Workflows

MsaPAD: Multiple Sequence Alignment - Inpu... (2)

BioVeL – Biodiversity Virtual e-Laboratory Workflow Documentation Name:Perform a Multiple DNA sequence alignment coding for multiple/single protein domains Capacities Programme of Framework 7: EC e-Infrastructure Programme – e-Science Environments - INFRA-2011-1.2.1 Grant Agreement No: 283359 Project Co-ordinator: Mr Alex Hardisty Project Homepage: [http://www.biovel.eu][1] [1]: http://www.biovel.eu ## 1 Description This workflow is used to submit the multip...

Created: 2014-07-30 | Last updated: 2015-06-12

Credits: Bachirb Giacinto Donvito Pasquale Notarangelo Saverio Vicario Graziano Pesole

Attributions:

sort_stereo_transient_list_into_cirs_and_c... (1)

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The workflow concept is below. Current workflow is proof of concept and works for default event.1. The initial query is to the stereo_hi_sw_transient list in a particular time range. From this catalogue we extract the longitude of the source of the transient, the longitude error, the start time (launch time of the transient) and the estimated time of arrival. The time of the event is then passed to the HELIO Instrument Location Service (ILS) to extract the Heliocentric Earth Equatorial longit...

Created: 2014-08-11

Credits: Eoincar

digital-preservation-migration-audio-ffmpe... (1)

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Converts any FFmpeg supported audio format to AAC

Created: 2014-08-13

digital-preservation-migration-audio-ffmpe... (1)

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Converts any FFmpeg supported audio format to MP3

Created: 2014-08-13

digital-preservation-migration-audio-ffmpe... (1)

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Converts MP3 to WAV

Created: 2014-08-13

digital-preservation-migration-audio-gstre... (1)

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Converts an audio file in MP3 to Flac using GStreamer

Created: 2014-08-13

digital-preservation-migration-audio-gstre... (1)

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Converts an audio file in MP3 to Ogg using GStreamer

Created: 2014-08-13

digital-preservation-migration-audio-gstre... (1)

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Converts an audio file in MP3 to WAV using GStreamer

Created: 2014-08-13

digital-preservation-migration-audio-mpg32... (1)

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Converts mp3 to wav

Created: 2014-08-13

digital-preservation-migration-audio-sox-a... (1)

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Converts any SoX supported audio format to WAV

Created: 2014-08-13

digital-preservation-migration-audio-sox-m... (1)

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Converts MP3 to WAV

Created: 2014-08-13

digital-preservation-migration-image-gimp-... (1)

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Converts TIFF to JPG

Created: 2014-08-13

digital-preservation-migration-image-gimp-... (1)

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Converts TIFF to PNG

Created: 2014-08-13

digital-preservation-migration-image-graph... (1)

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Converts TIFF to JP2000

Created: 2014-08-13

digital-preservation-migration-image-graph... (1)

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Converts TIFF to PNG

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts any Java Image IO supported image format to BMP

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts any Java Image IO supported image format to GIF

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts any Java Image IO supported image format to JPEG

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts HTML to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts HTML to TIFF

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts HTML to Text

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts any ImageMagick supported image format to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts any ImageMagick supported image format to Text

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts Text to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-image... (1)

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Converts Text to TIFF

Created: 2014-08-13

digital-preservation-migration-image-inksc... (1)

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Converts SVG to PDF

Created: 2014-08-13

digital-preservation-migration-image-inksc... (1)

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Converts SVG to PNG

Created: 2014-08-13

digital-preservation-migration-image-jaspe... (1)

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Converts JP2 to JPG

Created: 2014-08-13

digital-preservation-migration-image-netpb... (1)

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Converts TIFF to JPEG

Created: 2014-08-13

digital-preservation-migration-image-netpb... (1)

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Converts TIFF to PNG

Created: 2014-08-13

digital-preservation-migration-image-openj... (1)

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Converts any OpenJPEG supported image format to JPEG2000

Created: 2014-08-13

digital-preservation-migration-image-sanse... (1)

