Workflows

Retention Time Prediction with X!Tandem (1)

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This workflow identifies peptides from tandem mass spectra using X!Tandem as in a standard installation of the Trans-Proteomic Pipeline (TPP, version 4.6, but earlier versions should also work). The peptide-spectrum matches are validates using PeptideProphet (also from a standard installation of TPP) and peptides with at least a probability 0.95 are used to train a linear retention time predictor (Palmblad et al., 2002), whereby retention coefficients are also derived. These indirectly provid...

Created: 2012-09-03 | Last updated: 2012-09-03

Credits: Magnus Palmblad Yassene Eleni

Attributions: rt3.c

Associate Active Regions and Filaments to ... (1)

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This workflow is querying the HEC for the fastest 100 CME of a given list (input parameter); it calculates the latitude from the postion angle; last step is to query the HFC for Active Regions and Filaments for the given time where the bounding box of the feature contains the longitude (feature must be on the correct side of the Sun.) Inputs: HEC list name (must contain fields: v, time_start, pa_width, pa) Outputs: v, time_start, pa_width, pa of the 100 fastest CME, VOTables for associated A...

Created: 2012-09-03

Credits: Anja Le Blanc

READ_MULTI_FASTA_FILE (1)

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Read multi fasta file and split into a list of fasta sequences

Created: 2012-09-04 | Last updated: 2012-09-04

Credits: Mcasfrox

[untitled] (1)

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complete part one of assignment

Created: 2012-09-05 | Last updated: 2012-09-05

Credits: Mcasfrox

SNP Workflow (1)

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This workflow extracts information about the position of SNPs and the genes they are associated with

Created: 2012-09-05

Credits: Aishualex

SNP Workflow (1)

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This workflow extracts information about the position of SNPs and the genes they are associated with

Created: 2012-09-05

Credits: Vishalkpp

LASCO_CME_QUERY (1)

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This workflows queries the LASCO CME list and returns a VOTable with the following fields pa, pa_width, v_final and v_diff which is abs(v_init-v_final)/2

Created: 2012-09-05

Credits: Gab Eoincar Anja Le Blanc

Get SecchiRH composites images (1)

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 This workflow extracts the composite image from the http://secchirh.obspm.fr survey page.

Created: 2012-09-06 | Last updated: 2012-09-06

Credits: Baptiste Cecconi

timeToTimeRange (1)

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No description

Created: 2012-09-06

Goes Flare Check WF (3)

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No description

Created: 2012-09-06 | Last updated: 2012-09-06

Credits: Baptiste Cecconi HELIO

Attributions: Extract content of columns from VOTables

LASCO_CME_QUERY (2)

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This workflows queries the LASCO CME list and returns a VOTable with the following fields pa, pa_width, v_final and v_diff which is abs(v_init-v_final)/2

Created: 2012-09-06 | Last updated: 2012-09-06

Credits: Baptiste Cecconi

Attributions: Extract content of columns from VOTables

100CME_task1 (1)

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No description

Created: 2012-09-06 | Last updated: 2012-09-06

Credits: Baptiste Cecconi HELIO

Attributions: Extract content of columns from VOTables

xlmPath (2)

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xml path

Created: 2012-09-06 | Last updated: 2012-09-06

ACE Average Speed (1)

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No description

Created: 2012-09-06

Credits: Gab

WIND/Waves radio quicklook from CDAWeb WSD... (1)

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No description

Created: 2012-09-06

Credits: Baptiste Cecconi HELIO

Ulysses/URAP radio quicklook from CDAWeb W... (1)

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No description

Created: 2012-09-06

Credits: Baptiste Cecconi HELIO

Detect ellipse failures and get votable wi... (1)

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It detects if ellipse has failed by checking if the resulting data file exists. It adds a column (validellipse) that contains 1 if ellipse didn't fail and 0 if ellipse failed. It returns a votable that contains all the data with the new column and a votable that contains only the rows where ellipse didn't failed. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

Created: 2012-09-07

Credits: Julian Garrido

Cloud Parallel Processing of Tandem Mass S... (1)

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A workflow for searching LC−MS/MS mass spectrometry data using X!Tandem on the cloud. The workflow consists of 5 processors. The objectLogic processor prepares all inputs in the right format, i.e. keeping or converting strings into file object according to the following processor. The mzxmlDecomposer and pepxmlComposer run the decomposing/recomposing algorithms. objectLogic, mzxmlDecomposer and pepxmlComposer are Beanshell processors and they run locally. Xtandem runs X!Tandem on a remo...

