Workflows

nested_echo (2)

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Just calls the echoer

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

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

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

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

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 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 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

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

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

pubmed abstracts from pathways (1)

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Extraction of the abstracts from pubmed pubblications related to the pathways involving the input genes

Created: 2014-02-28

Credits: Massimo La Rosa Antonino Fiannaca

Attributions: NCBI Gi to Kegg Pathway Descriptions Pathway to Pubmed

ToMaR HDFS Input Directory Processing (2)

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This workflow allows processing an HDFS input directory using ToMaR. The "hdfs_working_dir" input port is the HDFS input directory which containes the data to be processed by ToMaR. The "toolspec" input port contains the toolspec XML describing operations that can be used (see "operation" input port). The "operation" input port defines the operation to be used in the current ToMaR job execution (see "toolspec" input port, an operation port used here must be defined in the tool specificatio...

Created: 2014-03-04 | Last updated: 2014-03-11

Credits: Sven

ARC2WARC Hadoop Job (1)

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Just a wrapper workflow for a Hadoop job converting ARC to WARC files.

Created: 2014-03-06

Credits: Sven

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: 2014-03-06

test_workflow (2)

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test_upload

Created: 2014-03-10 | Last updated: 2014-03-10

XPath From VOTable (1)

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A XPath From text version for VOTables. This is useful to extract certain information from the header of the VOTables but it could work for any XPath.

Created: 2014-03-12

Credits: David PS Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query

calculateCube by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method calculateCube. This calculates a 3DCube based on the paraboloid model of SINP around Earth (see http://smdc.sinp.msu.ru/index.py?nav=paraboloid/index).

Created: 2014-03-28 | Last updated: 2014-05-19

calculateDataPointValue by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method calculateDataPointValue. This method can be used to return the magnetic field (calculated by SINP PMM) in given points inside the planetary magnetosphere and in different time moments for each point.

Created: 2014-03-28 | Last updated: 2014-05-20

calculateDataPointValueMercury by SINP (6)

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Workflow for Taverna based on the IMPEx-FP7 method calculateDataPointValueMercury. This method can be used to return the magnetic field (calculated by SINP PMM) in given points inside the Hermean magnetosphere.

Created: 2014-03-28 | Last updated: 2014-05-19

Credits: Manuel Scherf

An iframe test (1)

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But this works

Created: 2014-03-28

Credits: Alan Williams

calculateCubeMercury by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method calculateCubeMercury. This method returns the magnetic field, calculated by SINP PMM, in grid points of a cube with chosen boundaries inside the Hermean magnetosphere with chosen sampling.

Created: 2014-03-31 | Last updated: 2014-05-19

getDataPointValue by FMI (3)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue. This method is used to compute values of various physical quantitites (e.g. density, magnetic field strengths etc.) for a given simulation run at a user given set of 3D points.

Created: 2014-03-31 | Last updated: 2014-05-19

getDataPointValue by LATMOS (5)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue. This is a generic method which can be used to return parameters for 0D, 1D, 2D, or 3D.

Created: 2014-03-31 | Last updated: 2014-05-19

getDataPointValue_Spacecraft by FMI (3)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue_Spacecraft. This method is used to compute values of various physical quantities (e.g. density, magnetic field strength etc.) along the path of a given spacecraft.

Created: 2014-03-31 | Last updated: 2014-05-20

getDataPointValue_Spacecraft by LATMOS (4)

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Workflow for Taverna based on the IMPEx-FP7 method getDataPointValue_Spacecraft. This method is used to compute values of various physical quantities (e.g. density, magnetic field strength etc.) along the path of a given spacecraft.

Created: 2014-03-31 | Last updated: 2014-05-19

getFieldline by FMI (3)

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Workflow for Taverna based on the IMPEx-FP7 method getFieldLine. This method computes field lines or stream lines inside the simulation box. The user will provide a set of 3D position coordinates which act as starting points for the field/stream line tracing. The tracing may be performed forwards, backwards or both. The method will return an URL to a VOTable file which contains the field/stream lines as a set of 3D position coordinates and the requested physical quantities at these points.

Created: 2014-03-31 | Last updated: 2014-05-19

getFieldline by LATMOS (3)

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Workflow for Taverna based on the IMPEx-FP7 method getFieldLine. This method computes field lines or stream lines inside the simulation box. The user will provide a set of 3D position coordinates which act as starting points for the field/stream line tracing. The tracing may be performed forwards, backwards or both. The method will return an URL to a VOTable file which contains the field/stream lines as a set of 3D position coordinates and the requested physical quantities at these points.

Created: 2014-03-31 | Last updated: 2014-05-20

getFileUrl by LATMOS (5)

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Workflow for Taverna based on the IMPEx-FP7 method getFileURL. This method fetches precomputed data, i.e. already calculated values along a given spacecraft trajectory.

Created: 2014-03-31 | Last updated: 2014-05-19

getMostRelevantRun by FMI (3)

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Workflow for Taverna based on the IMPEx-FP7 method getMostRelevantRun. This method is intended to help users to find those simulation runs in SMDB's tree.xml file whose input parameters best match the given solar wind conditions. For each simulation run in the tree.xml file the method computes a 'difference index'. This 'difference index' is a sum of individual difference indices (one for each solar wind parameter defined in the input parameter set).

Created: 2014-03-31 | Last updated: 2014-05-19

calculateDataPointValue by SINP (3)

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Workflow for Taverna based on the IMPEx-FP7 method calculateDataPointValue. This method can be used to return the magnetic field (calculated by SINP PMM) in given points inside the planetary magnetosphere and in different time moments for each point.

Created: 2014-03-31 | Last updated: 2014-05-19

calculateFieldline by SINP (5)

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Workflow for Taverna based on the IMPEx-FP7 method calculateFieldLine. This method can be used to return the field lines (calculated by SINP PMM), which start in given points inside the planetary magnetosphere and in different time moments for each point, and the magnetic field along these lines.

Created: 2014-03-31 | Last updated: 2014-05-19

Photohawk SSIM tiff/png/jpeg (4)

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SCAPE QA Object Component. Compares tiff/png/jpeg images using Photohawk SSIM.

Created: 2014-04-01 | Last updated: 2014-10-30

Demonstration of configurable iteration (2)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2014-04-03 | Last updated: 2014-07-09

Credits: Alex Nenadic

EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

Created: 2014-04-03 | Last updated: 2014-04-09

Credits: Alex Nenadic

Example for external tools with zip and unzip (1)

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This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

Created: 2014-04-03

Credits: Alex Nenadic

Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2014-04-03

Credits: Alex Nenadic

Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2014-04-03

Credits: Alex Nenadic

Example workflow for REST and XPath activi... (1)

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This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...

Created: 2014-04-03

Credits: Alex Nenadic

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2014-04-03

Credits: Alex Nenadic

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: 2014-04-03

Credits: Alex Nenadic

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2014-04-03

Credits: Alex Nenadic

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: 2014-04-03

Credits: Alex Nenadic

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: 2014-04-03

Credits: Alex Nenadic

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2014-04-03

Credits: Alex Nenadic

Numerically adding two values. (1)

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This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2014-04-03

Credits: Alex Nenadic

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2014-04-03

Credits: Alex Nenadic

Render gene via BioGPS (1)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2014-04-03

Credits: Alex Nenadic

Secure REST service call example (1)

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This is an example of a workflow that contains a call to a secure REST service that requires user to authenticate with HTTP Basic Authentication. You can use testuser/testpasswd as username and password for authentication when running the workflow.

Created: 2014-04-03

Credits: Alex Nenadic