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

XPath Pubmed Ids (2)

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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. The xml is then parsed to retrieve a list of PubMed ids

Created: 2011-03-23 | Last updated: 2011-03-30

Credits: Paul Fisher

Attributions: XPath Pubmed Ids

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes found from a set of differentially expressed probestes, in Human, Homo sapiens. The workflow requires an input human affymetrix probeset identifiers. 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 database.

Created: 2011-03-24 | Last updated: 2011-03-24

Credits: Paul Fisher

Extract unique proteins from blast results (4)

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The workflow parses uses the tab-delimited BLAST results to determine the unique proteins found in the target genome that have no similarity to the source genome.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.This workflow allows you to configure a BioMart query to fetch sequ...

Created: 2011-03-24 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Attributions: Parse unique proteins from Blast file

Drug Re-Purposing Workflow (6)

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The drug repurposing workflow system screens at least 20 bacterial proteomes against this set of proteins that are already being treated against using established drugs. By screening the bacterial proteomes it will be possible to find proteins of highly similar structure to those that are existing drug protein targets and so this will infer that it is highly likely that the drugs can be used as antimicrobials against these proteins of highly similar structure. Proteomes that will be screene...

Created: 2011-03-25 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

ADR-S (2)

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  The ADR-S pathway seeks to establish a connection between the clinical event and the drug through different paths: (i) through proteins in common among the proteins that are drug targets or metabolite targets and proteins associated to the clinical event (ii) through proteins that are drug targets or metabolite targets and proteins associated to the clinical event that participate in a common biological pathway. The workflow proceeds as follows: First, it checks if there are pr...

Created: 2011-03-28 | Last updated: 2011-08-09

Credits: Anna Bauer-Mehren

Threshold BLAST results (2)

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Thresholds tab-delimited BLAST results to a certain percent identity.

Created: 2011-03-28 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

NCBI Gi to Kegg Pathways (1)

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"This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings."This workflow gets a series of information relating to a list of KEGG genes supplied to it. It also removes any null values from a list of strings.

Created: 2011-03-28 | Last updated: 2011-03-28

Credits: Alibukhari

KEGG Pathways and Additional Information f... (2)

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Takes in a tab-delimited BLAST file and finds additional information about the target proteins from KEGG, Gene Ontology, Interpro and PubMed.

Created: 2011-03-29 | Last updated: 2011-03-30

Credits: Morgan Taschuk

Attributions: extract_uniprot_embl_gi.xml

gene subset extract (1)

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This workflow functions for matching a set of genes as a part of whole gene data set and aim to extract the subset as a separate list.

Created: 2011-03-29 | Last updated: 2011-03-29

Credits: Naser Paul Fisher

Print Analysis Information to HTML (2)

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Takes in a lot of parameters in order to construct an HTML header to display the information.

Created: 2011-03-29 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Compile Protein FASTA from Target to Drug ... (1)

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Uses a tab-delimited file with protein target and drug information (created in Ondex) to compile a protein FASTA file including each target.

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

Credits: Morgan Taschuk Andrewsmeaton

Vaccine Targets Workflow (3)

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Comparison of the genome of Bacillus anthracis to closely related strains will allow the discovery of proteins which may be involved in pathogenicity. Based on the biochemical pathways where the protein interacts, vaccines can be designed for these unique proteins. By gaining insight into the biochemical pathways that the unique proteins are involved in, the proteins can also be assessed for potential quality as vaccines. The key components of the vaccine finding system are the following: T...

Created: 2011-03-30 | Last updated: 2011-04-01

Credits: Morgan Taschuk A Team

Diabetes_workflow (1)

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No description

Created: 2011-03-31 | Last updated: 2011-03-31

Credits: Munasultan Banu

Diabetes Gene and SNP identification (1)

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No description

Created: 2011-03-31 | Last updated: 2011-03-31

IDDM Workflow (1)

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No description

Created: 2011-03-31 | Last updated: 2011-03-31

Credits: Banu Munasultan

Vaccine drug targeting (1)

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No description

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Matthieu Alexncl Kristiangardner123 Paulshreeve Matt Collison

Diabetes patways and SNPs (1)

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No description

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Sudeep Sahadevan

Drug Repurposing Targets (1)

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No description

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Matthieu Alexncl Kristiangardner123 Paulshreeve Matt Collison

IDDM_Workflow (1)

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No description

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Munasultan

Print Protein Information to HTML (1)

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Takes in a lot of parameters in order to construct an HTML table to display the information.

