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Taverna 2
Uploader
510?size=60x60 Us Wei Tan

Workflow caArray data retrieving (1)

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Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They ca be later used as training and test data set in many classification algorithms.Query all the gene expression data in a caArray experiment. Returns a evenly divided gene expression data set with corresponding class information. They can be later used as training and test data set in many classification algorithms.

Created: 2009-11-23

Credits: User Wei Tan

Taverna 2
Uploader
510?size=60x60 Us Wei Tan

Workflow genePattern data preprocessing (2)

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preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the default preprocess data set using genePattern preProces service, the input should be in genePattern STATML format.preprocess data set using genePattern preProces service, the input should be in genePattern STATML format. Configuration parameters can be adjusted by changing the string constants.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: User Wei Tan

Taverna 2
Uploader
510?size=60x60 Us Wei Tan

Workflow Support-Vector-Machine (SVM) based data cl... (2)

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Support-Vector-Machine based data classificationSupport-Vector-Machine based data classification using genePattern SVM service, the input should be in genePattern STATML format.

Created: 2010-05-24 | Last updated: 2010-05-24

Credits: User Wei Tan

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow 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: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify KEGG database list [myexperiments... (2)

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TAG: knowledgescope, kegg, bio2rdf, banff_manifesto, rdf

Created: 2009-11-28 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify search results from KEGG bfind SO... (3)

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This workflow use KEGG's SOAP service provided to do a BFIND serch within one of the KEGG's official database. The results are returned in RDF ntriples format. 

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify search results from all KEGG data... (3)

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Search all KEGG databases using bfind SOAP service and merge results into a bmuri list and a ntriples string. 

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify UniProt database list [myexperime... (1)

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TAG: knowledgescope, uniprotkb, bio2rdf, banff_manifesto

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify UniProt text search results [myex... (1)

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TAG: knowledgescope, uniprotkb, bio2rdf, search, rdf

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify UniProt text search results from ... (2)

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Search all UniProt databases using search URL service and merge results into a bmuri list and a ntriples string. 

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify EB-Eye databases list from EBI [m... (1)

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TAG: knowledgescope, eb-eye, bio2rdf, banff_manifesto, rdf, ebi, soap

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify namespace list from global search... (1)

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No description

Created: 2009-11-30 | Last updated: 2009-11-30

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify NCBI databases list [myexperiment... (1)

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List NCBI's database name. Using this URL service: http://www.ncbi.nlm.nih.gov/entrez/eutils/einfo.fcgi? This is NCBI's namespace list supported by Bio2RDF : pubmed protein nucleotide gene=geneid homologene mesh omim pccompound=cid pcsubstance=sid taxonomy unigene unists

Created: 2009-11-30 | Last updated: 2009-12-01

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify NCBI databases external reference... (1)

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Get NCBI external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify UniProt database external referen... (2)

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Get UniProt external database list from http://www.ncbi.nlm.nih.gov/projects/collab/db_xref.html 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify LSRN record name list [myexperim... (1)

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Get LSRN list from http://www.lsrn.org/lsrn/registry-2009-04-26-32404.rdf 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify GO database external reference [... (1)

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Get GO external database list from http://www.geneontology.org/doc/GO.xrf_abbs 

Created: 2009-12-01 | Last updated: 2009-12-01

Credits: User Francois Belleau

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Triplify namespace XREF list from GO, LSRN... (1)

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TAG: banff_manifesto, xref, bio2rdf, rdfTAG: banff_manifesto, xref, bio2rdf, rdf, mashup Triplify namespace XREF list from GO, LSRN, NCBI and UniProt [myexperiment:xref_namespace2rdf] TAG: banff_manifesto, xref, bio2rdf, rdf TAG: banff_manifesto, xref, bio2rdf, rdf

Created: 2009-12-01

Credits: User Francois Belleau

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow BiomartAndEMBOSSAnalysis (1)

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Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow EBI_InterProScan_T2 (1)

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Perform an InterProScan analysis of a protein sequence using the EBI’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: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Fetch today's xkcd comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Retrieve sequence in EMBL format (1)

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

Created: 2009-12-15

Credits: User Alan Williams

Taverna 2
Uploader
1217?size=60x60 Gb Alan Williams

Workflow Fetch Dragon images from BioMoby (2)

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Fetch images and annotations of snapdragons

Created: 2009-12-15 | Last updated: 2010-07-14

Credits: User EdwardKawas

Taverna 2
Uploader
9?size=60x60 Gb Stian Soiland-Reyes

Workflow Pattern: Return errors instead of null (1)

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 As Taverna can't (currently) handle null (see http://www.mygrid.org.uk/dev/issues/browse/TAV-653) - in Taverna 2 one can instead return exceptions on individual ports and inside lists. Exceptions are registered as error documents by Taverna, and are passed along. The ErrorBounce layer of processors downstream will prevent execution if they see this 'null'-exception - as showed in this example that the string concatination is just run for the two list elements that are not exceptio...

