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Taverna 2
Uploader
Avatar Maximilian Koch

Workflow FInd/filter idA and idB from MITAB (1)

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A workflow to filter idA and idB out of a MITAB file.

Created: 2015-11-05 | Last updated: 2015-11-05

Taverna 2
Uploader
Avatar Maximilian Koch

Workflow Query PSICQUIC and filter by idA and idB (... (1)

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Queries PSICQUIC and returns idA and idB.

Created: 2015-11-05

Taverna 2
Uploader
Avatar Maximilian Koch

Workflow Query for all PISCQUIC services (Name+URL) (1)

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No description

Created: 2015-11-05

Taverna 2
Uploader
Avatar Maximilian Koch

Workflow Define one query and retrieve Molecular In... (1)

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Define one query and retrieve Molecular Interactions from PSICQUIC Services registered in the PSICQUIC registry.

Created: 2015-11-05

Taverna 2
Uploader
3772?size=60x60 Nl Kristina Hettne

Workflow Get ontology parents (2)

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Retrieves the ontology parents of an entity including the relationship type, using the ChEBI identifier.

Created: 2015-11-16 | Last updated: 2016-04-26

Credits: User Kristina Hettne

Attributions: Workflow Get ontology parents

Taverna 2
Uploader
3655?size=60x60 Nl Magnus Palmblad

Workflow Get ENSEMBL cross-references for UniProt IDs (1)

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This small workflow uses the PICR (http://www.ebi.ac.uk/Tools/picr/) WDSL Web Service to look up ENSEMBL (ENSP) cross-references for UniProt IDs. The input is a list of UniProt IDs and the output a corresponding list of ENSEMBL IDs. This instance of the workflow specifically uses the ENSEMBL_HUMAN database and taxonID 9606 (Homo sapiens).

Created: 2015-11-16

Credits: User Magnus Palmblad

Taverna 2
Uploader
3739?size=60x60 Yassene

Workflow getDatabaseLinks (1)

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No description

Created: 2015-11-16 | Last updated: 2015-12-02

Taverna 2
Uploader
3739?size=60x60 Yassene

Workflow searchPublications (1)

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No description

Created: 2015-11-16 | Last updated: 2015-12-02

Taverna 2
Uploader
3739?size=60x60 Yassene

Workflow searchPublications (1)

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No description

Created: 2015-11-16 | Last updated: 2015-12-02

Taverna 2
Uploader
3739?size=60x60 Yassene

Workflow getDatabaseLinks (1)

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No description

Created: 2015-11-16 | Last updated: 2015-12-02

Taverna 2
Uploader
3739?size=60x60 Yassene

Workflow single_double_flattten (1)

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No description

Created: 2015-11-17 | Last updated: 2015-12-02

Taverna 2
Uploader
3655?size=60x60 Nl Magnus Palmblad

Workflow Author to Wordcloud (3)

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This small workflow demonstrates how to connect to and use Europe PMC (http://europepmc.org/RestfulWebService). The workflow searches the publications of an author, extracts the abstracts, counts the word frequencies and plot a wordcloud using the R package of the same name. The Rshell plot_wordcloud also applies text mining operations (transformation to lower case, removing punctuation, stripping whitespace and removing English stopwords) using the R package tm.

Created: 2015-12-02 | Last updated: 2015-12-07

Credits: User Magnus Palmblad

Taverna 2
Uploader
3655?size=60x60 Nl Magnus Palmblad

Workflow Author Citation Network (1)

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Map citation/reference network for one author using Europe PMC Web services. This workflow is intended to show the integration of several Web services, XPath XML parsing and use of the igraph package in R. Although the workflow is functional, the information in PubMed is incomplete. This means the results may be a subset of the correct citation graph.

Created: 2015-12-04 | Last updated: 2015-12-04

Credits: User Magnus Palmblad User Yassene

Taverna 2
Uploader
3655?size=60x60 Nl Magnus Palmblad

Workflow UniProt Protein Protein Network (1)

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This workflow uses the Europe PMC Web Services searchPublications and getDatabaseLinks to reconstruct a protein-protein network based on co-occurence in the scientific literature, arbitrary filtered by a PubMed query, e.g. the word "complex" appearing in the title or abstract. The workflow also looks up the second degree connections, i.e. proteins co-occuring with proteins co-occuring with the protein given as input, but not with this protein itself. The output is a (1) Pajek graph file, a GM...