Created: 2012-09-10

Credits: Yassene

Cloud Parallel Processing of Tandem Mass S... (1)

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A workflow for searching LC−MS/MS data using SpectraST on the cloud. The processor mzxmlDecomposer, pepxmlUnzip, and pepxmlComposer are identical to the one in the X!Tandem workflow (Figure 2). The only difference is that the Xtandem processor is exchanged with the Spectrast processor and the constant inputs are adjusted to SpectraST. This approach is also possible for other search engines as described in Data Decomposition and Recomposition Algorithms. More details can be found here:...

Created: 2012-09-10

Credits: Yassene

Cloud Parallel Processing of Tandem Mass S... (1)

An advanced scientific workflow for searching LC−MS data using SpectraST on the cloud. Uploading the libraries is optimized to achieve better performance, which makes this workflow more suitable for processing mzXML spectra files from human samples, as the corresponding NIST library needed by SpectraST is larger than 2 GB. Here we connect 3 nested workflows, in which the first 2, i.e., decomposeMzxml and uploadToCloud, run in parallel, while the third nested workflow, i.e. runSpectrastO...

Created: 2012-09-10 | Last updated: 2015-08-19

Credits: Yassene

Filter concepts with profiles (4)

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Purpose: Filter a list of concept id(s) by returning only those with a concept profile in the database.

Created: 2012-09-14 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Martijn Schuemie BioSemantics

The title (1)

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The description. This could be quite long.

Created: 2012-09-26

Credits: Stian Soiland-Reyes

Searching for near galaxies in NED service (2)

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This workflow needs as input an ascii table with a list of galaxies. This table contains the PGC name of the galaxy, the CIG number, the radius of searching, Z1 and Z2. The workflow uses the radius, Z1, Z2 and the PGC name of the galaxy to query NED service and get the html with the list of companions. This html is parsed and it is built a VOTable with the RA, DEC, Magnitud, Redshift, Separation, Velocity of each companion.

Created: 2012-09-26 | Last updated: 2012-10-09

Credits: Susana

Querying SDSS DR8 to get magnitude properties (2)

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This workflow gets a VOTable with the RA and DEC among others values of a list of galaxies. The workflow queries the SDSS DR8 VO conesearch service, to extract the objID, specObjID, ra, dec, u, g, r, i, z.

Created: 2012-09-26 | Last updated: 2013-03-08

Credits: Susana

Matchbox Evaluation (1)

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Matchbox evaluation against ground truth. The evaluation process first creates the matchbox output and ground truth lists. It then counts each page tuple from the matchbox output that is in the ground truth as correctly identified tuple (true positive). Those that are not in the ground truth are counted as incorrectly identified tuples (false positives), and finally, those that are in the ground truth but not in the matchbox output are counted as missed tuples (false negatives). The precision...

Created: 2012-10-02 | Last updated: 2012-10-02

Credits: Sven

Relation Extraction (1)

Perform relation extraction using AlchemyAPI. See here for more information: http://www.alchemyapi.com/api/relation/

Created: 2012-10-04 | Last updated: 2014-04-09

Credits: cneudecker

Sentiment Analysis (1)

Perform sentiment analysis using AlchemyAPI. See here for more information: http://www.alchemyapi.com/api/sentiment/

Created: 2012-10-04

Credits: cneudecker

Entity Extraction (1)

Perform entity extraction using AlchemyAPI. See here for more information: http://www.alchemyapi.com/api/entity/

Created: 2012-10-04

Credits: cneudecker

Concept Tagging (1)

Perform concept tagging using AlchemyAPI. See here for more information: http://www.alchemyapi.com/api/relation/

Created: 2012-10-04

Credits: cneudecker

OpenCalais (1)

Perform various enrichments using the OpenCalais API. See here for more information: http://www.opencalais.com/about

Created: 2012-10-04

Credits: cneudecker

Keyword Extraction (1)

Perform keyword extraction using AlchemyAPI. See here for more information: http://www.alchemyapi.com/api/keyword/

Created: 2012-10-05 | Last updated: 2014-04-09

Credits: cneudecker

Levenshtein edit distance words (1)

No description

Created: 2012-10-05

Credits: cneudecker

Tesseract 2.04 Basic Workflow (1)

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 Elementary workflow for execution on the on-line DAE platform. (requires an uncompressed tiff image URL as input or will fail otherwise)

Created: 2012-10-16

Credits: Bart Lamiroy

Ocrad 0.19 Basic Workflow (1)

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Elementary OCR workflow for execution on the on-line DAE platform. Implement v0.19 of the ocrad OCR engine. (requires an PGM or PMB input image URL) 

Created: 2012-10-16 | Last updated: 2012-10-16

Credits: Bart Lamiroy

Convert (1)

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Elementary workflow for execution on the on-line DAE platform. Converts an input image into another format by using the ImageMagick "convert" program.

