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

COVE Workflow (1)

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This workflow reads data from a netCDF file and sends out a message to COVE (collaborative ocean visualization environment). COVE reads the netCDF data and renders that.  

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

Credits: Trident

Ugi Reactions in Eppendorf tubes (1)

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Created: 2008-10-21

Credits: Danius Michaelides UsefulChem

Isolating the free amines of Ugi products ... (1)

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

Credits: Danius Michaelides UsefulChem

Astronomic Observation conditionals example (1)

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Created: 2008-10-13 | Last updated: 2008-10-13

Credits: Trident

get_elements_by_pathway (1)

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Retrieve all objects on specified pathway get_elements_by_pathway Input example: path:bsu00010

Created: 2008-10-08

Credits: Franck Tanoh

get_element_relations_by_pathway (1)

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Retrieve all objects and relations on specified pathway Input example: path:bsu00010

Created: 2008-10-08

Credits: Franck Tanoh

Cove_NetCDF_visualization (1)

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The Cove workflow reads oceanographic NetCDF data, does a simple processing step, writes the data out, then sends a web service message to the COVE visualization tool. It is a four step, sequential workflow.

Created: 2008-10-08 | Last updated: 2008-10-08

Credits: Trident

get_drugs_by_pathways (1)

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Retrieves all drugs on the specified pathway. input example: path:map07025 ; path:eco00020

Created: 2008-10-07

Credits: Franck Tanoh

color_pathway_by_elements (2)

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Color the objects (rectangles and circles on a pathway map) corresponding to the given 'element_id_list' with the specified colors and return the URL of the colored image. Example of inputs: pathway_id: path:bsu00010 element_list: (to add as list) 78 79 fg_color_list:(to add as list) red blue bg_color_list: (to add as list) green yellow

Created: 2008-09-30 | Last updated: 2008-10-01

Credits: Franck Tanoh

Extract elements from a list - single elem... (1)

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The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 2 and the toIndex is 3, so the service outputs the single element list ['c'].

Created: 2008-09-29

Credits: Alan Williams

Extract elements from a list - full extrac... (1)

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The extract_elements_from_a_list is passed the list ['a','b','c','d','e']. The fromIndex is 0 and the toIndex is 5, so the service outputs an identical list.

Created: 2008-09-29

Credits: Alan Williams

Test always fails - no parameters (1)

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The test always fails service generates a service failure when no parameter values are supplied.

Created: 2008-09-27

Credits: Alan Williams

Reverse complement DNA (1)

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The Reverse Complement DNA service takes the DNA sequence, here defaulted to 'gatcctccat' and outputs the corresponding reverse complement sequence, in this example, 'atggaggatc'.

Created: 2008-09-27

Credits: Alan Williams

Read GenBank file (1)

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The Get_web_page_from_URL downloads a file from myExperiment that contains GenBank data. That data is then saved to a temporary file generated by the create_and_populate_temporary_file beanshell. The path to the temporary file is then passed to the Read_GenBank_file service. That service reads the file and converts the GenBank data into Agave format. The result is then sent to the workflow's out port.

Created: 2008-09-27

Credits: Alan Williams

Fail if false - false value (1)

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The fail if true service throws an exception if given the value 'false'.

Created: 2008-09-27

Credits: Alan Williams

Encode byte[] to base64 (1)

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The encode byte[] to base 64 service encodes the bytes representing (in the local character set) 'hello'.

Created: 2008-09-27

Credits: Alan Williams

dbfetch tutorial (1)

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This workflow eases entry in the world of Taverna with one of the key tasks - the retrieval of plain data. The dbfetch offers sequence and structure data from a large variety of sources. A first execution of this workflow informs about these in the "getSupportedDBs" output. Also the formats and styles are listed. The two inputs allow for the specification of a query that leaves the format with "default" (which is different for every database, "native" would be a better fit), the style is alw...

Created: 2008-09-22

Credits: Steffen Möller

What's On Next (1)

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Queries the BBC to find out what's on next for a particular channel.

Created: 2008-08-28 | Last updated: 2008-08-28

Credits: Sean Bechhofer

BLASTP with simplified results returned (1)

Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers.

Created: 2008-07-22 | Last updated: 2008-07-22

Credits: Franck Tanoh

simple_xcms_pipeline (1)

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A (very) simple demo pipeline that takes an experiment ID, gets the data from the (currently in beta) metware metabolomics datawarehouse and runs XCMS.

