Workflows

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