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Taverna 2
Uploader
Avatar Gb Andrew David King

Workflow BlastandParse1 (1)

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This workflow allows you to configure a BioMart query to fetch sequences you want from Ensembl. These sequences are retrieved and a blast database of them is created (by default, in the directory you ran taverna from). Warning: This workflow assumes that you have blastall and formatdb installed on the machine, and that by default, these are both found or linked in /usr/local/bin. It also assumes that you have write permission to the directory you have run taverna from. The beanshells "creat...

Created: 2010-03-19

Credits: Network-member Baywatch Solutions

Attributions: Workflow fetchEnsemblSeqsAndBlast

Bioclipse Scripting Language
Uploader
Avatar Se Samuel Lampa

Workflow NMR Spectrum similarity search witn SWI-Pr... (1)

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With the SWI-Prolog (currently in experimental stage, and available from GitHub) plugin Prolog programs can be accessed inside Bioclipse’s scripting environment for querying and other processing of RDF triples. The prolog code in this Bioclipse script performs a simple spectrum similarity search based on a list of peak shift values, for which it tries to find spectra that contain peaks values close to those values, within a certian limit (<0.3 ppm in this case). The data which is u...

Created: 2010-03-13 | Last updated: 2010-03-19

Credits: User Samuel Lampa

Taverna 2
Uploader
4399?size=60x60 Gb Paul Fisher

Workflow Get Kegg Pathway information (1)

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This workflow gets a series of information relating to a list of KEGG pathways supplied to it. It also removes any null values from a list of strings. Example input: path:mmu04010 path:mmu05014

Created: 2010-03-10 | Last updated: 2010-03-10

Credits: User Paul Fisher

Taverna 2
Uploader
1505?size=60x60 Gb James Eales

Workflow Terms from collection of text files (1)

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This workflow will give you a set of candidate terms for each text file in a user-specified directory. You can also specify a c-value threshold that will restrict the terms to those with higher scores. This workflow was created using only nested workflows.  These workflow components work on their own and can be linked together to form more complex workflows such as this. You can view the text mining workflow components in this pack. If you receive errors when running this workflow then...

Created: 2010-02-22 | Last updated: 2011-12-13

Credits: User James Eales

Taverna 2
Uploader
1505?size=60x60 Gb James Eales

Workflow Load PDF from directory (1)

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This workflow will automate the reading of a set of PDF files stored in a single directory (the path to which should be supplied as a single input value). This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-19 | Last updated: 2011-12-13

Credits: User James Eales

Taverna 2
Uploader
1505?size=60x60 Gb James Eales

Workflow Load plain text from directory (1)

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This workflow will automate the reading of a set of text files stored in a single directory (the path to which should be supplied as a single input value).  It will assume that the text files are saved using the default character encoding for the system that Taverna is running on.  This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.  

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Taverna 2
Uploader
1505?size=60x60 Gb James Eales

Workflow Clean plain text (ASCII) (1)

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This workflow will remove any XML-invalid and non-ASCII characters (e.g. for sending to the ASCII-only Termine service) from any text supplied to the input port. This is a workflow component, designed to be used as a nested workflow inside a larger text mining or text processing workflow.

Created: 2010-02-18 | Last updated: 2011-12-13

Credits: User James Eales

Taverna 2
Uploader
Avatar Gb Michael Eiden

Workflow LipidMaps Query (1)

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This workflow retrieves database entries from LipidMaps for given exact mass and tolerance inputs.

Created: 2010-02-16

Bioclipse Scripting Language
Uploader
Avatar De http://...

Workflow In-silico Fragmentation of Naringenin (2)

This is the equivalent of the MetFrag Interface found on http://msbi.ipb-halle.de/MetFrag/ It takes a Speclipse Spectrum and a Bioclipse Molecule and runs MetFrag.  

Created: 2010-02-08

Credits: User http://sneumann.pip.verisignlabs.com/

Vision
Uploader
Avatar Jrensp

Workflow Autodock Vina (1)

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 This workflow requires MGLTools which contains the Vision workflow framework. MGLTools maybe downloaded from https://www.nbcr.net/pub/wiki/index.php?title=CADD_Pipeline. 

Created: 2010-02-04 | Last updated: 2010-02-09

Credits: User Jrensp

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Funded by: BioVeL, EPSRC, JISC, Microsoft

Affiliates: myGrid, Taverna, BioCatalogue
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