 | Last updated: 2014-06-24

JSTWebDav3Input (3)

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Some Broken

Created: 2013-12-11 | Last updated: 2013-12-17

ONB Web Archive Fits Characterisation usin... (2)

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Hadoop based workflow for applying FITS on the files contained in ARC web archive container files and ingest the FITS output in a MongoDB using C3PO. Dependencies: - Spacip (https://github.com/shsdev/spacip) - Tomar (https://github.com/openplanets/tomar) - C3PO (https://github.com/peshkira/c3po) Parameters: - hdfs_input_path: Path to a directory which contains textfile(s) with absolute HDFS paths to ARC files - num_files_per_invokation: Number of items to be processed per invokation - fits...

Created: 2013-12-09 | Last updated: 2013-12-10

Credits: Sven

Extract_citations (3)

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Corrected XPath

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

Extract_positions (2)

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Changed output port name

Created: 2013-12-01 | Last updated: 2013-12-01

Extract_data_providers (2)

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Changed output port name

Created: 2013-12-01 | Last updated: 2013-12-01

PostgresSQL/PostGIS Database for Historians (1)

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This diagram depicts the steps that the 'Mapping the Jewish Communities of the Byzantine Empire' project took to populate the project's PostgreSQL/PostGIS database. 

Created: 2013-11-27 | Last updated: 2013-11-27

Credits: Gethin Rees

Find master regulators in networks (GeneWays) (1)

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This workflow is designed to find master regulatory molecules upstream of an input list of genes. Input file is any gene or protein table.At the first step, the input table is converted into a table with Entrez Gene IDs.At the next step the Entrez genes are annotated with additional information, gene description and gene symbols.The annotated gene table is subjected to master regulator search in the GeneWays network. For each potential master regulator, FDR, Score, and Z-score are calculated....

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze promoters (GTRD) (1)

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This workflow is designed to search for putative transcription factor binding sites, TFBS, on the promoters of an input gene set.As input, any gene or protein table can be submitted. The input table contains genes under study, and it is called “Yes” set.At the first step, the input table is converted into a table with Ensembl Gene IDs.At the next step, promoters are analyzed for potential cis-regulatory sites. Promoters in this workflow are defined as sequences from -1000 to +100 ...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence for site enrichment (1)

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This workflow is designed to reveal TFBS  enrichment in any DNA sequence.  As input, any sequence collection in FASTA, EMBL or GeneBank format can be used. Yes and No sequence sets can be specified in the corresponding input fields.  As input, DNA sequences of any organisms and from any genome regions can be taken.At the first step Yes and No sequences are subjected to Site search on track analysis using the profile of positional weight matrices specified in the input form. The...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Mapping to ontologies (Gene table) (1)

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This workflow is designed to classify an input gene set to several ontologies and to identify terms, hits for which are overrepresented in the input set. The input file can be any gene or protein table.At the first step, the input table is converted into a table with Ensembl Gene IDs.This table with Ensembl Gene Ids is subjected to functional classification, which is done in parallel by the following ontologies: GO biological processes, GO cellular components, GO molecular functions, Reactome...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Compute differentially expressed genes (1)

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This workflow is designed to identify up-regulated, down-regulated and non-changed genes for experimental data with three and more data points for each experiment and control.  As input, normalized data with any types of IDs (Ensembl, gene symbols, EMBL, RefSeq) can be submitted.In the next step, p-values for up- and down-regulated probes are calculated for all probes using the “Up and Down Identification” analysis. This analysis applies Student’s T-test for p-value cal...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

ChIP-Seq - Identify and classify target genes (1)

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This workflow identifies and classifies target genes using positional information of peaks found by ChiP-Seq approach. As input, the peak regions in BED format, can be submitted. Actually, any dataset in BED format can be submitted as input track for this workflow.First, the track file is converted into a gene set using Track to gene set analysis. The Ensembl gene list is then annotated with additional information, gene descriptions and chromosomal location.The annotated Ensembl genes are sub...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, GeneBank (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in GeneBank format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individua...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, Fasta (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in Fasta format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual w...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Analyze any DNA sequence, EMBL (1)

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This workflow is designed to analyze a DNA sequence for potential binding sites. Sequences should be in EMBL format.What is the geneXplain type?The geneXplain platform is an online toolbox for a broad range of bioinformatic and systems biology applications. It is developed by geneXplain GmbH. The technology behind the geneXplain platform is BioUML (www.biouml.org), which has been built, improved and supported for many years at the Institute of Systems Biology in Novosibirsk. The individual wo...

Created: 2013-11-13 | Last updated: 2015-04-17

Credits: geneXplain

Imagemagick convert - tiff2tiff - compression (1)

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Converts tiff to tiff using imagemagick convert with the provided compression

Created: 2013-11-08

Credits: Markus Plangg

MatchboxHadoopAPI (1)

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The workflow MatchboxHadoopApi.t2flow enables using of matchbox tool on Hadoop with Taverna. This workflow is based on Python scripts and Hadoop Streaming API included in"pythonwf" folder of pc-qa-matchbox project on github (https://github.com/openplanets/scape/tree/master/pc-qa-matchbox/hadoop/pythonwf).For this workflow we assume that digital collection is located on HDFS and we have a list of input files in format "hdfs:///user/training/collection/00000032.jp2" - one ro...

Created: 2013-11-05

Credits: Roman SCAPE

Map genes to chromosomal location for T2WEB (1)

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This workflow maps a gene list on the genome using the biomart service. IMPORTANT NOTE: Keep in mind that for uploading files on t2web, you need to wait few minutes before executing the workflow. That's essential because the file needs first to be uploaded on the server.

Created: 2013-11-04

Credits: Eleni

get promoter region + operate on genomic i... (1)

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Finds the overlap between two datasets which contain genomic information (e.g. [gene id], chromosome name, gene start, gene end), 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. NOTE: The library(GenomicRanges) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Map genes to chromosomal location (1)

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This workflow maps a gene list to the genome using the biomart service, and afterwards computes a promoter region for each gene. The user needs to define the promoter region to be computed. The direction that a gene is transcribed is being taken into account in the "compute_promoter_region_with_strand" component. The variable "strand" is responsible for that. NOTE: The library(biomaRt) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133b.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Get differentially expressed genes for Arr... (1)

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****IMPORTANT****:if libraries: library(ArrayExpress), library(hgu133a.db), library(limma) are not installed in the local R installation, then they need to be installed before running this workflow. Original data come from Hodges et. al 2006 "Regional and cellular gene expression changes in human Huntington’s disease brain" This workflow loads the two necessary files (gene expression data & phenotype data), and creates the expression set object to be used by the R package limma, to test for ...

Created: 2013-11-04

Credits: Eleni

Download data from array express + create ... (1)

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This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Created: 2013-11-04

Credits: Eleni

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

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

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

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