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Category: Workflow Type: Taverna 2 Tag: workflow

Workflow Visualize PAV provenance as SVG (1)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2014-05-08

Credits: User Katy Wolstencroft User Aleksandra Pawlik

Uploader

Workflow Download data from array express + create ... (1)

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This workflow uses the array express library to download data from the array express repository and creates two separate files. The gene expression and the phenotype files. The files are saved in the directory that the user has to specify in the input. NOTE: The library(ArrayExpress) is a prerequisite for this workflow

Created: 2013-11-04

Credits: User Eleni

Workflow 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: User Sonja Holl User Yassene User Magnus Palmblad

Attributions: Workflow Retention Time Prediction with X!Tandem

Workflow ENM SVM workflow used for optimization (1)

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This workflow was used for the optimization of the SVM algorithm from the openModeller toolbox (http://openmodeller.sourceforge.net). The workflow uses 10-fold cross-validation and then calculates the average AUC, which can be used as fitness value during parameter optimization.

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

Credits: User Sonja Holl User Renato De Giovanni

Workflow ENM Maxent workflow used for optimization (1)

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This workflow was used for the optimization of the Maxent algorithm from the openModeller toolbox (http://openmodeller.sourceforge.net/). The workflow uses 10-fold cross-validation and then calculates the average AUC, which can be used as fitness value during parameter optimization.

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

Credits: User Sonja Holl User Renato De Giovanni

Uploader
Project Biovel

Workflow Biome-BGC MCE 1.4.1 (4)

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Biome-BGC is a process-based biogeochemical model that can be used to simulate carbon, nitrogen and water fluxes of different terrestrial ecosystems. Two models were implemented: Biome-BGC 4.1.1 MPI (Trusilova et al. 2009) and Biome-BGC MuSo 3.0 (Hidy & Barcza 2014). Its has about 40 and 60 various parameters. The only way to estimate or set these parameters is "calibration" (data-model-harmonization or model-data-fusion), which demands a hugh amount of computational capacity. Monte Carlo Exp...

Created: 2013-06-04 | Last updated: 2014-10-04

Credits: User Ferenc HORVATH User Zoltan BARCZA User Dora Krasser User Peter Ittzes Network-member BioVeL

Workflow Text-mining using OSCAR to obtain a list o... (1)

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This service extracts chemical names from text and obtains identifiers for these names. It outputs a HTML string that can be opened in a browser providing a table of information and links to ChemSpider.Known issues - Character limit ~3000 - Unable to produce InChIs or CSID for some names - Error sometimes encountered when a trivial and systematic name for the same compound are used - Some issues with identifiers being recognised but not able to be processedrequires access ...

Created: 2013-04-18

Credits: User Michael Smith User Mark Borkum

Attributions: Workflow InChIToCSID

Uploader

Workflow workflow to test Rshell (for internal purp... (1)

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 This is a workflow to test if Rserve is working properly, for internal purposes.  Takes as input two integers. output is the sum of integer 1 and integer 2  

Created: 2013-01-21 | Last updated: 2013-03-11

Credits: User Eleni

Workflow 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: User Julian Garrido

Workflow Build plots from galfit and ellipse results (2)

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Build plots from galfit and ellipse results (http://www.myexperiment.org/workflows/3068.html, http://www.myexperiment.org/workflows/3052.html).

Created: 2012-08-30 | Last updated: 2012-09-07

Credits: User Julian Garrido

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