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

Fundamental matrix (1)

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This component calculates the fundamental matrix from a stage matrix

Created: 2013-05-28

ref (2)

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ref

Created: 2013-05-28 | Last updated: 2013-05-28

From molecule name to SMILE and InchI usin... (2)

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Created: 2013-05-21 | Last updated: 2013-05-21

Credits: Luna De Ferrari

Chemical structure extractor - img2structure (1)

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Extracts images of chemical structures from PDFs and converts them to usable structure data using the OSRA binaries.An in-progress (incomplete) workflow.This workflow makes use of the External Tool node to access the OSRA structure recognition binaries.So you must have a functioning installation of OSRA and it's dependencies. This may require advanced compiler knowledge on your platform, and may not be a trivial task.OSRA 1.4 is free for both the source & binary distribution. OSRA 2.0...

Created: 2013-05-14 | Last updated: 2013-05-14

Credits: sauberns

Attributions: Chemical term extractor - text2structure

Variant discovery and reference correction... (1)

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Created: 2013-05-14 | Last updated: 2013-05-14

Credits: Robsyme

Retrieve object properties from NED and VO... (4)

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From an initial list of galaxy names, retrieve some of their properties from Virtual Observatory archives and services (NASA Extragalactic Database NED), and calculate others like Distance, based on the ones previously obtained (e.g. recession velocity, equatorial and galactic coordinates). The sample is filtered in a later step with criteria related to the angular size of the object and its declination. The goal is to build a sample of objects and their properties with up-to-date physical in...

Created: 2013-04-25 | Last updated: 2013-06-27

Perform Multi-SSA queries to an Spectral V... (2)

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Snippet showing how to use AstroTaverna "VO service perspective" and other tools for performing Multi-SSA queries to Spectral VO Services. The input is a VOTable with a list of source names and coordinates to perform the multi-query. Add_n_concat_tables tool is used to concatenate the list of responses issued from the multiquery. The result is a VOTable that may be renderized properly in the perspective Results, choosing Value Type as VOTable. It may also be sent via SAMP to other VO soft im...

Created: 2013-04-23 | Last updated: 2013-04-23

Retrieve the best position from an object ... (2)

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Snippet showing how to use Taverna REST Service tool for performing a query to a standard REST Service. In this particular case, the query is performed against NED_basic_posn REST Service from NASA Extragalactic Database (NED) Archive for the object M51. The result is a VOTable that may be renderized properly in the perspective Results, choosing Value Type as VOTable. More info on NED Web Serces: http://adsabs.harvard.edu/abs/2007ASPC..382..165M

Created: 2013-04-23 | Last updated: 2013-04-23

Credits: Jose Enrique Ruiz

Perform a SSA query to a Spectral VO Service (1)

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Snippet showing how to use AstroTaverna "VO service perspective" for performing SSA queries on Spectral VO Services. The result is a VOTable that may be renderized properly in the perspective Results, choosing Value Type as VOTable. In this particular case the Spectral Service queried is the Galexy Evolution Explorer (GALEX) SSA Service, with coordinates RA, DEC of 25, 22 and 1 degree in size.

Created: 2013-04-23

Credits: Jose Enrique Ruiz

Perform Multi-SIA queries to an Image VO S... (2)

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Snippet showing how to use AstroTaverna "VO service perspective" and other tools for performing Multi-SIA queries to Image VO Services. The input is a VOTable with a list of source names and coordinates to perform the multi-query. Add_n_concat_tables tool is used to concatenate the list of responses issued from the multiquery. The result is a VOTable that may be renderized properly in the perspective Results, choosing Value Type as VOTable. It may also be sent via SAMP to other VO soft imple...

Created: 2013-04-23 | Last updated: 2013-04-23

Credits: Jose Enrique Ruiz

Perform a SIA query to an Image VO Service (1)

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Snippet showing how to use AstroTaverna "VO service perspective" for performing SIA queries on Image VO Services. The result is a VOTable that may be renderized properly in the perspective Results, choosing Value Type as VOTable. In this particular case the Image Service queried is the Infrared Space Observatory (ISO) Data Archive SIAP Service, with coordinates RA, DEC of 30, 30 and 10 degrees in size.

Created: 2013-04-23

Credits: Jose Enrique Ruiz

Retrieve Bibliography from NED (1)

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This is a smal workflow that retrieves bibliography from Literature NED Web Service http://ned.ipac.caltech.edu/forms/SearchRefsByObjectName.html The input is a list of source names and the output is a VOTable with the info provided by NED, plus an extra column with the link pointing to the bliography in the NED website. This VOTable may be sent to Topcat via SAMP and the content of the "Link column" used as an action to display the website content in a browser when clicked. Note that the o...

Created: 2013-04-23

Credits: Jose Enrique Ruiz

Perform Multi-ConeSearch queries to a VO S... (1)

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Snippet showing how to use AstroTaverna "VO service perspective" and other tools for performing Multi-ConeSearch queries to a VO Services. The input is a VOTable with a list of source names and coordinates to perform the multi-query. Please *note how the AMIGACS block list handling is cofigured* with right click -> Configure running -> List Handling. Add_n_concat_tables tool is used to concatenate the list of responses issued from the multiquery. The result is a VOTable that may be renderiz...

