Workflows

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

caDSR metadata query in caGrid (1)

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This workflow shows the coordinated use of two services in CaGrid, i.e., the caDSR (Cancer Data Standards Repository) and EVS (Enterprise Vocabulary Services) services. caDSR is to define a comprehensive set of standardized metadata descriptors for cancer research terminology used in information collection and analysis. EVS provides resources and services to meet NCI needs for controlled terminology, and to facilitate the standardization of terminology and information systems across the Insti...

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

Credits: Wei Tan

Affimetrix microarray: part three (concat) (1)

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Collecting the results from the perumtation.

Created: 2008-12-05

Credits: Zhiming Zhao

Affimetrix microarray: part one (obs) (1)

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The R/MAANOVA package [1] is being adapted to carry out our computations. To enable R/MAANOVA to handle probe-sets with different probe numbers, which is necessary when using probe-set definitions other than the original one provided by Affimetrix, we will pre-process the input data by dividing it into groups, each group formed by genes reported by the same number of probes.

Created: 2008-12-05

Credits: Zhiming Zhao

Multi sequences NCBI BLAST (1)

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Run a BLAST analysis using the EBI's WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). This workflow wraps the EBI_NCBI_BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence file, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default.

Created: 2008-12-05

Credits: Whybiocc

Attributions: EBI_NCBI_BLAST EBI_NCBI_BLAST_with_prompts EBI_Blast2InterPro

Create Ugi Library 001 (1)

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Created: 2008-12-04

Credits: Jean-Claude Bradley

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 - 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

blastp using the MRS system (1)

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This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database name. Valid database names that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb". Output is returned in XML.

Created: 2008-11-28 | Last updated: 2008-11-28

Credits: Bas Vroling

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

Get ART2A classification result showing th... (1)

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This workflow load an ART2A classifcation results and creates a diagram showing the origin allocation within the different cluster or classes. This is usable for performing a chemical diversity analysis. The result is stored within an PDF which contains a diagram and a table of the classification result.

Created: 2008-11-17

Credits: Thomasku

ART2A Classification Workflow (1)

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This workflow loads a vector from a database and performs an ART2A classification. The ART2A classificator contains various options which are changeable within the stored workflow configuration file. There is no UI for these content available.

Created: 2008-11-17

Credits: Thomasku

Molecular Weight Distribution (1)

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This workflow calculates the molecular weight of molecules stored in a postgres sql database with the Pgchem::tigress chemoinformatics cardridge. The cardridge perform the molecular weight calculation. The get a moleculear weight distribution worker creates a chart of the available data.

Created: 2008-11-07

Credits: Thomasku

Analyse the Atom Typing Result (1)

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This workflow is used to analyse the result of the atom typing workflow. It creates a pdf document contains a diagram to visualise the outcome from the atom typing test to detect the for the cdk unknown atom types.

Created: 2008-11-06

Credits: Thomasku

Extract ChEBI molecules from TSV file and ... (1)

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This worklfow load a TSV file from the ChEBI database. (normally structures.tsv) After the extraction of the molecules from the TSV file all non MDL mol files are removed before the valid molecules are inserted into a database.

Created: 2008-11-06

Credits: Thomasku

Substructure Search On Database (1)

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This workflow takes as input a SMILES. This represents the substructure, for which the database gets searched. The output of this workflow is a PDF showing the 2D structures of the matched structure from the substructure search on the database.

Created: 2008-11-06

Credits: Thomasku

Extraction of atom typing problems after l... (1)

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This workflow load molecules from the database and than checks whether the perception of the atom types works or not. After the extraction of the database identifier from all molecules which caused problems during this process will the identifier be written to a file.

Created: 2008-11-05

Credits: Thomasku

Load Molecules from a database and create ... (1)

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This workflow loads molecules from a database. The 2D structure of these molecules are shown within a table of a PDF document.

Created: 2008-11-05

Credits: Thomasku

InsertMoleculesIntoDatabase (1)

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This workflow load molecules into a database. The molecules originally are stored in a MDL SD file. As workflow input an origin is added to each molecule which gets stored into the database. The output of the workflow shows logs from the database insert process.

Created: 2008-11-05

Credits: Thomasku

Iterative loading of molecules from databa... (1)

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This workflow loads molecules from a database in an iterative manner using the SQL commands LIMIT and OFFSET. After the loading each molecule goes through an atom typing perception before the Hueckel Aromaticity Detector tries to detect the aromaticity. All id of the aromatic molecules will be written wo a text file.

Created: 2008-11-03

Credits: Thomasku

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

XSL Transform (1)

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This WF downloads a web page and converts the content from HTML to XSL.

Created: 2008-10-21

Credits: Trident

NETCDFMean (1)

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This WF reads a netCDF file to a hyper cube data structure. Then this WF applies the mean transform to a variable in the netCDF file. The calculated mean is produced as part of the output.

Created: 2008-10-21

Credits: Trident

NetCDFDiff (1)

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This WF reads two netCDF files to two hyper cube data structures. Then this workflow uses the HyperCubeDiffTransform activity to perform difference operation between the values of a netCDF variable read from the two files. The WF generates a difference cube as output.

Created: 2008-10-21

Credits: Trident

If Sample (1)

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This WF is a sample which shows support of common programming constructs within Trident. The If workflow has two parts; the condition block which generates a TRUE or FALSE condition and two parallel branches for ‘If’ and ‘Else’.

Created: 2008-10-21 | Last updated: 2008-10-21

Credits: Trident