myExperiment - Workflows

Taverna 2

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Anja Le Blanc

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general query to DPAS; it gets a list of instruments and lists for start and stop times; for a query hessiEC, phoenix2; start times 2001-01-01 00:00:00, 2005-04-01 00:00:00; stop times 2001-01-05 00:00:00, 2005-05-1 00:00:00 it would perform to queries: hessiEC from 2001-01-01 00:00:00 to 2001-01-05 00:00:00 and phoenix2 from 2005-04-01 00:00:00 to 2005-05-1 00:00:00 There is only one output file with the results from both queries.

Created: 2010-04-19 | Last updated: 2010-04-19

Credits: Anja Le Blanc

Taverna 2

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Anja Le Blanc

HEC standard query (1)

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calls the HEC web service; inputs are start and stop time, which table should be queried and an optional where clause, as in an SQL statement output is of VOTable format

Created: 2010-04-16

Taverna 2

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Anja Le Blanc

DPAS simpel query workflow (1)

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call of the simpleQuery web service; all inputs are requested from the user; xml list as output file format

Created: 2010-04-16

Taverna 2

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Anja Le Blanc

Retrieve all data for all instruments for ... (3)

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This workflow looks up all instruments known to have worked during the requested periode of time (ICS), restructures results to make them fit instruments.xsd and requests data for this periode from DPAS. Result: VOTable with list of URLs to data.

Created: 2010-04-15 | Last updated: 2010-08-09

Credits: Anja Le Blanc

Attributions: Extracting data from VOTable format by using XPath query

Taverna 2

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AndrÃ© Csillaghy

Available instruments through DPAS (5)

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This workflow uses a DPAS servlet to obtain all available intrument keys in the DPAS (Data Provider Access Service) and formats the return as VOTable.

Created: 2010-04-15 | Last updated: 2012-03-16

Taverna 2

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Paul Fisher

Entrez Gene to KEGG Pathway (2)

This workflow takes in Entrez gene ids then adds the string "ncbi-geneid:" to the start of each gene id. These gene ids are then cross-referenced to KEGG gene ids. Each KEGG gene id is then sent to the KEGG pathway database and its relevant pathways returned.

Created: 2010-04-15 | Last updated: 2010-04-15

Credits: Paul Fisher

WSVLAM

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Adambel

Affymetrix Permutation-based Probe Level E... (1)

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Affymetrix Permutation-based Probe Level Estimation (APPLE). Goal: Because of its cost, microarray experiments are frequently designed using a relatively small number of biological or technical replicates. This can result in low statistical power when the number of differentially expressed genes is inferred. This worklfow investigates whether the statistical power of Affymetrix experiments can be increased, without the need to increase the number of hybridizat...

Created: 2010-04-13 | Last updated: 2010-04-14

Taverna 1

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Stian Soiland-Reyes

Find/show Taverna's home directory (1)

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Find Taverna's home directory and open that folder using Explorer/Finder/Gnome. This is the folder that is typically something like C:\Users\stain\AppData\Roaming\taverna-2.1.2, C:\Documents and settings\stain\taverna-2.1.2, /home/stain/.taverna-2.1.2 or /Users/stain/Library/Application support/taverna-2.1.2 This workflow should work on both Taverna 1 and Taverna 2. For Taverna 2 the beanshell script uses reflection to try to call ApplicationRuntime.getInstance().getApplicationHome() ...

Created: 2010-04-12 | Last updated: 2010-04-12

Credits: Stian Soiland-Reyes

Bioclipse Scripting Language

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Egon Willighagen

Download all data sets from a OpenTox API ... (3)

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Uses the OpenTox API (REST+RDF) to query all data sets, downloads them as MDL SD file, and opens the results in the Bioclipse molecules table.

Created: 2010-04-01 | Last updated: 2010-11-13

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Taverna 2

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Gregg Iceton

Compare two genomes for similarity (4)

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This workflow takes the file path to two genome nucleotide files in fasta format and requests a minimum similarity required from the user. The genomes are aligned according to the M-GCAT algorithm (http://alggen.lsi.upc.es/recerca/align/mgcat/intro-mgcat.html) and the genome similarity parsed out of the resultant log file. Output is either 0 (genome similarity less than required similarity) or 1 (genome similarity equal to or greater than the required similarity). NB - The file p...

Created: 2010-03-17 | Last updated: 2010-03-17

Credits: Gregg Iceton

Bioclipse Scripting Language

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Egon Willighagen

Calculate molecular mass for entries in a ... (1)

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Simple script to demonstrate how to iterate over entries in a MDL SD file and calculate some molecular property.

Created: 2010-03-08

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Taverna 2

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Fahad Alqahtani

Transciption (DNA into RNA) (1)

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This workflow allows a user to transcibe DNA into RNA.

