Workflows

Load affymetrix experiments results into S... (1)

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The affymetrix data source is not public.

Created: 2009-02-17

Credits: Francois Belleau

Sesame triplestore loader from a dereferen... (2)

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Load triples obtained from an URL in N3 or XML format and load them into your local Sesame Triplestore locally installed and available at http://localhost/sesame. The http://localhost/sesame/servlets/uploadURL service of Sesame is used in HTTP POST mode.

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: Sesame triplestore loader from tr... (2)

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INSERT IN GRAPH

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2rdf: Bind search, rdfise and load demo (1)

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INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> {     CONSTRUCT { ?s, ?p, ?o . }     FROM <http://soap.bind.ca/wsdl/bind.wsdl>     WHERE {         SELECT ?s         FROM <http://soap.bind.ca/wsdl/bind.wsdl>         WHERE {              ?s, ?p, ?o .        ...

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: Rdfiser for Bind protein interact... (1)

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CONSTRUCT{ <bmuri>, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { <bmuri>, ?p, ?o . }

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: Bind fulltext search service retu... (1)

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SELECT ?s FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE {   ?s, ?p, ?o .   FILTER ( regex(?o, "query")) . }

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath search, rdfise and load dem... (1)

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Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH < http://localhost/sesame/mem_rdf_db> {     CONSTRUCT{ ?s, ?p, ?o . }     FROM < http://www.pathwaycommons.org/pc/webservice.do>     WHERE {         SELECT ?s         FROM <http://www.pathwaycommons.org/pc/webservice.do>  ...

Created: 2009-02-19 | Last updated: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath search, rdfise and load dem... (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath describe interaction (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath reverse links (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Bio2RDF: CPath search in taxon (1)

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No description

Created: 2009-02-19

Credits: Francois Belleau

Lymphoma type prediction based on microar... (7)

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Scientific value Using gene-expression patterns associated with DLBCL and FL to predict the lymphoma type of an unknown sample. Using SVM (Support Vector Machine) to classify data, and predicting the tumor types of unknown examples. Steps Querying training data from experiments stored in caArray. Preprocessing, or normalize the microarray data. Adding training and testing data into SVM service to get classification result.

Created: 2010-05-11 | Last updated: 2010-05-11

Credits: Wei Tan Ravi Stian Soiland-Reyes

Get the list of GeneID for all pathways of... (1)

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No description

Created: 2009-04-28

Credits: Francois Belleau

Insert in local triplestore GeneID and KEG... (1)

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No description

Created: 2009-04-28

Credits: Francois Belleau

EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan on provided sequencesThis workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. 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: 2011-01-17 | Last updated: 2011-01-17

Credits: Katy Wolstencroft Hamish McWilliam Stian Soiland-Reyes

Attributions: EBI_InterProScan for Taverna 2 EBI_InterProScan for Taverna 2 EBI_InterProScan

EMBL-EBI ClustalW2_SOAP (2)

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Perform a ClustalW2 alignment of protein sequences using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap). 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: 2011-01-17 | Last updated: 2013-01-30

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: EMBL-EBI ClustalW2 (SOAP) EBI_ClustalW2

QSPR Model Discovery -- workflow structure... (2)

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replicates the structure of the QSPR model discovery workflow. Ref.: replicates the structure of the QSPR model discovery workflow. Ref.: http://www.openqsar.com/

Created: 2011-01-18 | Last updated: 2011-01-18

PRM With External Data (1)

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IN PROGRESS! Runs the PRM using data from an external on-line source.

Created: 2011-01-19 | Last updated: 2011-01-19

Credits: Nick Malleson

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Cow, Bos taurus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway data...

Created: 2011-01-21 | Last updated: 2011-01-21

Credits: Paul Fisher

SELECT3 (2)

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Select3 decides if a particular transition matches the selection criteria based on the line strength and line opacity in a given medium. To do that select3 requires a model of the medium (temperature, pressure, node spacing), chemical composition and boundary conditions. Only 1D models are supported at the moment. Select3 processes one transition at a time working in two modes: opacity and synthesis. In the first mode it computes line opacity, compares it to the reference (e.g. bf and ff opa...