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Converts any Apache Sanselan supported image format to BMP

Created: 2014-08-13

digital-preservation-migration-image-sanse... (1)

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Converts any Apache Sanselan supported image format to PNG

Created: 2014-08-13

digital-preservation-migration-image-tesse... (1)

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Converts TIF image to Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word to HTML

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word to OpenDocument Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word to PDF

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word to Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word (.docx) to Word

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word (.docx) to HTML

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word (.docx) to OpenDocument Text

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word (.docx) to PDF

Created: 2014-08-13

digital-preservation-migration-office-abiw... (1)

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Converts Word (.docx) to Text

Created: 2014-08-13

digital-preservation-migration-office-ffmp... (1)

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Converts Text to TIFF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Word to OpenDocument Text

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Word to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Presentation to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Presentation to Powerpoint

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Presentation to Flash

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Spreadsheet to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Spreadsheet to Excel

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Text to Word

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts OpenDocument Text to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint to OpenDocument Presentation

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint to Flash

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint (.pptx) to OpenDocument Presentation

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint (.pptx) to PDF

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Powerpoint (.pptx) to Flash

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Excel to OpenDocument Spreadsheet

Created: 2014-08-13

digital-preservation-migration-office-jodc... (1)

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Converts Excel to PDF

Created: 2014-08-13

digital-preservation-migration-office-pdfb... (1)

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Converts a PDF to a TXT

Created: 2014-08-13

digital-preservation-migration-office-pdfb... (1)

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Converts Text to PDF

Created: 2014-08-13

digital-preservation-migration-video-avide... (1)

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Converts any FLV to AVI

Created: 2014-08-13

digital-preservation-migration-video-avide... (1)

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Converts any WMV to MPEG2

Created: 2014-08-13

digital-preservation-migration-video-ffmpe... (1)

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Converts any FFmpeg supported video format to FLV

Created: 2014-08-13

digital-preservation-migration-video-ffmpe... (1)

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Converts any FFmpeg supported video format to MPEG2

Created: 2014-08-13

digital-preservation-migration-video-handb... (1)

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Converts any HandBrake supported video format to MPEG4

Created: 2014-08-13

digital-preservation-migration-video-menco... (1)

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Converts any Mencoder supported video format to MPEG2

Created: 2014-08-13

Example dbfetch (2)

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Run EBI's dbfetch

Created: 2014-09-03 | Last updated: 2014-09-03

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

FunctionalClusterDavid (1)

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This workflow takes a list of Entrez Gene IDs as input and submits them to the DAVID REST API for functional clustering using OG annotaiton, biological pathways and disease associations. Used for analysing a set of genes (i.e. those differentially expressed for a particular disease condition).

Created: 2014-09-05

Credits: Katy Wolstencroft

ImportConvertEnsembl (1)

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This workflow accepts a spreadsheet file as input and extracts a list of ENSEMBL Gene IDs from column A. The hsapiens_gene_ensembl service converts these IDs to Entrez_geneIds

Created: 2014-09-05

Credits: Katy Wolstencroft

entreztoKeggImage (1)

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This workflow accepts a list of Entrez Gene IDs. It dentifies which KEGG pathway each gene is involved with and displays the pathway diagrams

Created: 2014-09-05

Credits: Katy Wolstencroft

Photohawk SSIM tiff/png/jpeg-jp2 (3)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk SSIM.

Created: 2014-09-07 | Last updated: 2014-09-07

Credits: Markus Plangg

Photohawk MSE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk MSE.

Created: 2014-09-07

Credits: Markus Plangg

Photohawk AE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk AE.

Created: 2014-09-07

Credits: Markus Plangg

Photohawk MAE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk MAE.

Created: 2014-09-07

Credits: Markus Plangg

Photohawk PAE tiff/png/jpeg-jp2 (1)

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SCAPE QA Object Component. Compares tiff/png/jpeg to jp2 images using Photohawk PAE.

