Workflows

EBI_Whatizit (1)

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Perform a text-mining analysis of an input text document using the EBI's Whatizit tool (http://www.ebi.ac.uk/webservices/whatizit/info.jsf). Whatizit provides a number of text-mining pipelines which can can detect various terms of biological interest in text documents. For example finding gene names and mapping them to UniProtKB identifiers, finding chemical terms and mapping them to ChEBI, etc.

Created: 2008-07-09

Credits: Hamish McWilliam

countryExample_working (1)

This Workflow allows you to find a list of the cities in a particular country, the time zone that country is in, the conversion rate of the currency in that country and yours and the international dialling code for that country

Created: 2008-06-16

Credits: Katy Wolstencroft

EBI_DaliLite (1)

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Pairwise structure comparison using the DaliLite tool. The EBI's WSDaliLite web service (see http://www.ebi.ac.uk/Tools/webservices/services/dalilite) is used to access the tool.

Created: 2008-06-07

Credits: Hamish McWilliam

EBI_MAFFT (1)

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Perform a multiple sequence alignment using the MAFFT tool (see http://align.bmr.kyushu-u.ac.jp/mafft/software/). The EBI's WSMafft web service (see http://www.ebi.ac.uk/Tools/webservices/services/mafft) is used to access to tool. Note: the WSMafft 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 MAFFT services (REST or SOAP) should be used instead.

Created: 2008-06-03 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_MPsrch (1)

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Run a Smith-Waterman sequence search using the EBI’s WSMPsrch service (see http://www.ebi.ac.uk/Tools/webservices/services/mpsrch). Note: the WSMPsrch service used by this workflow was retired 27th January 2010. Equivalent functionality is available in the EBI's FASTA (REST or SOAP) and PSI-Search (REST or SOAP) services.  

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_Kalign (1)

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Multiple sequence alignment using the Kalign tool. This workflow uses the EBI's WSKalign service (see http://www.ebi.ac.uk/Tools/webservices/services/kalign) to access the Kalign tool. The set of sequences to align and the molecule type (protein or nucleic acid) are the input, the other parameters for the search (see Job_params) are allowed to default. Note: the WSKalign service used by this workflow is deprecated as of 21st September 2010 and should not be used in any new development. Thi...

Created: 2008-06-02 | Last updated: 2010-12-06

Credits: Hamish McWilliam

EBI_blastpgp_PSI-BLAST (1)

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Perform a PSI-BLAST iterative search using the EBI’s WSBlastpgp service (see http://www.ebi.ac.uk/Tools/webservices/services/blastpgp). The query sequence, database to search and users e-mail address are inputs, the other parameters for the search (see Job_params) are allowed to default. In most cases you will probably want to adjust the expectation thresholds and the maximum number of iterations for your specific query sequence and the database being searched.

Created: 2008-05-31

Credits: Hamish McWilliam

Termine Webservice (1)

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Termine is a service provided by the National Centre for Text Mining (NaCTeM) to assist in the discovery of terms in text. More information on the Termine service can be found here. This workflow represents the simplest method of using Termine. The input represents a text string with the output being an string containing a representation of the list of terms, with their C-Value scores (representing significance in the text), in a simple xml format. Other variations of this tools will be adde...

Created: 2008-05-19 | Last updated: 2008-05-19

Credits: Brian Rea National Centre for Text Mining (NaCTeM)

couple (1)

My Girl Friend and me ^o^/

Created: 2007-11-16 | Last updated: 2007-11-16

Credits: Hong Chang Bum

Microarray CEL file to candidate pathways (2)

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This workflow takes in a CEL file and a normalisation method then returns a series of images/graphs which represent the same output obtained using the MADAT software package (MicroArray Data Analysis Tool) [http://www.bioinf.manchester.ac.uk/MADAT/index.html]. Also retruned by this workflow are a list of the top differentialy expressed genes (size dependant on the number specified as input - geneNumber), which are then used to find the candidate pathways which may be influencing the observed ...

Created: 2007-10-03