Workflows

Fasta_string_to_fasta_list (1)

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Split a string containing a set of sequences in fasta format into a list for fasta formated sequences.

Created: 2008-06-06

Credits: Hamish McWilliam

EBI_FASTA (1)

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Run a FASTA or SSEARCH sequence similarity search using the EBI's WSFasta service (see http://www.ebi.ac.uk/Tools/webservices/services/fasta). Note: the WSFasta 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 FASTA services (REST or SOAP) should be used instead.  

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

Credits: Hamish McWilliam

Fetch today's xkcd comic (1)

Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.  I just uploaded this example so I can play around with the myexperiment api.

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

Credits: Alan Williams

Attributions: Fetch today's xkcd comic

Unique tags (2)

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This workflow takes a comma separated list of tags and removes duplicate entries. Tags may have multiple words in them. An example string is "carrots,handbags,carrots,cheese".

Created: 2008-03-11 | Last updated: 2008-03-11

Credits: Don Cruickshank

Attributions: Viking boat

Fetch PDB flatfile from RCSB server (1)

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Given aPDB identifier such as '1crn', this workflow fetches the PDB format flatfile from the RCSB

Created: 2008-01-25 | Last updated: 2008-03-05

Credits: Katy Wolstencroft

Retrieve SNPs from regions around known genes (1)

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Given a list of Gene IDs this workflow will query against the Ensembl human genome data to fetch the genomic region for each gene, extend that region by 1000bp in each direction and use this set of ranges, one per gene, to build a query against dbSNP to return the SNP identifier and location information (chromosome name, strand and position)

Created: 2007-11-07

Example of a conditional execution workflow (2)

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If the input is true the workflow returns the temperature in Celsius, if false the temperature in Fahrenheit is returned.

Created: 2007-10-03 | Last updated: 2008-01-27

BLASTP with simplified results returned (2)

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This workflow Performs a blastp search on protein sequence, extracts sequence id within the blast report and retrives the corresponding seuqences.

Created: 2007-10-03 | Last updated: 2008-03-06

Parse UniProt text file (2)

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This workflow performs a search through the SRS linking system to find the text files for a particular UniProt identifier. This UniProt text file is then parsed to extract a small list to summarise the file, primarily consisting of external identifiers. Example input for this workflow is: O35613

Created: 2007-10-03 | Last updated: 2009-12-03

Remove null values (2)

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This workflow removes any null values from a list of strings

Created: 2007-10-03 | Last updated: 2007-11-13

DOI2PMID (2)

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Converts Digital Object Identifiers into their corresponding PubMed identifiers, if they exist.

Created: 2007-10-03

NCBI Gi to Kegg Pathways (1)

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User inputs background and foreground colour to be used to highlight proteins in KEGG pathway image. User provides NCBI GI numbers. Worflow calculates KEGG ID and pathway ID and sends value to colour service, which adds colour to that KEGG id on pathway image. Also outputs kegg description, pathway description and url of image.

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

Credits: Ian Laycock nclteamc

Attributions: color_pathway_by_objects NCBI Gi to Kegg Pathways

find events in xray and radio (7)

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instruments: hessiEC, phoenix2 attention: hessi name has changed!

Created: 2010-03-16 | Last updated: 2010-03-16

Credits: Anja Le Blanc

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: 2009-07-03 | Last updated: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: Fetch PDB flatfile from RCSB server Fetch PDB flatfile from RCSB server

Analysing workflows (3)

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This workflows analyses workflows stored at the myExperiment site. It is used in the paper submitted to the Workshop on Scientific Workflow 2009. The workflow shows the task usage in the Taverna workflows stored at the myExperiment site The amount of services used The amount of local processors used The amount of scripting tasks The amount of sub workflows Furthermore it classifies the local services based on their intended function. The workflow has two inputs: ...

Created: 2009-05-06 | Last updated: 2009-05-06

Credits: Wassinki Pieter Neerincx Katy Wolstencroft Marco Roos

AffyArrayNormalization (2)

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The AffyArrayNormalization web services normalise raw Affymetrix GeneChip data. They are wrappers around Philip de Groot's normalization R script to provide remote programmatic access. This example workflow demonstrates the use of the AffyArrayNormalization services. The flow is as follows: A client executes the AffyArrayNormalization_submit service with two inputs: a User object and a collection of URLs linking to CEL files. The User object contains a user ID, a password and an ...

Created: 2009-02-16 | Last updated: 2009-02-16

Credits: Pieter Neerincx Philipg

MediGRID FEAT Workflow (1)

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This workflow is a translation of the VLeMed workflow to the GWorkflowDL format, which is used in MediGRID. The translation of the "cross product" iteration strategy is currrently under work and not yet finished. So this workflow only varies the parameters p1, p2, and p3.

Created: 2009-02-13

Credits: Andreas Hoheisel

Attributions: feat_workflow

FLOSS Communication Centralization Plot, U... (2)

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The analysis in this workflow represents the basis of the analysis in our paper, Social dynamics of FLOSS team communication across channels. This workflow uses WSDL components to select periodized data from the FLOSSmole database and generate sociomatrices. The workflow parses the threaded list structure into a communication network based on reply-to relationships. In the analysis process, an unit weighting is applied to the edges. The weighted sociomatrices are then dichotomized according ...

Created: 2009-02-07

Credits: Andrea Wiggins Crowston James Howison

What is known about HIV using Bio2RDF's SP... (2)

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched.  The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, two SPARQL queries analyze the obtained graph.  Finally you can submit queries to the RDF mashup about HIV as you like.  Enjoy. This is the queries present in t...

Created: 2009-02-05 | Last updated: 2009-02-05

Credits: Francois Belleau

BlatBlastCombi (2)

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This workflow combines the blat and blast workflows. It takes as input a database name (Danio_rerio_Genome for Zebra Fish for example) and and a set of Fasta sequences. It first tries to perform a blat (at www.bioinformatics.nl). When this service returns nothing, a blast is done (also at www.bioinformatics.nl). The resulting reports are combined.   To run this workflow, a certificate to access www.bioinformatics.nl needs to installed (Some services use an SSL connection). Look at the ...

Created: 2009-02-03 | Last updated: 2009-02-03

Credits: Wassinki