Created: 2012-10-16 | Last updated: 2012-10-16

Credits: Bart Lamiroy

Standford Named Entity Detection (1)

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 Elementary OCR workflow for execution on the on-line DAE platform. Takes a text file as input. Implements a Named entity detection algorithm by Jenny Finkel and Christopher Manning as described in Jenny Rose Finkel, Trond Grenager, and Christopher Manning. 2005. "Incorporating Non-local Information into Information Extraction Systems by Gibbs Sampling". Proceedings of the 43nd Annual Meeting of the Association for Computational Linguistics (ACL 2005), pp. 363-370. ...

Created: 2012-10-16

Credits: Bart Lamiroy

NCC Document Layout Segmentation (1)

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Segments a black-and-white input image into text, line drawing and picture images. Contribution by the NCI/CADD group at the National Institutes of Health for the ICDAR 2011 Document Analysis Algorithm Contributions in End-to-End Applications Contest.

Created: 2012-10-16

Credits: Bart Lamiroy

NCC Image Binarization (1)

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Converts color or grayscale image to black-and-white. Winning contribution by the NCI/CADD group at the National Institutes of Health for the ICDAR 2011 Document Analysis Algorithm Contributions in End-to-End Applications Contest.

Created: 2012-10-16

Credits: Bart Lamiroy

DAE Random Image Selector (1)

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DAE Webservice providing n random images from a given data set. 

Created: 2012-10-16

Credits: Bart Lamiroy

APIS EPN-TAP Query (1)

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Use this workflow to query APIS (Auroral Planetary Imaging and Spectroscopy) using the EPN-TAP protocol.

Created: 2012-10-18

Credits: Baptiste Cecconi

Retrieve_Pubmed_Publication_by_kegg_pathwa... (1)

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This workflow shows in your browser pubmed articles related to input pathway

Created: 2012-10-18

Credits: Massimo La Rosa Antonino Fiannaca

get_Disease_Id_by_Pathway (1)

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retrieve Disease Id related to a gien pathway in KEGG db

Created: 2012-10-19

Credits: Massimo La Rosa Antonino Fiannaca

When did the fastest type II CME happened? (1)

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Simple query to the HELIO Event Catalogue to extract the start and end time of the fastest CME from the Wind Type II catalogue. Also it extracts the Xray Class from the flare associated to the CME

Created: 2012-10-21

Credits: David PS Eoincar

Attributions: Extract content of columns from VOTables

Forward CME propagation model (SHEBA) - de... (1)

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Extract Objects, HitOrMiss, ETAs and plots for a selected run of the SHEBA forward CME.

Created: 2012-10-21

Credits: David PS

Attributions: CME backwards propagation

Check registry for wrongly registed and un... (2)

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HELIO registry contains a list of tables available in the HEC. The HEC contains a table with available talbes itself. This workflow shows the differences between these two lists.

Created: 2012-07-24 | Last updated: 2012-07-24

Credits: Anja Le Blanc

Check the content of the Registry for mism... (1)

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This workflow check for tables which are registered in the HELIO registry but not available in the UOC and for tables which are in the UOC but which are not registred.

Created: 2012-07-25

Credits: Anja Le Blanc

Create configuration files from a template... (1)

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This workflow uses astrotaverna artifacts. It creates files by using a template whose keys are replaced by data from a votable. A configuration file is created for every row in the votable. The keys must appear also in the vocabulary file and match column names in the votable. A column in the votable must contain the name of the result configuration file.

Created: 2012-07-26 | Last updated: 2012-09-04

Credits: Julian Garrido

Run sextractor using a votable (2)

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It runs sextractor and adjust the paramenters specified. This workflow has a dependency on the stil library (http://www.star.bris.ac.uk/~mbt/stil/). Sextractor is called by an bash script as 'sex'. Sextractor is called for every row in the votable. Columns where the configuration file and the image file name are defined must be especified. These files should be accesibles from taverna. ExperimentFolder provides the root folder for the experiment. If the configuration files contain refer...

Created: 2012-07-26 | Last updated: 2012-09-07

Credits: Julian Garrido

Create votable from sextractor results (2)

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The workflow creates a votable from the results provided by sextractor (votables). It returns this table and an aditional table that is joined to the input table. It requires a votable that contains a column with the file name resulting from running sextractor and such files accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

Created: 2012-07-26 | Last updated: 2012-08-21

Credits: Julian Garrido