Workflows

Multiple Protein Alignment Profiling(1) (4)

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Designed from an example workflow at Traverna, this workflow retrieves a set of sequences from UniProt, then simultaneously scans for transmembrane regions and performs a multiple alignment using EMMA. The alignment is then plotted to a set of PNG images, followed by a profile analysis using prophecy and prophet tools.

Created: 2010-01-13 | Last updated: 2010-11-17

Credits: Carol Lushbough Alan Williams

Attributions: A workflow version of the EMBOSS tutorial

BioMart and Emboss Analysis (T2) (1)

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This is the Taverna 2 version of the Biomart and Emboss Analysis workflow http://www.myexperiment.org/workflows/158   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. Previous versions of this workflow only returned sequences with an ID mapped to a MIM_morbid_accession. This was primarily to reduce the numbe...

Created: 2009-09-15

Credits: Katy Wolstencroft Alan Williams

Attributions: BiomartAndEMBOSSAnalysis

Get Kegg Gene information (2)

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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.   Example input for this workflow is given below (new line separated): mmu:13163 hsa:1616

Created: 2009-01-26 | Last updated: 2009-12-14

Credits: Paul Fisher

Workflow Pattern - Structured Loop (2)

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This workflow is a GWorkflowDL representation of a structured loop that updates the variable "x" in each iteration. 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 calculation is done only by using the GWorkflowDL's syntax and semantics.

Created: 2008-12-09

Credits: Andreas Hoheisel

QSAR workflow to measure the time used for... (1)

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This workflow loads molecules from a database. Each molecule goes through the atom typing, gets its explecite hydrogens and the detection of the hueckel aromaticity. After that different qsar properties will be calculated. The output of this workflow will be a qsar vector as a csv file and a file which contains the time needed to calculate each qsar property.

Created: 2008-08-29 | Last updated: 2008-08-29

Credits: Thomasku

Nucleotide_ORF_translation (1)

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From a nucleotide sequence get the protein translations of the open reading frames (stop to stop) that are longer than a specifed minimum length. EMBOSS getorf is used to find the ORFs and perform the translations. The getorf tool is accessed via Soaplab (see http://www.ebi.ac.uk/Tools/webservices/soaplab/overview).

Created: 2008-06-06

Credits: Hamish McWilliam

Attributions: Sequence_or_ID

EBI_Phobius (2)

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The Phobius tool predicts transmembrane domains and signal peptide region from a protein sequence. This workflow uses the EBI's WSPhobius web service (see http://www.ebi.ac.uk/Tools/webservices/services/phobius) to access the tool. The predicted features are returned in a UniProtKB style feature listing.

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

Credits: Hamish McWilliam

EBI_NCBI_BLAST_with_prompts (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, database, BLAST program and user e-mail. Other parameters (e.g. matrix, sort, gap penalties, etc.) are allowed to default. Note: the WSNCBIBlast service used by this workflow is deprecated as of 21st September 2010 and should not be use...

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

Credits: Hamish McWilliam

Attributions: EBI_NCBI_BLAST

feat (3)

This is an attempt to implement the feat application from the fsl fMRI package www.fmrib.ox.ac.uk/fsl/fsl/whatsnew.html into a Scufl workflow. Details are still being polished but the general structure is here. The main problem that we have with such workflows concerns data provenance. Each of the services is typically iterated on hundreds of data sets and keeping track of the produced files is a pain.

Created: 2008-03-18 | Last updated: 2008-05-19

Credits: Glatard

myExperimentBeanshellCollection (2)

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Public collection of generic Beanshells curated by the myExperimentBeanshellCollection group on myExperiment. Visit http://www.myexperiment.org for details and updates. To use this collection of beanshells in Taverna: Right click "Available Processors" in the "Design Perspective" Choose "Add new Workflow scavenger..." Provide the URL to this beanshell collection on www.myExperiment.org or if you downloaded this to your hard disk, provide a "file" URL to the absolute path of this file (O...

Created: 2008-03-06 | Last updated: 2008-03-25

Credits: myExperimentBeanshellCollection