Created: 2011-04-01

Credits: Morgan Taschuk

UniProt to Gene Ontology (1)

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Used parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from Gene Ontology and outputs it in text format.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Use UniProt to retrieve InterPro data (1)

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Used parsed Uniprot results (see workflowUsed parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve results about the protein from InterPro.

Created: 2011-04-01

Credits: Morgan Taschuk

Parsed UniProt to PubMed (1)

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Uses the parsed Uniprot results (see workflow http://www.myexperiment.org/workflows/26.html) to retrieve information from PubMed.

Created: 2011-04-01 | Last updated: 2011-04-01

Credits: Morgan Taschuk

Quality control processing of GEO datasets (2)

The workflow performs a quality control process on gene expression data sets stored in the Gene Expression Omnibus database. The QC process is performed using Bioconductor R packages. A variety of statistics are produced by the workflow including a diagnostic plot from snm normalisation and nucleotide composition bias.

Created: 2011-04-06 | Last updated: 2011-04-11

Credits: Peter Li Bhmecham

Blast Report from ID (1)

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This workflow retrieves a fasta sequence or blast report from an id. Firstly, given some inputs (e.g. ids:EDL10223.1, format:fasta, style:default and db:emblcds), it returns the sequence in fasta format associated to those inputs using the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch). Next, we obtain a Blast report from this fasta sequence and some others parameters. The final result in that case corresponds with the same fasta sequence introduced...

Created: 2011-04-07 | Last updated: 2011-04-07

Credits: Hectorj2f

GRASS-GIS orchestration using pyWPS (2)

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Generic workflow that run r.watershed, with auxiliary services: r.math and geotiff2png. Watershed accumulation is calculated from DEM using r.watershed, the accumulation result is then filtered using r.math with equation:output=(if(a>10,a,null())) Generic workflow that run r.watershed, with auxiliary services: r.math and geotiff2png. Watershed accumulation is calculated from DEM using r.watershed, the accumulation result is then filtered using r.math with equation: output=(if(a>10,...

Created: 2011-04-18 | Last updated: 2011-04-25

Credits: Jorgejesus

M_Super_aln_boot_phylo_New (1)

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This workflow performs a generic protein sequence analysis. A multiple sequence alignment and finally a phylogenetic analysis.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.This workflow performs "parallel" generic protein sequence ana...

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

Credits: Achille Zappa

Attributions: EMBL-EBI ClustalW2 (SOAP)

Remove_Duplicates (1)

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This workflow removes any duplicates from a list of inputs, merges the unique values, and then removes any null values.

Created: 2011-04-21 | Last updated: 2011-04-21

Credits: Paul Fisher

Gene expression interpretation by the Glob... (1)

This workflow adds meaning to gene expresion values by performing a standard and a literature weighted Global Test. Gene expression is expected to be from Affymetrix microarrays, for which an RMA normalization and entrez Gene ID mapping/summation is performed. Original workflow is by Dennis Leenheer, edits by Marco Roos. Scripts by Kristina Hettne, acknowledging Rob Jellier, Jelle Goeman, and Peter-Bram 't Hoen. The workflow was created for the LUMC BioSemantics group, part of the Human Gen...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Marco Roos

[untitled] (1)

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This workflow allows the user to search for processes that are involved with a certain gene. Using microarray-files (CEL-files), consisting of wild type and KO mice to which a stimulant is induced, the user can get an idea of the processes involved. (This is done using the global test and the literature weighted global test.) The results are then given as a text-file. Warning: workflow is not working (needs some revisions), all input is currently hardcoded! (You will have to change the file...

Created: 2011-04-26 | Last updated: 2011-04-26

Credits: Dennis Leenheer

Voronoi polygon generation using GRASS-GIS... (1)

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Generic example on how to deal with vectorial data. Major pitfall is the need to process ProcessOutputs using Xpath plugin. A random point file in GML 2.1.2 is sent to the v.voronoi service and after it is sent to a service that runs v.out.svg generating a SVG image that can be rendered in Taverna (need to set output to SVG image)

Created: 2011-04-27 | Last updated: 2011-04-27

Credits: Jorgejesus

CGR from multiple fasta files (1)

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 The workflow generates Chaos Game Represenations (CGR) image from multiple fasta files. See http://www.g-language.org/wiki/cgr for more information about the Chaos Game Representations.