Created: 2015-12-04

Credits: User Magnus Palmblad User Yassene

Taverna 2
Uploader
3655?size=60x60 Nl Magnus Palmblad

Workflow SImple Europe PMC Search (1)

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This very simple workflow searches Europe PMC using the searchPublications Web Service and a conditional XPath to retrieve the article titles for all cited work matching the search query.

Created: 2015-12-04

Credits: User Magnus Palmblad

Taverna 2
Uploader
3655?size=60x60 Nl Magnus Palmblad

Workflow Connecting to Europe PMC (1)

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This very simple workflow connects to Europe PMC using the searchPublications Web Service.

Created: 2015-12-04

Credits: User Magnus Palmblad

Taverna 2
Uploader
3655?size=60x60 Nl Magnus Palmblad

Workflow Search Europe PMC and get ChEBI annotations (3)

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This workflow first conducts a search and downloads the PMIDs for all publications in PubMed and PMC that match a particular query using the Europe PMC Articles API. In a second phase, the workflow fetches the ChEBI annotations for all these publications using the Europe PMC Annotations API.

Created: 2018-02-09 | Last updated: 2018-02-12

Credits: User Magnus Palmblad

Taverna 2
Uploader
Avatar choon

Workflow Get (3)

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No description

Created: 2018-05-27 | Last updated: 2018-05-27

Taverna 2
Uploader
Avatar Harish

Workflow Demo (1)

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No description

Created: 2019-06-25 | Last updated: 2019-06-26

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Killer whale demography (1)

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This workflow analyzes the demography and population growth of resident killer whale populations. Originally created for comparative studies of Northeastern Pacific populations at risk, Southern Resident Killer Whales (SRKW) and the Northern Resident Killer Whales (NRKW), the workflow can be used for other killer whale populations or cetaceans counting with census data and life cycles that can be represented using the matrix models described in this document. This workflow perform the follow...

Created: 2014-09-24

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Andres Araujo User Jon Giddy User Francisco Quevedo

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow Workflow_waveform-compare_2.0.2 (2)

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xcorrSound waveform-compare component - minor edits

Created: 2014-09-25 | Last updated: 2014-09-26

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow xcorrSound_overlap-analysis_2.0.2 (1)

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This component uses xcorrSound overlap-analsis to find the overlap between two input wav files and output an analysis report in a txt output format.

Created: 2014-09-26 | Last updated: 2014-09-26

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow xcorrSound_sound-match_2.0.2 (1)

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This component uses xcorrSound sound-match to find occurrences of the first (small) input wav file in the second (larger) wav file and output the result in a txt output format.

Created: 2014-09-26 | Last updated: 2014-09-26

Taverna 2
Uploader
3190?size=60x60 Dk Bolette Jurik

Workflow Characterise_Audio_using_FFprobe (1)

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The workflow takes an inputfilepath as input parameter. It relies on FFprobe being installed locally, when it is run. It has been tested with ffprobe version 0.10.3. It outputs bitrate, bitsPerSample, channels, duration and audio sampling frequency (hz) as well as an activity report (raw FFprobe STDOUT+STDERR).

Created: 2014-09-26 | Last updated: 2014-09-26

Taverna 2
Uploader
4562?size=60x60 Nl Maria Paula Balcazar-Vargas
Project Biovel

Workflow Resident killer whale-chinook salmon inter... (1)

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The resident killer whale-chinook salmon interactions workflow provides an environment to calculate a two-sex stage-structured matrix with no density dependence and with vital rates as random variables or as functions of Chinook abundance from specific stock aggregates and to (i) quantify the differences in demographic rates between killer whale (Orcinus orca) population that explain population growth; (ii) to determine the relative influence of vital rates and Chinook (Oncorhynchus tshawytsc...

Created: 2014-09-26

Credits: User Maria Paula Balcazar-Vargas User Antonio Velez-Espino User Andres Araujo User Jon Giddy User Francisco Quevedo

Attributions: Workflow Killer whale demography

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Funded by: BioVeL, EPSRC, JISC, Microsoft

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