Workflows

InterProScan (SOAP) (1)

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Perform an InterProScan search using the EMBL-EBI’s InterProScan (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/pfa/iprscan_soap). The query sequence to use is the input, the other parameters for the search are allowed to default.

Created: 2010-12-03 | Last updated: 2013-03-28

Attributions: EBI_InterProScan

HTTP Basic authentication example workflow (1)

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This workflow shows an example access to a resource protected by HTTP Basic authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

HTTP Basic authentication + HTTPS example ... (1)

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This workflow shows an example access to a resource protected by HTTP Basic authentication and HTTPS. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

HTTP Digest authentication example workflow (1)

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This workflow shows an example access to a resource protected by HTTP Digest  authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.  

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

Credits: Alex Nenadic

HTTP Digest authentication + HTTPS example... (1)

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This workflow shows an example access to a resource protected by HTTP Digest  authentication and HTTPS. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

WS-Security example workflow (1)

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This workflow shows an example access to various secure Web services protected by WS-Security authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

WS-Security + HTTPS example workflow (1)

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This workflow shows an example access to various secure Web services protected by WS-Security authentication. Use testuser/testpasswd whenever prompted for username and password. Check http://www.mygrid.org.uk/dev/wiki/display/story/Taverna+2.x+test+secure+services+and+workflows for more details about the secure services used in the workflow.

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

Credits: Alex Nenadic

EMBL-EBI ClustalW2 (SOAP) (1)

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Perform a ClustalW2 alignment using the EMBL-EBI’s ClustalW2 (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/msa/clustalw2_soap).

Created: 2010-12-06 | Last updated: 2013-03-28

Attributions: EBI_ClustalW2

Cosine vector space (2)

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This workflow calculates the cosine vector space between two sets of corpora. The workflow then removes any null values from the output. this is some extra text vbeing added

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Cosine vector space

Rank Phenotype Terms (2)

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This workflow counts the number of articles in the pubmed database in which each term occurs, and identifies the total number of articles in the entire PubMed database. It also identified the total number of articles within pubmed so that a term enrichment score may be calculated. The workflow also takes in a document containing abstracts that are related to a particular phenotype. Scientiifc terms are then extracted from this text and given a weighting according to the number of terms that ...

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Attributions: Rank Phenotype Terms

Pathway to Pubmed (2)

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This workflow takes in a list of KEGG pathway descriptions and searches the PubMed database for corresponding articles. Any matches to the pathways are then retrieved (abstracts only). These abstracts are then returned to the user.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Extract Scientific Terms (2)

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This workflow takes in a document containg text and removes and non-ascii characters. The cleaned text is then sent to a service in dresden to extract all scientific terms. These terms represent a profile for the input document. Any null values are also removed.

Created: 2010-12-08 | Last updated: 2011-01-11

Credits: Paul Fisher

Merge QSAR descriptor CSV files (3)

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This workflow merges QSAR descriptor CSV files into a single CSV file. The workflow loads the CSV files from hard disk and builds a single QSAR descriptor vector. Afterwards the vector is converted in one single CSV file and saved to hard disk.

Created: 2010-12-09 | Last updated: 2011-07-21

Curate QSAR descriptor CSV file (2)

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This workflow erases descriptor entries which were not calculated. The QSAR data is loaded from a CSV file and afterwards processed by the Curate_QSAR_Vector worker. At the end the curated CSV file is written to hard disk.

Created: 2010-12-09 | Last updated: 2011-07-21

ART-2a Classification Result As PDF (2)

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This workflow classifies a given CSV file with the ART-2a algorithm. The results are visualized in a PDF file. The QSAR data is loaded from a CSV file and converted into a fingerprint items list which is the suitable data type for the ART-2a algorithm.

Created: 2010-12-09 | Last updated: 2011-07-21

ART-2a Classification Considering Differen... (2)

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This workflow classifies the given CSV files with the ART-2a algorithm. The results are visualized in a PDF file. The QSAR dara is loaded from CSV files and merged together by the Merge_QSAR_Vectors worker. Afterwards they are converted into a fingerprint items list which is the suitable data type for the ART-2a algorithm.

Created: 2010-12-13 | Last updated: 2011-07-21

Biomart and Blast (1)

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart) Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service

Biomart and Blast with concatinated gene id (1)

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Perform Rodent BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). Finally (to showcase Taverna pipelining) - the Ensembl gene ID is added as a prefix on the BLAST report. Referenced in the Taverna knowledge blog.

Created: 2010-12-13 | Last updated: 2010-12-13

Attributions: BLAST using DDBJ service Biomart and Blast

Biomart and 2x BLAST (1)

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Perform Roden and Invertebrates BLAST sequence alignments (using DDBJ Blast) on the gene sequences for a (semi-random) selection of genes from Human sapiens chromosome 22. (Using Biomart). blast_ddbj_invertebrates and blast_ddbj_rodents should execute in parallel as they don't depend on each other.

Created: 2010-12-13 | Last updated: 2010-12-13

Compound Library Screen For Reaction Enume... (2)

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This workflow performs a compound library screen for molecules which match the given template reaction. The reaction is loaded from a RXN file and the Reaction_Reactant_Splitter splits the reaction into its reactants. The compound library is loaded iteratively from a SD file. Afterwards a substructure search is performed for each reactant and the results are saved as SD files.

Created: 2010-12-14 | Last updated: 2011-07-21

Get Molecular Weight Distribution From QSA... (2)

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This workflow calculates a molecular weight distribution from given QSAR vector. The QSAR data containing the molecular weight values is read from a CSV file and converted into a QSAR vector. Finally, the Get_molecular_Weight_Distribution_From_QSAR_vector extracts the weight data and saves it as CSV files.

Created: 2010-12-15 | Last updated: 2011-07-21

Lemmatization (3)

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The workflow lemmatizes the text in the input port. Takes text as input and returns (language dependent) lemmatized text as output. All the words in the resulting text are in the same order as in the original text, but they are transformed to their dictionary form. The workflow asks for the language of lemmatization. Currently, 12 languages are supported: en,sl,ge,bg,cs,et,fr,hu,ro,sr,it,sp.

Created: 2010-12-17 | Last updated: 2010-12-23

Credits: Petra Kralj Novak

Attributions: Select from a list of possible web service parameter values

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2010-09-06

Credits: George

Attributions: Multiple Choice Quiz

Principle Component Analysis (PCA) over mi... (1)

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Principle Component Analysis (PCA) over microarray data. Data is uploaded through caGrid transfer ultility.

Created: 2010-09-10 | Last updated: 2010-09-10

Credits: Wei Tan

Example workflow for REST and XPath activi... (1)

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Note that this workflow depends upon the REST and XPath plugins. This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch d...

Created: 2010-09-13 | Last updated: 2010-09-13

Credits: Sergejs Aleksejevs