Workflows in this Topic

1 (2)

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Trivial workflow which will initially fail, retry twice then fall over to the alternative specified for the FailingThing process.

Created: 2007-11-06 | Last updated: 2007-11-20

Credits: Antoon Goderis Carole Goble A. Random Scientist try it out

Attributions:

Success-Abandonment-Classification (3)

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Retrieves data from FLOSSmole and from the Notre Dame SourceForge repository to compute project statistics based on releases, downloads and project lifespan. Project statistics are then used to classify projects according to the criteria set up in English & Schweik, but comparison criteria are parameterized so that a different set of criterion thresholds can be used to evaluate the project characteristics.

Created: 2008-02-06 | Last updated: 2008-07-02

Credits: Andrea Wiggins James Howison

FLOSS Communication Centralization Plot, E... (4)

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The analysis in this workflow represents the basis of the analysis in our paper, Social dynamics of FLOSS team communication across channels. This workflow uses WSDL components to select periodized data from the FLOSSmole database and generate sociomatrices. The workflow parses the threaded list structure into a communication network based on reply-to relationships. In the analysis process, an edge weighting is applied so that older messages receive less weight using an exponential decay fun...

Created: 2009-02-07

Credits: Andrea Wiggins Crowston James Howison

FLOSS Communication Centralization Plot, U... (2)

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The analysis in this workflow represents the basis of the analysis in our paper, Social dynamics of FLOSS team communication across channels. This workflow uses WSDL components to select periodized data from the FLOSSmole database and generate sociomatrices. The workflow parses the threaded list structure into a communication network based on reply-to relationships. In the analysis process, an unit weighting is applied to the edges. The weighted sociomatrices are then dichotomized according ...

Created: 2009-02-07

Credits: Andrea Wiggins Crowston James Howison

feat (3)

This is an attempt to implement the feat application from the fsl fMRI package www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html into a Scufl workflow. Details are still being polished but the general structure is here. The main problem that we have with such workflows concerns data provenance. Each of the services is typically iterated on hundreds of data sets and keeping track of the produced files is a pain.

Created: 2008-03-18 | Last updated: 2008-05-19

Credits: Glatard

Fetch today's xkcd comic (1)

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.  I just uploaded this example so I can play around with the myexperiment api.

Created: 2008-05-05 | Last updated: 2008-05-05

Credits: Alan Williams

Attributions: Fetch today's xkcd comic

getUPIForSequence workflow (2)

Given a sequence retrieve the UPI (UniProt Archive (UniParc)) identifier.

Created: 2008-06-06 | Last updated: 2008-06-06

Credits: Franck Tanoh

countryExammple_unfinished (1)

This Workflow is unfinished, but when connected up, it will allow you to find a list of the cities in a particular country, the time zone that country is in, the conversion rate of that country and yours and the international dialling code for that country

Created: 2008-06-16

Credits: Katy Wolstencroft

countryExample_working (1)

This Workflow allows you to find a list of the cities in a particular country, the time zone that country is in, the conversion rate of the currency in that country and yours and the international dialling code for that country

Created: 2008-06-16

Credits: Katy Wolstencroft

parse_uniprot_2.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

sub_gene_info_to_uniprot.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

remove_duplicates.xml (1)

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No description

Created: 2008-07-12 | Last updated: 2008-07-12

Credits: Paul Fisher

Data Set Metadata Generator (1)

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This workflow generates ePrints XML import files with data set metadata for the FLOSSmole project. It reads in an input file generated from a Notre Dame SourceForge dump SQL query and uses regular expressions to parse the filename for the data set's source repository, download URL, and basic description. It also translates the epoch date into a sql format suitable for import, and the file size from bytes into larger units, e.g. GB, MB, etc. These data are inserted into an XML eprint record te...

Created: 2008-08-19 | Last updated: 2008-08-19

Credits: Andrea Wiggins

bget (1)

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Retrieve database entries specified by a list of entry_id. Number of entry_id retrieves at a time is restricted up to 100 Example of input: eco:b0002 hin:tRNA-Cys-1

Created: 2008-09-29

Credits: Franck Tanoh

Sample grid workflow (1)

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This is a sample workflow submitting jobs to the EGEE grid using the Generic Application Service Wrapper (GASW). The job submission service has to be installed locally.

Created: 2008-10-24 | Last updated: 2008-10-31

Credits: Glatard

firstwf (1)

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No description

Created: 2008-11-13

Credits: Rory

GWorkflowDL: Simple Test Workflow (1)

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This is a trivial test workflow modeled using the Grid Workflow Description Language (GWorkflowDL), which can be executed by means of the Grid Workflow Execution Service (GWES).

