Workflows

Test for Orthologues (1)

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Warning: The files are hardcoded in to the beanshell of this workflow. Given an orthlog file for an organism from http://www.ebi.ac.uk/integr8/FtpSearch.do? orgProteomeId=22602, find proteins that are orthologous to proteins in another oragnsims, e.g., B.subtils. Outputs percent.

Created: 2010-03-19

Credits: Baywatch Solutions

Fetch Fasta and Genbank files (1)

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Fetches fasta and genbank files for a given identifier., e.g., CP000256

Created: 2010-03-19

Credits: Baywatch Solutions

Fetch EMBL File (1)

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Fetches an EMBL file using the EMBL id. Creates file to a specified location.

Created: 2010-03-19

Credits: Baywatch Solutions

Square A List Of Numbers (1)

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Simple workflow which squares a list of numbers.

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

Credits: Paul Miller

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: - 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 otput: a TP53 somatic mutation database unique IDs list associated with the input effect (done via a call to the getP53MutationIdsB...

Created: 2010-01-15

Credits: Achille Zappa

Get TP53 Mutations By Intron (1)

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This workflow takes the intron and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByIntron web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Special requirements on input data are: - The intron range of numb...

Created: 2010-01-15

Credits: Achille Zappa

Get TP53 Mutations By Exon (1)

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This workflow takes the exon and the TP53 somatic mutation database as input and retrieve the full TP53 somatic mutation description(s) by first retrieving the TP53 somatic mutation database unique IDs associated with the input (done via a call to the getP53MutationIdsByExon web service) and then using IDs for retrieving the full TP53 somatic mutations descriptions (done via a call to the getP53MutationsByIds web service). Special requirements on input data are: - The exon range of numbers is...

Created: 2010-01-15

Credits: Achille Zappa

Get TP53 Mutation Function Entries And TP... (1)

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This workflow retrieves from two different databases two distinct set of entries starting from the same inputs data (i.e. the Mutated Aminoacid encoded at the codon in which the mutation occurred, and the Codon Number where the mutation occurs). Input data: Mutant Amino Acid encoded at the codon in which the mutation occurred and Codon Number where the mutation is located. Special requirements on input data are: - the MutAA (Mutated Amino Acid) in three letters code (Gly, Ala, Trp, Phe etc.)...

Created: 2010-01-15 | Last updated: 2010-01-15

Credits: Achille Zappa

Fetch Dragon images from BioMoby (2)

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Fetch images and annotations of snapdragons

Created: 2009-12-15 | Last updated: 2010-07-14

Credits: EdwardKawas

Retrieve sequence in EMBL format (1)

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

Created: 2009-12-15

Credits: Alan Williams

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-12-15

Credits: Alan Williams

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2009-12-15

Credits: Alan Williams

Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2009-12-15

Credits: Alan Williams

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2009-12-15

Credits: Alan Williams

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2009-12-15

Credits: Alan Williams

BiomartAndEMBOSSAnalysis (1)

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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: 2009-12-15

Credits: Alan Williams

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: 2009-12-15

Credits: Alan Williams

workflow1 (1)

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blast dando o ID de uma proteinablast dando o ID de uma proteina ex: database is ‘SWISS’, for program, ‘blastp’, and for ID ‘1220173blast dando o ID de uma proteina ex: database is SWISS’, for program, blastp, and for ID 1220173

Created: 2009-11-16

Credits: Jorgep

blastp using the MRS system (1)

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This blastp workflow uses the blast service of MRS (http://mrs.cmbi.ru.nl). Inputs are a sequence (only amino acids, not a fasta sequence) and a database. Databases that can be used are "sprot", "uniprot", "trembl", "pdb", "refseq", "ipi" and "gpcrdb".

Created: 2009-11-10

Credits: Bas Vroling

Search GeNS DataType (1)

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 This workflow returns a single GeNS identifier corresponding to the given data type.    Disclaimer: This workflow is just a simple example designed for academic purposes.

Created: 2009-09-15

Credits: Pedro Lopes

Search GeNS BioEntity (1)

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 This workflow returns a list of know associations between an organism and a data type. All identifiers correspond to GeNS database identifiers.    Disclaimer: This workflow is just a simple example designed for academic purposes.

Created: 2009-09-15 | Last updated: 2009-09-15

Credits: Pedro Lopes

hbr (1)

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Created: 2009-06-29

Credits: Hbrphd

FirstExampleWorkflow (1)

This is my first test example of Taverna Workflow.

Created: 2009-06-24

Credits: Jelena (Obradovic) Dreskai

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2009-03-08

Credits: Pvilaca