Created: 2008-07-14 | Last updated: 2008-07-14

Credits: Markf

metabolic_pathway.xml (1)

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A list of Kegg entires are supplied to the Kegg database which then retrieves the associated metabolic pathways for each entry supplied. e.g. Ids takes in a value of 351, whilst abbr takes in a value of hsa. Thus hsa:351 corresponds to neurodegenerative disorders and alzheimers disease pathways. [fisherp@cs.man.ac.uk]

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

Credits: Paul Fisher

EBI_CiteXplore (1)

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Perform a literature search using the EBI's CiteXplore service (http://www.ebi.ac.uk/citexplore/), and get the results in a minimal XML format containing the citation information (i.e. title, author, journal, etc.), the identifier of the citation in the source database (PubMed/Medline, Agricola, Patent Abstracts, CBA, CiteSeer, etc.) and information about abstract and full article availablity including URLs.

Created: 2008-07-09

Credits: Hamish McWilliam

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

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

EBI_ScanPS (1)

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Perform a Smith-Waterman sequence similarity search using the ScanPS tool (see http://www.compbio.dundee.ac.uk/Software/Scanps/scanps.html). In the case the EBI's WSScanPS web service (see http://www.ebi.ac.uk/Tools/webservices/services/scanps) is used to run the tool. Note: the WSScanPS service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.  

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: Hamish McWilliam

GlobPlotExample (1)

This is a sample for how to get the new GlobPlot native disorder and globularity prediction webservice working. At the moment it seems you need all the parameters - even the optional ones filled in, to work in taverna.

Created: 2008-04-30 | Last updated: 2008-04-30

Credits: Niall Haslam

Html output test (1)

Workflow for testing the html rendering on myExperiment

Created: 2008-03-04 | Last updated: 2008-09-08

Credits: David Withers

AmrPlusPlus Paired Workflow (9)

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Created: 2016-08-05 | Last updated: 2016-11-18

Credits: Chris

Use Case B, KNIME workflow (1)

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Workflow used to obtain data for the research paper ‘The application of the Open Pharmacological Concepts Triple Store (Open PHACTS) to support Drug Discovery Research’, PLoS One. 2014 Dec 18; 9(12):e115460. PMID: 25522365; authored by Joseline Ratnam, Barbara Zdrazil, Daniela Digles, Cuadrado-Rodriguez E, et al. This workflow can be used to retrieve data and perform the analysis described in use case BRequirements:- Knime v2.9- Open PHACTS Knime nodes version 1.0.0 (DON'...

Created: 2014-11-20 | Last updated: 2015-11-03

Credits: Barbara Zdrazil Emiliano Cuadrado Daniela Digles Lars Richter Open PHACTS

Indigo-pains-recursive (2)

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*** Update 20151130 - using KNIME 3 nodes and the 'RDKit' version of PAINS queries ***The old Indigo library (1.1.13) could not take advantage of the parallelizing nodes in KNIME the way the RDKit library could. One way to speed up the PAINS workflow when using the Indigo library was to use a recursive loop that constantly shrank the list of structures being presented to the next PAINS query as structures were knocked out of the main list.Using the WEHI-10k reference set (embedded in ...

Created: 2013-08-13 | Last updated: 2015-12-01

Credits: sauberns

Attributions: Indigo-pains RDKit-pains-parallel

Uczenie z macierza kosztow (1)

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Przeplyw pokazuje wykorzystanie operatora MetaCost, umozliwiajacego wprowadzenie macierzy kosztow do procesu uczenia klasyfikatora na przykladzie naiwnego klasyfikatora Bayesa.

Created: 2011-05-25 | Last updated: 2014-03-23

Algorytmy k-Means i k-Medoids (1)

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Przeplyw pokazuje zastosowanie algorytmow k-Means i k-Medoids do przeprowadzenia analizy skupien. Analizie podlega zbiór danych Iris, przy czym oryginalne dane zostaly przetransformowane z przestrzeni 4-wymiarowej do przestrzeni 2-wymiarowej za pomoca operatora Singular Value Decomposition. Redukcja liczby wymiarow ma na celu uproszczenie wizualizacji wynikowych modeli.

Created: 2011-05-11 | Last updated: 2013-08-19

Odkrywanie regul asocjacyjnych za pomoca a... (1)

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Workflow pokazuje sposób wykorzystania operatorow Apriori i PredictiveApriori (z narzedzia Weka) do odkrywania regul‚ asocjacyjnych. Operator Set Role zostal wykorzystany do tego, aby atrybut Play (który w oryginale jest zmienna celu) byl potraktowany jak zwyczajny atrybut.

Created: 2011-03-31 | Last updated: 2013-05-30

BiomartAndEMBOSSDisease (4)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions with mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned. 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: 2011-01-27 | Last updated: 2012-09-04

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

EMBL-EBI ClustalW2 (SOAP) (1)

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Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).

