Workflows

Vector field lines in the planetary models... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the field lines for the vector field requested for the starting points provided for a particular planetary model.

Created: 2013-09-10

Credits: David PS

Particle trajectories in the planetary mod... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the particle trajectories for the defined particle (initial position, velocity, mass and charge) for a particular planetary model.

Created: 2013-09-10

Credits: David PS

Interpolate values on planetary models pro... (2)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the value of different variables, at the cordinates that a spacecraft pass through for the time range provided, for a particular planetary model. The orbital values of the spacecraft are obtained by AMDA.

Created: 2013-09-10 | Last updated: 2013-09-10

Credits: David PS

Interpolate values on planetary models pro... (1)

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This is a simple workflow using one of the webservice provided by IMPEx. It calculates the value of different variables, at the cordinates provided, for a particular planetary model.

Created: 2013-09-10

Credits: David PS

VOTable on the net maker for IMPEx (1)

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This simple workflow is a way to create a simple votable that uses the standards from IMPEx and provides an URL for the created VOTable enabling re-use of it through the IMPEx services

Created: 2013-09-10

Credits: David PS

RCOMM 2013 Challenge: 2. Solution (Re-infe... (1)

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This process is the solution for one of the RCOMM 2013 data mining challenge tasks which participants had to solve within 10 minutes. The task was this: Given (1) a variant of the Golf data set (found in the //Samples/data folder) where the attribute Outlook is missing, (2) a decision tree model built on the complete Golf data set, and (3) a utility data set containing only the three distinct values of Golf, create an example set based on the incomplete data set from (1) containing all po...

Created: 2013-09-09

RCOMM 2013 Challenge: 1. Generate input data (1)

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This process generates the input for one of the RCOMM 2013 data mining challenge tasks. For a description, please refer to the solution process.

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

BioCyc:Reaction Scheme (1)

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The purpose of this workflow is to determine all the enzymes/genes that participate in a radius of 2 reaction steps around a given metabolite. Broadly, the scheme involves the following steps: 1. determine all the reactions that the given metabolite participates in 2. determine all the compounds that participate in these reactions 3. filter certain compounds like H2O, ATP etc to avoid non-specific connections 4. determine all the reactions that the compounds passing through step 3 participate...

Created: 2013-09-06

Credits: Harish Dharuri

BioCyc:Pathway Scheme (1)

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The purpose of the workflow is to determine all the genes operating in BioCyc pathways that the input metabolite participates in. The overall idea is to generate a set of genes that potentially influence the levels of a metabolite due to the common pathways that they share.

Created: 2013-09-06

Credits: Harish Dharuri

Print R expression (3)

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This is a very small nested workflow to convert an R expression to the same textual representation that you see displayed when using the R command line.

Created: 2013-09-05 | Last updated: 2013-10-16

Credits: Jon Giddy

BioVeL workshop reduced full workflow (1)

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The workflow is a reduced version of the main workflow. It can be used to call web services to support biodiversity research. It fetches data from GBIF. The occurrences are then used to create a model using OpenModeller, test the model and to project the model. The projection of the model is currently a "native projection" i.e. it uses the same layers as those used to create the model. The services within the workflow will allow non-native projections

Created: 2013-09-04

Credits: Katy Wolstencroft Alan Williams

Attributions:

Convert Taverna list of RExpr to R list - v2 (2)

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This workflow accepts a Taverna list of arbitrary R expressions and returns a single R expression representing an R list containing the original expressions. This workflow relies on the current Taverna behaviour of an R expression being represented by a list of strings containing the deparsed expression. If this changes, this workflow will likely break. The first BeanShell converts each R expression (actually a list of strings) to a single string. This uses implicit iteration to do this for...

Created: 2013-09-04 | Last updated: 2013-10-14

Credits: Jon Giddy BioVeL

Hello World (1)

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One of the simplest workflows possible, outputting the String Constant "Hello world!"One of the simplest workflows possible. No workflow input ports, a single workflow output port "greeting", outputting "Hello, world!" as produced by the String Constant "hello".

Created: 2013-09-04

Credits: Raul Palma

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

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

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

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

Find Labels in WikiPathways that are IUPAC... (1)

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This scripts parses a directory with WikiPathways GPML files. For each "label" it checks if the label contains an IUPAC name (using OPSIN), calculated the InChIKey (using JNI-InChI/CDK), and looks up a ChemSpider identifiers (using the ChemSpider web service).

Created: 2013-08-20

Credits: Egon Willighagen

Extracts metabolites from GPML pathway fil... (1)

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Extracts metabolites from a collection of GPML pathway files downloaded from WikiPathways, and opens structures with IUPAC names in a molecules table, using the CDK and OPSIN.

Created: 2013-08-16

Credits: Egon Willighagen

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

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

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

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

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

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

Extracts metabolites from a GPML pathway d... (1)

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This Groovy scripts starts with a WikiPathways identifier, downloads the GPML, and uses the Groovy XmlParser to extract metabolites for which it reports the label, and if available, database and identifier.

