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Licence: by-sa

Workflow Retrieve Protein Sequence and BLAST (1)

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Retrieves a protein sequence in Fasta format from Genbank and then performs a BLAST on that sequence

Created: 2007-11-09 | Last updated: 2008-06-05

Credits: User Katy Wolstencroft

Workflow Compare genome, extract proteins which are... (1)

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  Takes GI number for source (non-pathogenic) and target (pathogneic) genomes, extracts list of all proteins from each genome using GenBank database. Outputs prtoeins in FastA format. Creates database from source proteins using formatdb (locally installed) and blasts (local installed) proteins from target against this database. Extracts protens which are unique (no blast hits) to the target (pathogenic) genome based on eValue set by user. Takes unique proteins from target and blasts aga...

Created: 2010-03-19 | Last updated: 2010-03-19

Credits: User Ian Laycock Network-member nclteamc

Attributions: Workflow fetchEnsemblSeqsAndBlast Workflow NCBI Gi to Kegg Pathways Workflow color_pathway_by_objects

Workflow 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: User Carol Lushbough User Alan Williams

Attributions: Workflow A workflow version of the EMBOSS tutorial

Workflow 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: User Katy Wolstencroft User Alan Williams

Attributions: Workflow BiomartAndEMBOSSAnalysis

Workflow 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: User Paul Fisher

Workflow 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: User Andreas Hoheisel

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Blob Installing java certificates for services using SSL

Created: 2008-10-15 09:05:44 | Last updated: 2009-02-16 07:37:39

Credits: User Wassinki

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This jar file, designed by sun microsystems, helps you to install certificates for java to access services using a secure socket. The complete documentation of this small java tool, including its source, can be found at: http://blogs.sun.com/andreas/entry/no_more_unable_to_find In this document, I will explain how to create a keystore holding the certificate required to access services provided by www.bioinformatics.nl . To install the certificate for www.bioinformatics.nl, do the follow...

File type: Java archive

Comments: 1 | Viewed: 1710 times | Downloaded: 1469 times

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Workflow 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: User Thomasku

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Workflow feat (3)

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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: User Glatard

Workflow 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: Network-member myExperimentBeanshellCollection

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