Created: 2011-01-22 | Last updated: 2011-02-27

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2011-01-27 | Last updated: 2011-01-27

Credits: Maninder

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

Define one query and retrieve Molecular In... (3)

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Define one query and retrieve Molecular Interactions from PSICQUIC Services registered in the PSICQUIC registry.

Created: 2011-01-31 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Select redundant accessions (1)

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Simple workflows to select accessions which appear more than once. Chose threshold to specify how many times an accession has to appear to be selected. This workflow uses a list of Comma-separated values as input. The accessions selected is the result which is presented in a String of Comma-separated values.

Created: 2011-01-31 | Last updated: 2011-01-31

Credits: Rafael C. Jimenez

Rank Phenotype Terms (1)

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This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Created: 2011-02-01 | Last updated: 2011-02-01

Credits: Paul Fisher

Attributions: Cosine vector space Rank Phenotype Terms

Using a Create_List script with a dot-prod... (1)

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Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b]. The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...

Created: 2011-02-02 | Last updated: 2011-02-02

Credits: Stian Soiland-Reyes

PubMed Search (1)

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This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. Those abstracts found are returned to the user

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Remove Non-ASCII (1)

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THis workflow removes any non-ascii characters from a segment of text. Any characters that are found are removed. Letters either side f the non-ASCII are concatenated - this may cause the loss of word meaning

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Read files from Directory (1)

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This workflow reads files from a given directory, based on a known file extension (e.g. .txt), and then outputs the contents of each file in a single value/single list.

Created: 2011-02-03 | Last updated: 2011-02-03

Credits: Paul Fisher

Gene to Pubmed (4)

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This workflow takes in a list of gene names and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2011-02-08 | Last updated: 2011-02-10

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms

Pathway and Gene to Pubmed (2)

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This workflow takes in a list of gene names and KEGG pathway descriptions, and searches the PubMed database for corresponding articles. Any matches to the genes are then retrieved (abstracts only). These abstracts are then used to calculate a cosine vector space between two sets of corpora (gene and phenotype, or pathway and phenotype). The workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMe...

Created: 2011-02-10 | Last updated: 2011-02-18

Credits: Paul Fisher

Attributions: Cosine vector space Extract Scientific Terms Rank Phenotype Terms Cosine vector space Rank Phenotype Terms Pathway to Pubmed Extract Scientific Terms Gene to Pubmed

Associate hessi flares with active regions (3)

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This workflow is querying the HFC ActiveRegions list and HEC hessi_flare list. It requires a time periode and a search radius arround the centre of an Active Region as inputs It produces two outputs: HFCout is a modified VOTable where a field is added with the number of associated hessi flares. combined_output is a 2 dimensional list with an VOTable for each Active region and one with an VOTable for all associated flares for that Active Region.

Created: 2011-02-11 | Last updated: 2011-10-24

Credits: Anja Le Blanc

Calculate Sun data from date (2)

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caluculates B0 (radians), position angle and sun radius (arcsec) B0 - heliographic latitude of the centre of disk position angle - of the north end of the axis of rotation, measured +ve if east of the north point of the disk radius - the apparent radus of the Sun in arcsec This is created using the calculations from the IDL routine get_sun.pro

Created: 2011-02-15 | Last updated: 2011-03-02

Credits: Anja Le Blanc

StRAnGER Web Service Workflow (1)

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 StRAnGER is a web-based application, which performs functional analysis of high-throughput genomic datasets, starting from a list of significant genes derived from statistical and empirical thresholds, by utilizing the GO database and the KEGG pathway database as well as established statistical methods in order to relate the identified significant genes with important nodes in the GO tree structure or map those genes to over-represented metabolic pathways.

Created: 2011-02-15 | Last updated: 2011-02-15

Credits: Elico stranger

QSAR Descriptor Calculation Workflow (2)

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This workflow calculates QSAR properties and saves them as a CSV file. The molecules are read iteratively from a SD file. Additionally it writes out the molecules with unknown atom types, salt counter ions, curated molecule library with UUIDs and the used calculation time of every QSAR descriptor as a CSV file.Furthermore explicit hydrogens are added and a Hueckel aromaticity detection is performed.