Created: 2008-11-25

Credits: Andreas Hoheisel

GWorkflowDL: Generic execution of programs (1)

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This workflow is an example of the execution of an arbitrary command line program. This workflow transfers a tar.gz package containing the linux program "date" to a free Grid resource, unpacks, and executes it. After execution the URL to the file with the standard output is available on "stdout", the standard error on "stderr".

Created: 2008-11-25 | Last updated: 2008-11-25

Credits: Andreas Hoheisel

Make 28 CPUh load on the Grid (1)

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This workflow makes 28 CPU hours load on a Grid. Therefore it calls 100 times (represented by 100 input tokens) the program "makeload", which makes 1000 Seconds load each. The processing is done recurrent, so you can use this workflow to benchmark the speedup of your Grid environment, or just to heat up your computer center... This workflow also serves as an example of a typical parameter study modeled with GWorkflowDL. Of cause this workflow can only be invoked with a X509 certif...

Created: 2008-11-25 | Last updated: 2008-12-17

Credits: Andreas Hoheisel

AUGUSTUS Workflow for predicting genes in ... (1)

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AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences. Currently, it has been trained to predict genes in human, Drosophila melagonaster, Arabidopsis thaliana, Brugia malayi, Aedes aegypti, Coprinus cinereus, Tribolium castaneum, Schistosoma mansoni, Tetrahymena thermophila, Galdieria sulphuraria and Zea mays. In addition the species parameters of the following species are a courtesy of Jason Stajich: Caenorhabditis elegans, Saccharomyces cerevisiae, Ustilago ma...

Created: 2008-11-25 | Last updated: 2008-12-05

Credits: MediGRID

Workflow Pattern - Structured Loop (2)

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This workflow is a GWorkflowDL representation of a structured loop that updates the variable "x" in each iteration. This workflow is equivalent to the following pseudo code: x:=0; for ( i:=0; i<=99; i++) { x:=x+i; } x_result:=x; Please remark that this demonstration workflow does not invoke any external services at all. The calculation is done only by using the GWorkflowDL's syntax and semantics.

Created: 2008-12-09

Credits: Andreas Hoheisel

Workflow Pattern - Structured Loop (B) (2)

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This workflow is an alternative GWorkflowDL representation of a structured loop that updates the variable "x" in each iteration and which models the control flow separately from the index "i". Here a version of the graph with manual graph layout: This workflow is equivalent to the following pseudo code: x:=0; for ( i:=0; i<=99; i++) { x:=x+i; } x_result:=x; Please remark that this demonstration workflow does not invoke any external services at all. The c...

Created: 2008-12-09

Credits: Andreas Hoheisel

Attributions: Workflow Pattern - Structured Loop

Workflow Pattern - Structured Loop (C) (2)

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This workflow is a GWorkflowDL representation of a structured loop that counts from 0 to 99.   This workflow is equivalent to the following pseudo code: for ( i:=0; i Please remark that this demonstration workflow does not invoke any external services at all.

Created: 2008-12-09

Credits: Andreas Hoheisel

Attributions: Workflow Pattern - Structured Loop (B)

Workflow Pattern - Sequence (1)

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This workflow is a GWorkflowDL representation of a sequence that sequentially invokes A and B. This workflow is equivalent to the following pseudo code: end_A = A(); end_B = B(end_A);

Created: 2008-12-03

Credits: Andreas Hoheisel

Workflow Pattern - Parallel Split (AND-Split) (1)

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This workflow is a GWorkflowDL representation of a parallel split that invokes A and B recurrently without synchronization. This workflow is equivalent to the following pseudo code: new Thread( end_A = A() ); new Thread( end_B = B() );

Created: 2008-12-03 | Last updated: 2008-12-03

Credits: Andreas Hoheisel

Workflow Pattern - Synchronization (AND-Join) (2)

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This workflow is a GWorkflowDL representation of a synchronization (AND Join) that waits until A and B finish their execution. This workflow is equivalent to the following pseudo code: threadA = new Thread( end_A = A() ); threadB = new Thread( end_B = B() ); threadA.join(); threadB.join();

Created: 2009-01-19

Credits: Andreas Hoheisel

Workflow Pattern - Exclusive Choice (XOR-S... (2)

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This workflow is a GWorkflowDL representation of an exclusive choice (XOR Split) that invokes either A or B. This workflow is equivalent to the following pseudo code: x = XOR_Split; if (x=="true") { end_A = A(x); } else { end_B = B(x); }

Created: 2008-12-09

Credits: Andreas Hoheisel

Workflow Pattern - Simple Merge (XOR-Join) (1)

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This workflow is a GWorkflowDL representation of a simple merge (XOR Join) that invokes C when either A or B has been invoked. The structure of the GWorkflowDL representation of a simple merge is identical to the multi merge pattern!