Created: 2011-04-29 | Last updated: 2011-04-29

Credits: cory (Kazuki Oshita)

[untitled] (1)

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No description

Created: 2011-05-05 | Last updated: 2011-05-05

Credits: Yahmet82

External Tool: Numerically adding two valu... (1)

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The workflow is an examples for the External Tools / UseCase plugin to integrate external tools. It wraps the "bc" command line calculator. Internally, it executes the following script: if [ ! -r "$1" ]; then echo "Cannot read file indicated by first argument '$1'." ; exit -1 ; fi ; if [ ! -r "$2" ];then echo "Cannot read file indicated by second argument '$1'." ; exit -1 ; fi if [ -x /usr/bin/bc ]; then ...

Created: 2011-05-06 | Last updated: 2011-05-06

Credits: Steffen Möller

Dot viewing (1)

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No description

Created: 2011-05-12

Generate Atom Signatures of molecules give... (1)

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Reference: Natural Product-likeness Score and Its Application for Prioritization of Compound Libraries Peter Ertl,* Silvio Roggo, and Ansgar Schuffenhauer Novartis Institutes for BioMedical Research, CH-4002 Basel, Switzerland http://peter-ertl.com/reprints/Ertl-JCIM-48-68-2008.pdf    The natural product likeness scorer implemented by Peter Ertl was originally devised to screen large compound libraries for natural product likeness in drug designing studies. His work is re...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: Kalai

Scoring small molecules for metabolite lik... (2)

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 Prerequisite:   - CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow the atom_signatures file of Natural product(NP), Synthetic Molecules(SM) and query structures are needed - This could be generated from GenerateAtomSignatures.t2flow http://www.myexperiment.org/workflows/2120/download?version=1   Description of input ports : NP_file: needs precomputed Atom_signatures of desired Natural product structu...

Created: 2011-05-13 | Last updated: 2012-03-18

Credits: Kalai

Plotting distribution of natural product l... (1)

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 Prerequisite:  CDK -Taverna Plugin 0.5.1 http://www.ts-concepts.de/cdk-taverna2/plugin/ - To run this workflow you need a Score file which is written to text file.  - This could be generated from ScorerActivity.t2flow http://www.myexperiment.org/workflows/2121/download?version=1   Description of input ports : score_file: Path to file name that has pre computed scores. Note: While passing file as input it could be passed as list of many files or single fi...

Created: 2011-05-13 | Last updated: 2011-05-13

Credits: Kalai

Molecular Interactions from IntAct PSICQUI... (2)

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Get molecular interaction data in psi-mitab25 from IntAct through its PSICQUIC service. As input you can use an Uniprot Acc like "P99999" or a MIQL query like "alias:(KHDRBS1 OR HCK)". This workflow finds by itself how many queries needs to make (SOAP service limited to 200 binary interactions per call) to be able to return all the results in one file.

Created: 2011-05-17 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

Example for external tools with gzip and g... (1)

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This workflow is self-contained. It has a fixed URL from which a text file is downloaded (output as Original_file). That file is gzipped (output as Compressed_File) and then gunzipped again (output as Decompressed_File). The workflow wraps external tools from taverna.nordugrid.org and needs a beta version of Taverna 2.3 or later.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: Steffen Möller Alan Williams

EBI PICR, find cross-references for protei... (2)

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Find cross-references (based on 100% sequence identity) for protein accessions from more than 95 distinct databases. For instance input a list of IPI accessions and find cross-references for Swissprot and Ensembl. Mappings can be limited by source database, taxonomic ID and activity status.

Created: 2011-05-18 | Last updated: 2011-05-29

Credits: Rafael C. Jimenez

Get names of proteins similar to RNA bindi... (1)

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A very simple demo workflow using some existing SADI services. It finds UniProt proteins of GO function "RNA Binding", it then runs a BLAST service to find similar UniProt proteins and then outputs their names.

Created: 2011-05-18 | Last updated: 2011-05-18

Credits: hindlem

get human and mouse phenotypes for a gene (2)

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This workflow gets phenotype annotations associated with human genes and the mouse orthologs from human (GWAS Central) and mouse (EuroPhenome and MGI) databases.

Created: 2011-05-20 | Last updated: 2012-03-29

Credits: Tim Beck

Download Structures from PubChem given che... (1)

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This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: Kalai Michael Gerlich

Attributions: Download Entries from PubChem

Probabilistic Model Checking (PMC): plot r... (1)

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/2266).

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: trybik