Workflows

Executes Python script (4)

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Snippet showing how to use Taverna Tool in Service template folder for executing a Python script. This workflow needs Python to be installed on the local system, and declared in the PATH enviromental variable, so any python script could be executed from a terminal.

Created: 2011-07-14 | Last updated: 2013-04-22

Credits: Jose Enrique Ruiz

Epitope-based Vaccine Design Workflow usin... (3)

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Population-based vaccine design workflow in KNIME. AlleleFrequency is used to specify the geographical region or population of interest and returns a tab-separated list of HLA alleles with their corresponding occurrence probability within the selected population. This file, together with a FASTA file containing protein sequences, or a file containing peptides is used as input to EpitopePrediction, which generates a file containing the predicted binding affinities of the (generated) peptides a...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: Benjamin Schubert

HLA ligandomics workflow using OpenMS and ... (2)

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HLA ligandomics workflow combining native KNIME, OpenMS, and ImmunoNodes nodes. The workflow extracts MS data from PRIDE and performs mass spectra identification with X!Tandem, annotates the results with details of the given target/decoy database, calculates false discovery rates and filters for 5% FDR using OpenMS’ nodes. The identified peptides are annotated with their respective binding affinity predicted by NetMHC using the EpitopePrediction node. Finally, simple summary statistics ...

Created: 2016-11-30 | Last updated: 2017-04-11

Credits: Mathias Walzer

Environment (2)

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From a previously selected cube of galaxies residing in a remote database, we provide extragalactic environment parameters for all galaxies sample. This workflow takes as input the path of the tabular *.pckl Python pickle dataset created in the previous workflow, as well as the database connection settings and several criteria on how to filter the potential companions of the target galaxies. It provides a file with the SDSS identifiers of each target galaxy of the sample, environmental estim...

Created: 2013-01-04 | Last updated: 2013-01-14

Credits: Juandesant Jsm

Intialize Sample (2)

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This workflow saves a tabular *.pckl Python pickle dataset in the local file system, containing values calculated on physical parameters associated to potential companions of a sample of target galaxies. These original physical parameters are extracted from a postgreSQL database, containing information of all galaxies covered by the SDSS spectroscopic survey. The workflow first access the external database located in the AMIGA server and selects the target galaxies from the sample (those havi...

Created: 2013-01-04 | Last updated: 2013-01-05

Credits: Juandesant Jsm

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

Sort 1000 fastest CMEs from a given list a... (1)

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The fastest 1000 CME of the input list are bined in categories by factor of 10 according to their pa_width value. List must contain fields v and pa_width. Output VOTable with the counts in the categories.

Created: 2012-08-30 | Last updated: 2012-08-30

Credits: Anja Le Blanc

Monthly counts for event occurences betwee... (1)

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This workflow provides monthly counts of events in HEC between the beginning of year_start and the end of year_end. Returns the result as comma separated file (csv) and as list of lists.

Created: 2012-08-23

Credits: Anja Le Blanc

Attributions: Counts number of events per month in HEC table Split VOTable into its values

Counts number of events per month in HEC t... (1)

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This workflow counts the monthly number of events in a HEC table from the begining of year year_start to the end of year year_end. Returns a VOTable with the count

Created: 2012-08-22

Credits: Anja Le Blanc

Monthly counts for feature occurences betw... (1)

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This workflow provides monthly counts of features in HFC between the beginning of year_start and the end of year_end. Returns the result as comma separated file (csv) and as list of lists.

Created: 2012-08-22

Credits: Anja Le Blanc

Attributions: Number of recorded features in catalogue per month Split VOTable into its values