Created: 2008-12-03 | Last updated: 2009-01-19

Credits: Andreas Hoheisel

Workflow Pattern - Multi Choice (OR Split) (2)

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This workflow is a GWorkflowDL representation of a multi choice (OR Split) that invokes either A or B or A and B.

Created: 2008-12-09

Credits: Andreas Hoheisel

TextGrid: Test workflow (2)

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This is a first test workflow that demonstrate, how to use the GWES for a document-style Web Service within TextGrid.

Created: 2008-12-17

Credits: Andreas Hoheisel

TextGrid: Test workflow (on ingrid) (1)

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Test workflow that invokes CRUD read on ingrid.

Created: 2008-12-17

Credits: Andreas Hoheisel

Workflow Pattern - Structured Synchronizin... (2)

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This workflow is a GWorkflowDL representation of a structured synchronizing merge that invokes either A or B or A and B and merges to one branch afterwards.

Created: 2009-01-19

Credits: Andreas Hoheisel

Workflow Pattern - Multi Merge (2)

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This workflow is a GWorkflowDL representation of a multi merge that invokes C after each invocation of A or B.

Created: 2009-01-19 | Last updated: 2009-01-19

Credits: Andreas Hoheisel

Workflow Pattern - Structured Discriminator (2)

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This workflow is a GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored. This is only one out of various possibilities to model this workflow pattern. Notice alternative representation of this pattern at http://www.myexperiment.org/workflows/632

Created: 2009-01-19 | Last updated: 2009-01-19

Credits: Andreas Hoheisel

Workflow Pattern - Cancelling Discriminator (1)

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This workflow is a GWorkflowDL representation of a cancelling discriminator that cancels the invocation of B if A has been executed and vice versa. This is only one out of various possibilities to model this workflow pattern. Please regard that this workflow example uses a separate method for cancelling the invocation of the activity. This is very useful if the invocation of the activity is done asynchronously as it is often implemented for long running methods. It may be necessary to propag...

Created: 2009-01-06

Credits: Andreas Hoheisel

Workflow Pattern - Structured Partial Join (1)

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This workflow is a GWorkflowDL representation of a structured partial join (N-out-of-M join) that invokes D after N=2 invocations of A or B or C (M=3). All next (M-N) invocations of A or B or C are ignored. This is only one out of various possibilities to model this workflow pattern.

Created: 2009-01-06

Credits: Andreas Hoheisel

Workflow Pattern - Structured Discriminato... (1)

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This workflow is an alternative GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored. The pattern is resets if both, A and B have been invoked. Please note that the transitions "C", "ignore", and "release" have different priorities (not shown in the graph) that make the net deterministic (except the occurrence of "A" and &q...

Created: 2009-01-19 | Last updated: 2009-01-20

Credits: Andreas Hoheisel

Workflow Pattern - Blocking Discriminator ... (1)

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This workflow is a GWorkflowDL representation of a blocking discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored and the AND transition is blocked. The pattern is resets if both, A and B have been invoked. Then the next token on "begin" can be processed. Please note that the transitions "C", "ignore", and "release" have different priorities (represented by p0, p1, an...

Created: 2009-01-20

Credits: Andreas Hoheisel

Workflow Pattern - Structured Discriminato... (1)

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This workflow is an alternative GWorkflowDL representation of a structured discriminator (1-out-of-M Join) that invokes C after the first invocation of A or B (M=2). All next (M-1) invocations of A or B are ignored for the same data group. Other tokens on the place "begin" can be processed recurrently if they belong to another data group. Please note that the transitions "C" and "ignore" have different priorities (not shown in the graph) that make the net determ...

Created: 2009-01-20

Credits: Andreas Hoheisel

feat_workflow (2)

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No description

Created: 2009-02-03

Credits: Glatard

MediGRID FEAT Workflow (1)

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This workflow is a translation of the VLeMed workflow to the GWorkflowDL format, which is used in MediGRID. The translation of the "cross product" iteration strategy is currrently under work and not yet finished. So this workflow only varies the parameters p1, p2, and p3.