Created: 2011-02-18 | Last updated: 2011-07-21

Reaction Enumeration (1)

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This workflow performs a reaction enumeration. Therefore it loads a generic reaction rxn file and two educt lists. The SD files contain the educt lists for the enumeration. The products of the enumerated reaction are stored as RXN files and also a PDF will be created which visualizes the resulting reactions.

Created: 2011-02-18 | Last updated: 2011-07-21

Converting from heliocentric coordinate sy... (1)

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Converting from heliocentric coordinate system with coordinates in arcsec to coordinates in longitude latitude Based on the IDL script xy2lonlat.pro http://hesperia.gsfc.nasa.gov/ssw/gen/idl/solar/xy2lonlat.pro Stonyhurst Heliographic Coordinate System to Helioprojective-Cartesian Coordinate System

Created: 2011-02-18 | Last updated: 2011-02-18

Credits: Anja Le Blanc

Associate goes X ray flares with active r... (1)

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This workflow is querying the HFC ActiveRegions list and HEC goes_xray_flare list. It requires a time periode and a search radius arround the centre of an Active Region as inputs It produces two outputs: HFCout is a modified VOTable where a field is added with the number of associated hessi flares. combined_output is a 2 dimensional list with an VOTable for each Active region and one with an VOTable for all associated flares for that Active Region.

Created: 2011-02-18 | Last updated: 2011-02-18

Credits: Anja Le Blanc

Associate flares with active regions (1)

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This workflow is querying the HFC ActiveRegions list and HEC flare lists (names retrieved from the ontlogoy) It requires a time periode and a search radius arround the centre of an Active Region as inputs It produces two outputs: HFCout is a modified VOTable where a field per flare list is added with the number of associated flares. combined_output is a 2 dimensional list with an VOTable for each Active region and each one with an VOTable for all associated flares for that Active Region.

Created: 2011-02-22 | Last updated: 2011-08-24

Credits: Anja Le Blanc

Attributions: Associate goes X ray flares with active regions Associate hessi flares with active regions

Extract content of columns from VOTables (3)

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Extracts all values from all columns which are passed from the input ColumnNames

Created: 2011-02-24 | Last updated: 2012-08-20

Credits: Anja Le Blanc

Taverna-eScienceCentral integration demo (1)

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show how a eSC workflow can be embedded into a Taverna workflow

Created: 2011-02-25

[untitled] (1)

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gdalinfo test

Created: 2011-02-27 | Last updated: 2011-02-27

Credits: Jorgejesus

Converting from coordinates in longitude l... (1)

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Based on lonlat2xy.pro Converts from Helioprojective-Cartesian Coordinate System to Stonyhurst Heliographic Coordinate SystemBased on lonlat2xy.pro http://hesperia.gsfc.nasa.gov/ssw/gen/idl/solar/lonlat2xy.pro Converts from Helioprojective-Cartesian Coordinate System to Stonyhurst Heliographic Coordinate System

Created: 2011-03-02 | Last updated: 2011-03-02

Credits: Anja Le Blanc

MDES simple execution (2)

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workflow to query MDES, obtaining the DES results and from it extracting the VOTable and the PNG plot for the time range queried.

Created: 2011-03-02 | Last updated: 2014-03-12

Credits: Anja Le Blanc

WPS orchestration example, image metadata ... (1)

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1 image inputs (GeoTIFF, JPEG,PNG), metadata from gdalinfo and histogram analisys, histogram result is a PNG image in base64 coding (default WPS service encoding) that will be converted to binary.

Created: 2011-03-03 | Last updated: 2011-03-03

Credits: Jorgejesus

DevinTheDevil (1)

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DevinTheDevil computes level populations for one or more ions of astrophysical interest using the XSTAR atomic database (uaDB).

Created: 2011-03-08

InterproScan without Looping (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text or png. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. This workflow will not work properly until we add looping.

Created: 2011-03-16 | Last updated: 2012-08-29

Credits: Katy Wolstencroft

Pathways and Gene annotations forQTL region (2)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in Human, Homo sapiens. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG pathway ...

Created: 2011-03-17 | Last updated: 2011-08-30

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

XPath Pubmed Ids (1)

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This workflow takes in a search term (as used in the normal PubMed interface) and retrieves a list of PubMed ids in xml

Created: 2011-03-23 | Last updated: 2011-03-23

Credits: Paul Fisher