Created: 2014-09-07

Credits: Markus Plangg

Optimization of retention time prediction (1)

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The workflow uses RTCalc from the TPP toolbox to perform two different retention time predictions. The third branch uses a linear retention time predictor (Palmblad et al., 2002). The workflow has a flag that switches on a specific branch.

Created: 2013-08-13 | Last updated: 2013-09-04

Credits: Sonja Holl Yassene Magnus Palmblad

Attributions: Retention Time Prediction with X!Tandem

X!Tandem and PeptideProphet on the Grid (1)

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The workflow performs the execution of X!Tandem and PeptideProphet from the TPP toolbox on the Grid. The execution is performed by the UNICORE Plugin for Taverna. mzXMLDecomposer/Composer is used to run the execution of X!Tandem in parallel. extract_values extract relevant information from thetandem.interact.pep.xml File. The file can then remain on the remote storage.

Created: 2013-08-13 | Last updated: 2013-09-04

Credits: Sonja Holl Yassene Magnus Palmblad

Attributions: de Bruin et al. Workflow 1 Cloud Parallel Processing of Tandem Mass Spectrometry Based Proteomics Data: X!Tandem

Biomarker Identification via RFE on the Grid (2)

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The first two components split the original data set into several sub-sampling sets. The RFE component performs the machine learning approach by executing several instances of a SVM, each of which consuming one sub-sample data set. The execution of the SVM takes place in a distributed computing environment, using the UNICORE-Taverna Plugin. The calc_objFunc component calculates the F-measure of the ranked gene list compared to a 'gold standard'.

Created: 2013-08-13 | Last updated: 2013-09-24

Credits: Sonja Holl

Attributions: Biomarker Identification via EFS on the Grid

Biomarker Identification via EFS on the Grid (2)

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The first two components split the original data set into several sub-sampling sets. The EFS component performs the machine learning approach by executing several instances of a SVM, each of which consuming one sub-sample data set. Another level of SVM execution is added by taking bootstapping into account. The execution of all SVMs takes place in a distributed computing environment using the UNICORE-Taverna plugin. The calc_objFunc component calculates the F-measure of the ranked gene list ...

Created: 2013-08-13 | Last updated: 2013-09-24

Credits: Sonja Holl

Attributions: Biomarker Identification via RFE on the Grid

Imagemagick convert - tiff2tiff - compression (1)

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Converts tiff to tiff using imagemagick convert with the provided compression

Created: 2013-08-15

Credits: Markus Plangg

Generate Spectral Library (1)

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This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 Unported License (CC BY-SA). Copyright© 2012 Yassene Mohammed Please send your feedback, questions, comments and suggestions for improvement to y.mohammed@lumc.nl 14 November 2012 Yassene

Created: 2013-08-16

Credits: Yassene Magnus Palmblad

EBI NCBI BLAST filter e-value and length (1)

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The workflow queries the NCBI BLAST web service and extracts the e-values and length of the results. One of the sub-workflows filters the length first and afterwards the e-value and the other sub-workflow filters first the e-value and then the length. As the result may be different, this workflow was used for optimization purposes to find the sub-workflow performing best.

Created: 2013-08-23 | Last updated: 2014-02-06

Credits: Sonja Holl

Attributions: EBI_NCBI_BLAST

Get concept suggestions from term (1)

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This workflow suggests concept ids that match the query term. The user can run this workflow with any term of interest as for example "human", "htt", "Transcription" etc, and will get suggestions for concept ids together with descriptions. Then can choose the concept id that matches the best to her/his needs and use it to the rest of the CPA workflows.

Created: 2013-08-31

Credits: Eleni BioSemantics

UnigeneID to KEGG Pathways (1)

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This workflow accepts a list of Unigene gene identifiers and returns descriptions of gene functions and a list of all pathways each gene is involved in (plus pathway image) from the KEGG database. This workflow replaces the earlier SOAP version with the new KEGG REST services

Created: 2013-09-03

Credits: Katy Wolstencroft Alan Williams Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

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.

Created: 2013-09-03

Credits: Alan Williams Paul Fisher

Attributions: Pathway to Pubmed