Created: 2010-12-06 | Last updated: 2013-03-28

Attributions: EBI_ClustalW2

A Basic example R workflow (3)

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This workflow uses an R service running on localhost to calculate sin(0.45)

Created: 2010-11-26 | Last updated: 2014-08-20

Credits: Alan Williams

genePattern data preprocessing (2)

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preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the default preprocess data set using genePattern preProces service, the input should be in genePattern STATML format.preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the string constants.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: Wei Tan

Keyword search against chEMBL (1)

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Created: 2010-03-24

Credits: Annsofie Anderssson

KEGG pathway analysis (1)

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The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et al., 2010), described in the KEGG API available at: http://www.genome.jp/kegg/docs/keggapi...

Created: 2010-03-19

Credits: Baywatch Solutions

Kegg pathway diagrams (missing part 3) (2)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram. Colour all enzyme boxes with colours specified. This workflow still has one problem. The list of colours have to be specified. I would like ideally to only except one background and one foreground colour and expand that to a list with length equivalent to the number of enzymes found - just duplicating the specified colours. However with almost no Taverna documentation to speak of, none of...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Gregg Iceton

Retrieve Genome Seqn using gi nos (1)

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Retrieves the genome seqn for both the target and source strains using gi nos

Created: 2010-03-19

Credits: Ian Laycock nclteamc

Extract proteins from xml blast results (1)

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The workflow extracts a list of proteins from the target genome that may be known drugs using the blast similarity results.

Created: 2010-03-19

Credits: Ian Laycock nclteamc

Parse unique proteins from Blast file (1)

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The workflow parses uses the blast results to determine the unique proteins found in the target genome that have no similairty to the source genome. Using these unique protein ids, and the original target protein fasta file, a fasta file of unique proteins is created.

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Ian Laycock nclteamc

Extract proteins using a gi - output as fa... (1)

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The workflow uses the gi id to retrieve a xml format of the genbank entry. Using a beanscript, the workflow then parses the required data for the creation of the protein fasta file.

Created: 2010-03-19

Credits: Ian Laycock nclteamc

KEGG Pathway Analysis (1)

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The KEGG pathway analysis of the workflow takes a list of UniProt accession numbers in any of the following formats with the following prefixes: External database Database prefix ----------------- --------------- NCBI GI ncbi-gi: NCBI GeneID ncbi-geneid: GenBank genbank: UniGene unigene: UniProt uniprot: It performs this using the web service bconv, provided by the KEGG database (Kanehisa et a...

Created: 2010-03-19

Credits: Baywatch Solutions

Run MGCAT for Global Sequence Comparison (1)

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Runs the M-GCAT tool for Global Sequence Comparison. M-GCAT: http://alggen.lsi.upc.es/recerca/align/mgcat/ intro-mgcat.html

Created: 2010-03-19

Credits: Baywatch Solutions

Invocation of Gene Pattern modules using R (1)

 A workflow to invoke a Gene Pattern module using an R script. Note that a FTP URL for the data to be analysed is required, not the data itself!

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: Peter Li

Visualise KDA output data with Cytoscape (2)

This workflow retrieves a data file on a web server directory and launches Cytoscape to visualise it.

Created: 2010-03-18 | Last updated: 2010-03-18

Credits: Peter Li

Convert to KEGG ID (1)

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Convert another database ID to a KEGG ID. Valid namespaces are NCBI_gi, GebBank, UniProt, UniGene, PMID or OMIM.

Created: 2010-03-17 | Last updated: 2010-03-17

Credits: White duncan100

Log out from Alitora system (1)

A nested workflow to be used for logging out of Alitora

Created: 2010-03-17 | Last updated: 2010-03-17

Credits: Peter Li

Log into Alitora system (1)

A nested workflow to be used for logging into Alitora

Created: 2010-03-17

Credits: Peter Li

Split multi-sequence FASTA file into list (1)

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Splits a flat file containing multiple fasta sequences into a list of fasta sequences.

Created: 2010-03-16

SPARQL query for QSAR data (1)

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Created: 2010-03-16

Credits: Annsofie Anderssson

Cross-references search, duplicated genes ... (1)

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This workflow is composed of 3 steps: -First, it search for Ensembl gene Ids matching a list of identifier, using the GenOuest Xref webservice. -Then it uses the Duplicated Genes Database webservice to search for duplication information about each found gene. -Finally, it uses the GenOuest Xref webservice to fetch external identifier for each found gene (GO term in this example).