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

Credits: User Stian Soiland-Reyes

Taverna 2
Uploader
9?size=60x60 Gb Stian Soiland-Reyes

Workflow Dummy example of looping (3)

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Example of looping over asynchronous services. The dummy beanshell scripts represents the operations of an asynchronous submit-status-results style service, such as EBI's InterProScan and NCBI Blast. createJob creates a temporary file with the content "0". Filename retuirned as a "job ID". checkStatus reads the job, and return state "RUNNING" as long as the content is less than 10, increasing the number for each call. (As no actual job is being run) getResults reads the file content, with...

Created: 2010-01-27 | Last updated: 2013-10-08

Credits: User Stian Soiland-Reyes

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow Rdfise Riken SciNes Database Repository [m... (1)

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This workflow rdfise Riken SciNes Database Repository available at https://database.riken.jp/sw/links/en/crib151s2i/. There is a bug with main page listing databases: version 2p and 3p are similar to 1p.

Created: 2010-02-01 | Last updated: 2010-02-01

Credits: User Francois Belleau

Taverna 2
Uploader
Avatar Yuhuichen

Workflow 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

Taverna 2
Uploader
Avatar Yuhuichen

Workflow 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
Uploader
Avatar Yuhuichen

Workflow 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
Uploader
4399?size=60x60 Gb Paul Fisher

Workflow Get Gene Ids for Human (1)

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This workflow gets a list of gene ids (number depending on Ret_Max_value variable) for Homo sapiens. The species may be changed according to that desired, by altering the term_value string constant

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

Credits: User Paul Fisher

Taverna 2
Uploader
4174?size=60x60 Ca Francois Belleau

Workflow PDB2KEGG step 1done during BH2010 (1)

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No description

Created: 2010-02-13

Credits: User Francois Belleau

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

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
1505?size=60x60 Gb James Eales

Workflow Clean plain text (1)

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This workflow will remove any XML-invalid characters (these characters often appear in the output of PDF to text software) 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
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 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 PDF to plain text (1)

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This workflow will extract the plain text content of PDF files supplied to the input port.  You can connect the Load PDF from directory workflow to this workflows input. We recommend you send the output from this workflow to the Clean plain text workflow, because the PDF to text process can add characters into the text that are XML-invalid and therefore can not be sent to most services as plain text.  Another way round this problem is to encode the text as Base64 using the handy loc...

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

Credits: User James Eales

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

Workflow Sentence splitting (1)

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This workflow will attempt to split up text into sentences, returning a list of sentences to the output port.  The sentence splitting service makes use of the OpenNLP sentence detector and has been trained to work on english text. This workflow can be used to provide input to the Termine with c-value threshold workflow. 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 Termine with c-value threshold (1)

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This workflow accepts a list of sentences from a single document and returns the terms found by the TerMine web service. It also allows you to set a threshold c-value score so that only terms with a user-controlled probability (of being a real term) are returned as an output.   To get sentences to supply to this workflow you can use the sentence splitting workflow.  The TerMine service (used in this workflow) only accepts text in ASCII encoding, so you should also use the Clean p...

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

Credits: User James Eales

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

Workflow Terms from collection of PDF files (2)

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This workflow will give you a set of candidate terms for each PDF document 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 t...

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

Credits: User James Eales

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
Avatar Rodriguez

Workflow Tutorial Taverna (1)

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No description

Created: 2010-02-26 | Last updated: 2010-02-26

Credits: User Rodriguez

Taverna 2
Uploader
Avatar Rodriguez

Workflow Taverna Tutorial2 (1)

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No description

Created: 2010-02-26 | Last updated: 2010-02-26

Credits: User Rodriguez

Attributions: Workflow EBI_InterProScan for Taverna 2

Taverna 2
Uploader
1650?size=60x60 Sa Fahad Alqahtani

Workflow 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
Uploader
482?size=60x60 Gb Rory

Workflow Get locations from postcode (1)

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 This workflow will return all the areas that correspond to a postcode. Enter the first part of the postcode only, e.g. SW19

Created: 2010-03-08 | Last updated: 2010-03-08

Credits: User Rory

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