Created: 2013-08-11 | Last updated: 2013-08-11

Credits: Egon Willighagen

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: Sonja Holl Renato De Giovanni

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: Sonja Holl Renato De Giovanni

WebCrawl-RapidMiner (1)

WebCrawl-RapidMiner

Created: 2013-08-06

Find isotopes with a certain exact match (1)

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This script lists all isotopes matching a certain exact mass (given a certain error) and outputs the symbol, atomic number, and exact match of the search hits.

Created: 2013-07-30 | Last updated: 2013-07-31

Credits: Egon Willighagen

Query EVS by chromosomal position (1)

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The workflow takes a list of chromosomal positions (in the format chr:pos e.g. 2:139574) and returns a selection of data in the Exome Variant Server (http://evs.gs.washington.edu/EVS/).

Created: 2013-07-26 | Last updated: 2013-07-26

Credits: Sirisha Hesketh

PubMed Search and Solr storage (5)

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Based on the work of Fisher: This workflow takes in a search term, are passed to the eSearch function and searched for in PubMed. I extended by removing outputs and text extraction and addded an automatic Solr storage process using a post.jar, specified by the user. Before running this workflow, make sure that a solr server is up and running and the variable attached to the SolrImport process contains the correct path. Dependencies: - Solr

Created: 2013-07-25 | Last updated: 2013-08-26

Credits: Sander van boom

Attributions: PubMed Search

I'm sorry I did not mean to :) (1)

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lsi

Created: 2013-07-25 | Last updated: 2013-08-19

wf4ever_document_extraction_and_storage (1)

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The workflow uses parts of the existing BioAid workflow by Marco Roos (http://www.myexperiment.org/workflows/74.html) The workflow stores found articles in a Solr database. Make sure that Solr is running in the correct directory (stored in the Solr_directory value).

Created: 2013-07-24 | Last updated: 2013-08-29

wf4ever_PDF2TXT2Solr_Database (1)

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This workflow extracts the text of a .pdf file and stores it in a .txt file. Then it stores the .txt file in a Solr database.

Created: 2013-07-24

Running a picard tool in the #KNIME workfl... (1)

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Running a picard tool in the #KNIME workflow engine . See my blog http://plindenbaum.blogspot.fr/2013/07/running-picard-tool-in-knime-workflow.html

Created: 2013-07-18

Credits: PL

Find asteroids in images from CAHA observa... (1)

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It analyzes images from CAFOS instrument in Calar Alto Observatory. It uses SkyBot catalog in order to identify objects in the Solar System. It includes a double check to avoid objets that are not asteroids (comparing with USNO and 2MASS catalogs). The result is a VOTable of asteroids

Created: 2013-07-17

Credits: Julian Garrido

Attributions:

Imagemagick convert - tiff2tiff - compression (2)

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Converts tiff to tiff using imagemagick convert with the provided compression

Created: 2013-07-08 | Last updated: 2013-07-08

Credits: Markus Plangg

OPS REST services (1)

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Library of REST services developed for the Open Pharmacological Space (OPS) by the OpenPHACTS project. Usage: 1. Copy-paste a service into your workflow 2. Add an output to responseBody 3. Run the workflow (this will produce output in XML) 4. Copy the XML output 5. Go back to the design window and add the XPath widget to the canvas 6. Link the responseBody output to the XPath widget input 7. Paste the XML output to the example window in the XPath configure window 8. Select the desired eleme...

Created: 2013-07-06

Credits: Marco Roos Open PHACTS

Find pathways in which two genes co-occur ... (1)

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This workflow finds all pathways in which two gene symbols co-occur. This workflow was created as an exercise for the "Managing and Integrating Information in the Life Sciences course 2013" at the LUMC, which is organized by the Netherlands Bioinformatics Center (NBIC).

Created: 2013-06-28 | Last updated: 2013-06-28

Free text search to Concept Wiki URI (4)

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Free text search of concept wiki using the Openphacts "Map free text to a concept url based on semantic tag" ie /search/byTag. Search for either compounds or targets depending on the input uuid for "searchType" and filter by source authority with the "branch" input

Created: 2013-06-24 | Last updated: 2013-06-24

Credits: Ian Dunlop Katy Wolstencroft Marco Roos paul groth

MusicClassificationExperiment (1)

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Performs a scientific experiment of classifying music into genres

Created: 2013-06-20

Credits: Rudolf Mayer

OPS_FreetextToTargetInfo (1)

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Workflow to retrieve target information for the concepts as refered to by humans (the input). Known issues: It produces error values for the concepts returned by ConceptWiki that are apparently not present in OPS (e.g. for "ezh2" and limit=10, it gives 7/10 error values vs "ezh2 (homo sapiens)" giving 2 valid values).

Created: 2013-06-18

Credits: Marco Roos Katy Wolstencroft paul groth

Fraunhofer IAIS mydec (4)

This workflow is provided by the Succeed EU project. For more information about Succeed, please visit http://succeed-project.eu/. For more information about mydec, please visit http://www.iais.fraunhofer.de/mydec.html

Created: 2013-06-04 | Last updated: 2014-02-07

Credits: cneudecker