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EBI_NCBI_BLAST (1)

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Perform a BLAST search using the EBI’s WSNCBIBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/ncbiblast). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search (see Job_params) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement NCBI BLA...

Created: 2008-05-31 | Last updated: 2010-12-06

Credits: Hamish McWilliam

SifterWorkflow_Prod_Neu (2)

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Phylogenomic workflow with SIFTER. The workflow first runs an iterative Blast search against the RefSeq database (Pruitt et al. 2007) (only fully sequenced organisms) and filters the results to get putative orthologous and in-paralogous proteins. These sequences are used to build a multiple alignment with MAFFT (Katoh et al. 2005). After filtering out alignment columns with more than 60% gaps, a phylogenetic tree is build. If there are less than 20 proteins in the alignment Phyml (Guindon an...

Created: 2007-11-23 | Last updated: 2008-04-29

Credits: Anika Joecker

Translate Nucleotide sequence into Peptide... (2)

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Translate Nucleotide sequence into Peptide sequence using EBI Service. Find nucleotide sequence from EBI wsdbfetch(using ref.seq Id NM_005700) 2. Translation nucleotide sequence(from 1) into peptide sequence using EBI EMBOSS4 transeq.

Created: 2007-10-03

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Taverna 2.1 starter pack

Created: 2009-12-10 16:04:54 | Last updated: 2009-12-18 11:15:36

12 items in this pack

Comments: 0 | Viewed: 521 times | Downloaded: 237 times

Perform a search through NCBI eUtils eSearch (3)

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This workflow takes in a search term and a database (e.g. snp, gene, protein) in which to perfom the search over. The result is an xml file containing summary information about the search term. Example input for this workflow are given below: database: pubmed terms: cancer AND diabetes

Created: 2009-11-27 | Last updated: 2009-12-03

EBI WU-BLAST with program and database sel... (3)

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Run a BLAST analysis using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). This workflow wraps the EBI_WU-BLAST workflow to provide a basic user interface which prompts for the required inputs: sequence, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. The values presented in the selection menus for the program and database are obtained from the service, using the provided me...

Created: 2009-07-04 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Attributions: EBI_WU-BLAST

Retrieve sequence in EMBL format (3)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2009-06-17

Credits: Franck Tanoh Tomoinn Stuart Owen

EBI_ClustalW2_phylogentic_tree (2)

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Create a Neighbor-joining phylogenetic tree, with Kimura distance corrections, from a sequence alignment using the EBI's WSClustalW2 service (see http://www.ebi.ac.uk/Tools/webservices/services/clustalw2).

Created: 2009-04-07

Credits: Hamish McWilliam

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile and returns the corresponding 3D image of the protein.

Created: 2008-03-05 | Last updated: 2008-03-31

Credits: Tomoinn

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: 2008-03-05 | Last updated: 2008-03-25

Credits: Tomoinn

Multiple Blastp (2)

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This is a workflow to automate multiple BLASTp jobs on a large list of protein sequences in FASTA format.

Created: 2007-11-20 | Last updated: 2008-01-10

Credits: Kieren Lythgow

Get weather information (3)

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Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure. The default value Stian's home country.

Created: 2008-06-17 | Last updated: 2008-06-20

Credits: Franck Tanoh Stian Soiland-Reyes

Attributions: Get weather information Get cities by country name

Escherichia coli : From cDNA Microarray Ra... (1)

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This workflow takes in a CDNA raw file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the R and bioconductor. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed changes in the microarray data. By identifying the candidate pathways, more detailed...

Created: 2008-05-08 | Last updated: 2008-05-12

Credits: Saeedeh Paul Fisher

Attributions: HUMAN Microarray CEL file to candidate pathways

conditional branch (2)

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Example of a conditional execution workflow. use 'false' or 'true' as input

Created: 2007-10-03

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

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Taverna 2.1 beta 2

Created: 2009-07-02 12:51:11 | Last updated: 2009-09-21 14:48:06

6 items in this pack

Comments: 0 | Viewed: 177 times | Downloaded: 65 times

Workflow Pattern - Structured Loop (B) (2)

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This workflow is an alternative GWorkflowDL representation of a structured loop that updates the variable "x" in each iteration and which models the control flow separately from the index "i". Here a version of the graph with manual graph layout: This workflow is equivalent to the following pseudo code: x:=0; for ( i:=0; i<=99; i++) { x:=x+i; } x_result:=x; Please remark that this demonstration workflow does not invoke any external services at all. The c...

Created: 2008-12-09

Credits: Andreas Hoheisel

Attributions: Workflow Pattern - Structured Loop

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Example workflow for KEGG web service

Created: 2008-09-29 13:28:02 | Last updated: 2008-10-08 16:37:49

14 items in this pack

Comments: 0 | Viewed: 430 times | Downloaded: 86 times

Identification of differential genes using... (1)

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This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data which are then analysed by the LIMMA Bioconductor package in an R script. This produces a list of significant differentially expressed genes which is then analysed using the Go Term Finder tool to generate a PDF report of the common GO terms associated with the genes. A CSV file containing the list of sign...

Created: 2008-07-02 | Last updated: 2008-07-02

Credits: Peter Li

tmap_single_sequence (2)

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Simple workflow using tmap to find transmembrane regions, using a single sequence as input.

Created: 2008-06-01 | Last updated: 2008-06-02

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

Sequence_or_ID (1)

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Given a sequence or sequence entry identifer (e.g. uniprot:wap_rat), return the sequence in fasta format. If a sequence identifier, in database:identifier format, is input the EBI's WSDbfetch web service (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) is used to retrive the sequence in fasta format. Otherwise the input is assumed to be a sequence and if passed through the Soaplab EMBOSS seqret service to force the sequence into fasta format.

Created: 2008-06-01

Credits: Hamish McWilliam

Protein_alignment_transmembrane (1)

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Transmembrane domain prediction using EMBOSS tmap with an input sequence alignment of homolouges: Sequence similarity search (SSS) to find homologues Fetch sequences of hits Multiple sequence alignment (MSA) of hit sequences EMBOSS tmap with alignment from 3. Uses the EBI web services: WSFasta (see http://www.ebi.ac.uk/Tools/webservices/services/fasta) WSDbfetch (see http://www.ebi.ac.uk/Tools/webservices/services/dbfetch) WSClustalW2 (see http://www.ebi.ac.uk/Tools/webservices/servic...

Created: 2008-06-01

Credits: Hamish McWilliam

Attributions: EBI_FASTA EBI_ClustalW2 EBI_dbfetch_fetchBatch

EBI_WU-BLAST (1)

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Perform a BLAST search using the EBI's WSWUBlast service (see http://www.ebi.ac.uk/Tools/webservices/services/wublast). The default parameters search UniProtKB using blastp. To change the job parameters see Job_params. Note: the WSWUBlast service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. This service is will be retired during 2011. EBI's replacement WU-BLAST services (REST or SOAP) should be used instead.  

Created: 2008-05-30 | Last updated: 2010-12-06

Credits: Hamish McWilliam

Identification of differential genes using... (2)

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This workflow starts by retrieving the names of microarray datasets from the Maxd database. The user has to select sets of control and test data for analysis using t-tests by R. A list of significant differentially expressed genes is then analysed using the Go Term Finder tool which generates a list of GO terms associated with the genes. A CSV file containing the list of significant genes is also generated.

Created: 2008-04-15 | Last updated: 2008-07-01

Credits: Peter Li