Created: 2010-03-05 | Last updated: 2010-03-05

Taverna 2

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Yuhuichen

CaliBayes_Client (1)

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A workflow for consuming CaliBayes web services. CaliBayes: www.calibayes.ncl.ac.uk

Created: 2010-02-03 | Last updated: 2010-02-03

Taverna 2

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Yuhuichen

SBML shorthand to SBML converter (1)

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converts SBML shorthand to SBML document via BASIS web services BASIS: www.basis.ncl.ac.uk:81/Basis SBML shorthand: http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/

Created: 2010-02-03 | Last updated: 2010-02-03

Taverna 2

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Yuhuichen

SBML to SBML shortand converter (1)

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converts SBML document to SBML shorthand via BASIS web services BASIS: www.basis.ncl.ac.uk:81/Basis SBML shorthand: http://www.staff.ncl.ac.uk/d.j.wilkinson/software/sbml-sh/

Created: 2010-02-03 | Last updated: 2010-02-03

Bioclipse Scripting Language

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Egon Willighagen

Convert a SMILES string into a connection ... (1)

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Bioclipse script that converts a SMILES string into a LaTeX table of the connection table of the molecule.

Created: 2009-12-16

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Taverna 2

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Alan Williams

EBI_InterProScan_T2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBIâ€™s WSInterProScan service (see http://www.ebi.ac.uk/Tools/webservices/services/interproscan). The input sequence to use and the user e-mail address are inputs, the other parameters for the analysis (see Job_params) are allowed to default. InterProScan searches a protein sequence against the protein family and domain signature databases integrated into InterPro (see http://www.ebi.ac.uk/interpro/). A set of matches to the s...

Created: 2009-12-15

Credits: Alan Williams

Taverna 2

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Francois Belleau

demo_dbpedia_search2graph (1)

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Do a full text search in DBpedia and load triples from results into a local Virtuoso graph.Do a full text search in DBpedia and load result resource triples into a local Virtuoso graph.

Created: 2009-11-27

Credits: Francois Belleau

Taverna 2

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David Withers

Beanshell Test (1)

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A test workflow that uses beanshell services

Created: 2009-11-10

Taverna 2

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Jelena (Obradovic) Dreskai

getGoTermsFromUniprotId (1)

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This service is invoking UniprotAPI to retrive GOTerms associated with the list of UniprotIds provided in the input. It is using Axis2 webservice created using UniprotAPI and published with wsdl. Example uniprotIds for input: "A2ABK7", "A2ABK8", "A2ABK9"

Created: 2009-07-09 | Last updated: 2009-07-09

Credits: Jelena (Obradovic) Dreskai

Taverna 1

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Tilsith

Retrieve sequence in EMBL format (1)

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

Created: 2009-05-25

Credits: Tilsith

Taverna 1

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Alan Williams

Warn - message parameter (1)

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The warn service displays a warning dialog with no title but message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Warn - title parameter (1)

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The warn service displays a warning dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Warn - no parameters (1)

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The warn service displays a prompt with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the warn service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Tell - message parameter (1)

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The tell service displays an informative dialog with no title but with message 'Some message'. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Tell - title parameter (1)

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The tell service displays an informative dialog with 'Some title' but no message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Tell - no parameters (1)

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The tell service displays an informative dialog with no title or message. When the user presses OK the string 'answer' is passed to the answer port of the tell service and so to the output of the workflow.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

String list difference - yielding non-empt... (1)

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The string list difference service takes in ['a','b','c'] and ['a','e','c'] and returns the list ['b','e'].

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Select - title and message parameters (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with ''Some title' and 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Select - message parameter (1)

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The split_string_into_string_list_by_regular_expression parses the string 'a,b,c,d,e' and outputs the list ['a','b','c','d','e']. The select service displays a dialog with no title but with 'Some message'. The user is able to select from the values ['a','b','c','d',e']. When the user presses OK the value the user selected is passed to the answer port of the select service and so to the output of the workflow. If the user clicks Cancel then a service failure is generated.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Pad numeral with leading 0s - too short ta... (1)

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The pad numeral with leading 0s takes the input '12' and because the specified target length of 1 is too short, yields the output '12'.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

Pad numeral with leading 0s - specified ta... (1)

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The pad numeral with leading 0s takes the input '12' and pads it to the specified target length of 4, yielding the output '0012'.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Alan Williams

List files by regex - single answer (1)

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The create_temporary_directory beanshell creates a temporary directory and outputs the path to that directory. The populate_directory beanshell creates several files within the temporary directory. Once the directory has been populated, it is examined by the List_files_by_regex service and the file path to the one file matching 'c.*' i.e. starting with 'c' is output.

Created: 2008-09-27

Credits: Alan Williams

Taverna 1

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Stian Soiland-Reyes

Pathway to Pubmed (1)

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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.