Created: 2010-03-16 | Last updated: 2010-03-16

Credits: abretaud

Calculating frequencies of gene expression... (1)

This workflow retrieves data from the MaxD microarray database and calculates the frequencies of gene expression levels using an R script

Created: 2010-03-15

Credits: Peter Li

Kegg pathway diagrams (1)

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Find pathways in which all the genes in the list are involved. For each pathway draw the pathway diagram.for each protein draw a diagram of the Kegg pathway that its protein is involved in and where available visualise the structures

Created: 2010-03-13

Credits: Jannetta

M_Fetch_e-T_phylo_boot - (BETA) (1)

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This workflow performs a generic protein sequence analysis. In order to do that a novel protein sequence enters into the software along with a list of known protein identifiers chosen by the biologist to perform a homology search, followed by a multiple sequence alignment and finally a phylogenetic analysis.

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: Achille Zappa Hamish McWilliam

Get locations from postcode (1)

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 This workflow will return all the areas that correspond to a postcode. Enter the first part of the postcode only, e.g. SW19

Created: 2010-03-08 | Last updated: 2010-03-08

Credits: Rory

Rdfise Riken SciNes Database Repository [m... (1)

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This workflow rdfise Riken SciNes Database Repository available at https://database.riken.jp/sw/links/en/crib151s2i/. There is a bug with main page listing databases: version 2p and 3p are similar to 1p.

Created: 2010-02-01 | Last updated: 2010-02-01

Credits: Francois Belleau

Search CABRI human and animal cell lines c... (1)

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This workflow takes the cell line name and the catalogue(s) name(s) as input and retrieve the full cell line description(s) by first retrieving the cell lines' unique IDs associated with the input (done via a call to the getCellLineIdsByName web service) and then using IDs for retrieving the full cell lines descriptions (done via a call to the getCellLinesByIds web service).

Created: 2010-01-15 | Last updated: 2010-01-15

Credits: Achille Zappa

Retrieve full descriptions of bacteria str... (1)

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This workflow retrieves the full description of bacteria strains that are available in the CABRI network services (see www.cabri.org). Input are the name of the involved CABRI catalogues (text/plain string with one catalogue name per line) and the scientific name of the desired bacteria strain (a text/plain string including genus and species separated by a blank space). Data are retrieved from the CABRI Web Services in two steps. First, all bacteria strains IDs are retrieved by using the ge...

Created: 2010-01-15

Credits: Achille Zappa

Search TP53 Somatic Mutation catalogue by ... (1)

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This workflow takes the intron, the effect and the TP53 somatic mutation database as input and retrieves the full TP53 somatic mutation description(s) by first retrieving two different outputs and arranging them according to the boolean operators (and, or and butnot): - first output: a TP53 somatic mutation database unique IDs list associated with the input 'intron' (done via a call to the getP53MutationIdsByIntron web service) - second output: a TP53 somatic mutation database unique IDs list...

Created: 2010-01-15

Credits: Achille Zappa

Search TP53 Somatic Mutation catalogue by ... (1)

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This workflow takes the exon, the effect and the TP53 somatic mutation database as input and retrieves the full TP53 somatic mutation description(s) by first retrieving two different outputs: - first output: a TP53 somatic mutation database unique IDs list associated with the input exon (done via a call to the getP53MutationIdsByExon web service) - second output: a TP53 somatic mutation database unique IDs list associated with the input effect (done via a call to the getP53MutationIdsByEffe...

Created: 2010-01-15

Credits: Achille Zappa

Pattern: Return errors instead of null (1)

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 As Taverna can't (currently) handle null (see http://www.mygrid.org.uk/dev/issues/browse/TAV-653) - in Taverna 2 one can instead return exceptions on individual ports and inside lists. Exceptions are registered as error documents by Taverna, and are passed along. The ErrorBounce layer of processors downstream will prevent execution if they see this 'null'-exception - as showed in this example that the string concatination is just run for the two list elements that are not exceptio...

Created: 2010-01-04 | Last updated: 2010-01-04

Credits: Stian Soiland-Reyes

Triplify GO database external reference [... (1)

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Get GO external database list from http://www.geneontology.org/doc/GO.xrf_abbs 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify LSRN record name list [myexperim... (1)

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Get LSRN list from http://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify NCBI databases list [myexperiment... (1)

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List NCBI's database name. Using this URL service: http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? This is NCBI's namespace list supported by Bio2RDF : pubmed protein nucleotide gene=geneid homologene mesh omim pccompound=cid pcsubstance=sid taxonomy unigene unists

Created: 2009-11-30 | Last updated: 2009-12-01

Credits: Francois Belleau

Triplify EB-Eye databases list from EBI [m... (1)

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TAG: knowledgescope, eb-eye, bio2rdf, banff_manifesto, rdf, ebi, soap

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: Francois Belleau

Triplify UniProt text search results [myex... (1)

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TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: Francois Belleau

Triplify UniProt database list [myexperime... (1)

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TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: Francois Belleau