Workflows

Blast_and_Interproscan (5)

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This workflow performs an NCBI blast at the EBI. It accepts a protein sequence as input. Default values have been set for the search database (Uniprot), the number of hits to return (10), and all scoring and matrix options. These can be changed in the workflow by altering the string constant values if required. The sequences for the top 10 hits are retrieved from the UniProt database and analysed using InterproScan (also from the EBI) to determine functional domains and motifs in each sequenc...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft

clustal_phylogeny (3)

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This workflow accepts a ClustalW protein sequence alignment and produces a phylogenetic tree, using the EBI clustalw_phylogeny web service, which implements phylip.

Created: 2013-01-28 | Last updated: 2013-03-11

Credits: Katy Wolstencroft

Blast_Align_and_Tree (2)

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This workflow accepts a protein sequence as input. This sequence is compared to others in the Uniprot database, using the NCBI BLAST Web Service from the EBI (WSDL), and the top 10 hits are returned (Nested workflow:EBI_NCBI_BLast). For each extracted hit, the Uniprot REST service returns the protein sequence in FASTA format. The workflow concatenates the 10 protein sequences and submits them as input to the EBI CLustalw service (Nested workflow EMBL_EBI_clustalw2_SOAP). These sequences are ...

Created: 2013-01-28 | Last updated: 2013-01-30

Credits: Katy Wolstencroft Hamish McWilliam

Attributions: Protein_search_fetch_align_tree

Migration ffmpeg audio to wav pcm_s32le (1)

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Converts audio to wav using ffmpeg with codec pcm_s32le

Created: 2013-01-24

Credits: Markus Plangg

GET statuses/home_timeline | Twitter (1)

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Returns a collection of the most recent tweets and retweets posted by the authenticating user and the users they follow. Uses the OAuth plugin for Taverna Workbench.

Created: 2013-01-22

Credits: Mark Borkum

workflow to test Rshell (for internal purp... (1)

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 This is a workflow to test if Rserve is working properly, for internal purposes.  Takes as input two integers. output is the sum of integer 1 and integer 2  

Created: 2013-01-21 | Last updated: 2013-03-11

Credits: Eleni

Environment (2)

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From a previously selected cube of galaxies residing in a remote database, we provide extragalactic environment parameters for all galaxies sample. This workflow takes as input the path of the tabular *.pckl Python pickle dataset created in the previous workflow, as well as the database connection settings and several criteria on how to filter the potential companions of the target galaxies. It provides a file with the SDSS identifiers of each target galaxy of the sample, environmental estim...

Created: 2013-01-04 | Last updated: 2013-01-14

Credits: Juandesant Jsm

Intialize Sample (2)

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This workflow saves a tabular *.pckl Python pickle dataset in the local file system, containing values calculated on physical parameters associated to potential companions of a sample of target galaxies. These original physical parameters are extracted from a postgreSQL database, containing information of all galaxies covered by the SDSS spectroscopic survey. The workflow first access the external database located in the AMIGA server and selects the target galaxies from the sample (those havi...

Created: 2013-01-04 | Last updated: 2013-01-05

Credits: Juandesant Jsm

Non-redundant protein alignments (1)

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Execute BLASTP program to search protein databases using a protein query: Input file from iPlant Discovery Environment Save the data extract of similar sequences created by BLASTP Execute XMKNR to a compute a non-redundant set from a large collection of protein sequences. Input from the data extract created by BLASTP. Perform multiple sequence alignments using Clustal Omega and TCoffee Input from data extract created by XMKNR To execute this workflow, you need to be logged into the Bio...

Created: 2012-12-19 | Last updated: 2012-12-19

Credits: Carol Lushbough

Ingest.t2flow (1)

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 characterisation of NeXus files

Created: 2012-12-19

Credits: Arifshaon