Created: 2009-02-13

Credits: Andreas Hoheisel

Attributions: feat_workflow

caviar cardiac application (1)

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Applications details in the following paper: Ketan Maheshwari, Tristan Glatard, Joel Schaerer, Bertrand Delhay, Sorina Camarasu, Patrick Clarysse, Johan Montagnat. "Towards Production-level Cardiac Image Analysis with Grids" in Proceedings of the HealthGrid'09, Berlin, 28-30 june 2009 The 3 green boxes are run on the EGEE grid. Addional Beanshells have been added to transfer results from EGEE Storage Elements to a web server, to allow for better interactivity.

Created: 2009-05-23 | Last updated: 2009-05-23

Credits: Glatard

GATE Monte-Carlo simulations (3)

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Application description is found in the following papers: Jan S et al, GATE: a simulation toolkit for PET and SPECT. Phys. Med. Biol. 49 (2004) 4543-4561 Sarrut D. and Guigues L. Region-oriented CT image representation for reducing computing time of Monte Carlo simulations. Med Phys. 35(4):1452-1463. 2008 Two components (fgate and merge, merge being disabled in experiments conducted for the heteropar and JGC papers) are run on the EGEE grid. A quite elaborated workflow is ma...

Created: 2009-05-23 | Last updated: 2009-08-13

Credits: Glatard

Execute GWorkflowDL workflow using Taverna 2 (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench.

Created: 2009-06-30 | Last updated: 2009-06-30

Credits: Andreas Hoheisel

Execute GWorkflowDL workflow using Taverna... (1)

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This workflow makes use of the "Grid Workflow Execution Service" (GWES) in order to exececute a GWorkflowDL workflow by means of the Taverna Workbench 2. As the GWES is deployed as a regular SOAP service, the WSDL can be imported as a normal service into the Taverna Workbench. This workflow contains all the input parameters as string constants, so it can be started right away without user inputs.

Created: 2009-06-30

Credits: Andreas Hoheisel

Attributions: Execute GWorkflowDL workflow using Taverna 2

DPAS general query with sorted field (1)

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same as DPAS general query. Calling the DPAS sortedQuery web service. additional input: partialSorting input boolean true or false false all result entries are sorted by start measurementTime true each request is sorted by measurement time; no overall time order, but queries stay in the order they there asked.

Created: 2010-04-19 | Last updated: 2010-04-19

Credits: Anja Le Blanc

EBI_InterProScan for Taverna 2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2010-07-08 | Last updated: 2010-07-08

Credits: Benb

FIELD-II ultrasound simulation (1)

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Workflow implementing ultrasound simulation using FIELD-II http://server.electro.dtu.dk/personal/jaj/field/. Developped by the Virtual Imaging Platform (http://www.creatis.insa-lyon.fr/vip).

Created: 2011-04-18

Credits: Glatard

Computed Tomography with Sindbad (1)

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This workflow implements computed tomography (CT) simulation with the Sindbad software. It is developped by the Virtual Imaging Platform (http://www.creatis.insa-lyon.fr/vip).

Created: 2011-04-18 | Last updated: 2011-04-18

Credits: Glatard

Positron Emission Tomography simulation wi... (1)

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This workflow implements Positron Emission Tomography simulation with PET-Sorteo http://sorteo.cermep.fr/. It is developped by the Virtual Imaging Platform (http://www.creatis.insa-lyon.fr/vip).

Created: 2011-04-18 | Last updated: 2011-04-18

Credits: Glatard

Magnetic Resonance Image simulation with S... (1)

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Created: 2011-04-18 | Last updated: 2011-04-18

Credits: Glatard

[untitled] (1)

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This is simly a test fortest

Created: 2011-06-19 | Last updated: 2011-06-19

Credits: Merdmann

Population Plot with R (1)

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This script pulls the population of every country and creates a plot of them. This is based on the script at http://www.myexperiment.org/workflows/1728.html , with a few modifications for labelling axes and the title.

Created: 2011-10-08

Credits: Atminer

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: 2012-01-03 | Last updated: 2014-03-03

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: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

Attributions: Hello World

WCP-04 Exclusive choice - if/else branching (1)

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The choice of executing choiceA or choiceB is determined by using String_List_Intersection and String_List_Difference. If in="true" then the intersection will yield a non-empty list, triggering execution of choiceA. This list will however not differ from the input, and so choiceB will iterate over an empty list (ie. not execute). Note how using 'difference' for the else-case here means that if you run the workflow with in="bob", choiceB would still run. Some early if/el...

Created: 2012-02-20 | Last updated: 2012-02-20

Credits: Stian Soiland-Reyes

Attributions: Example of a conditional execution workflow Example of conditional invocation