Created: 2013-04-22

Perform a ConeSearch query to a VO Service (2)

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Snippet showing how to use AstroTaverna "VO service perspective" for performing ConeSearch queries on VO Services. The result is a VOTable that may be renderized properly in the perspective Results, coosing Value Type as VOTable.

Created: 2013-04-22 | Last updated: 2013-04-22

Use of temporary files to execute local to... (1)

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Snippet showing how to use AstroTaverna tool "Fill template from VOTable" for creating temporary files filling a template provided by the user. The input is two templates a one VOTable with information on where to store files created from filling the templates. The VOTable also contains data values to fill the templates. This snippet is particularly useful when a local tool needs different configuration files when looping through different executions.

Created: 2013-04-22

Add a common row to a VOTable (1)

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Snippet showing how to use AstroTaverna tool for adding a common row to a whole VOTable. The input are two VOTable, the main one has a lis of sources and coordinates, to which is appended a common row "Object Type" with common values "Messier Object". Right click on tool may change configuration to append the common row to left or right side of main VOTable.

Created: 2013-04-22

Transformation of reference coordinate system (1)

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Snippet showing how to use AstroTaverna tool for reference coordinate system transformation. The input is a list of source names and coordiantes and the output is a VOTable with two added columns for Galactic Latitude and Galactic Longitude.

Created: 2013-04-22

Chemical term extractor - text2structure (1)

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This workflow demonstrates how to extract biological and chemical terms (text!) from a PDF file using the KNIME text processing nodes and attempts to convert the chemistry terms to structures.Requirements:KNIME 2.7.4KNIME Labs nodes - Text ProcessingCommunity Nodes - RDKit (to view structures)See http://tech.knime.org/communityStart by selecting the folder containing the PDF documents. Alternatively, you can use a folder with Word docs.

Created: 2013-04-22 | Last updated: 2013-04-22

Credits: sauberns

Attributions: Chemical structure extractor - img2structure

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: Michael Smith Mark Borkum

Attributions: InChIToCSID

Validate_Compare_Compare_List (1)

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QA for file migrated to wav. The QA steps include File Format Validation, Significant Property Comparison and xcorrSound waveform-compare file content comparison (all CLI). Input the migrated wav and a "compare-to-wav" file.

Created: 2013-04-15

Credits: Bolette Jurik

Select columns from VOTable (2)

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Snippet showing how to use AstroTaverna tool for selecting/filtering columns from a VOTable.

Created: 2013-04-12 | Last updated: 2013-04-12

Select rows from VOTable (1)

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Snippet showing how to use AstroTaverna tool for selecting/filtering rows from a VOTable. Functions provided by STILTS Library may be used. http://www.star.bris.ac.uk/~mbt/stilts/sun256/sun256.html#staticMethods

Created: 2013-04-12

Joins two VOTables with the same numer of ... (1)

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Snippet showing how to use AstroTaverna tool for joining two VOTables. The input is two VOTables with the same number of rows. The result if using sample values provided will be an horizontally duplicated VOTable.

Created: 2013-04-12

Concatenates two VOTables with the same nu... (2)

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Snippet showing how to use AstroTaverna tool for concatenating two VOTables. The input is two VOTables with the same number of columns. The result if using sample values provided will be a vertically duplicated VOTable.

Created: 2013-04-12 | Last updated: 2013-04-12

Adding a column to a VOTable using a mathe... (1)

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Snippet showing how to use AstroTaverna tool for adding columns based on expressions of existing columns. The input is a VOTable with five columns. A new column is added considering the maximum value of the three last columns. All functions provided by STILTS Library may be used. http://www.star.bris.ac.uk/~mbt/stilts/sun256/sun256.html#staticMethods

Created: 2013-04-12

Coordinate units conversion (3)

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Snippet showing how to use AstroTaverna tool for coordinate units conversion "Coordinates_units_conversion_in_VOTable". The input is a VOTable with three columns: SourceName, RA_J2000, DEC_J2000 in units degrees. Two conversions are performed on the coordinates for Right Ascension, first from degrees to radians, and a second one from radians to RA hours:minutes:seconds. Choices on the units to convert from and to may be set up in service configuration: right click on box "Coordinate units con...

Created: 2013-04-12 | Last updated: 2013-04-22

Resolving coordinates from a source names ... (2)

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Snippet showing how to use AstroTaverna tool for coordinates resolving. The input is a list of source names and the output is a VOTable with three columns: SourceName, RAJ2000, DECJ2000.

Created: 2013-04-12 | Last updated: 2013-04-22

Table format coversion: ASCII to VOTable (2)

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Snippet showing how to use AstroTaverna tool for table format conversion

Created: 2013-04-12 | Last updated: 2013-04-12

Retrieving information from HST ConeSearch... (1)

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This workflow retieves information from Hubble Space Telescope VO Services in the form of VOTables. The input of the workflow is an ASCII file with a list of source names. This file is converted to a VOTable, and coordinates added with an extra-column needed to query SIAP Image service. The final result are two different VOTables issued as the response of both VO Services, Images VOTable has been previously filtered.

Created: 2013-04-12

Crossmatching VOTables (2)

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Snippet showing how to use AstroTaverna tool for crossmatching two VOTables VOTable samples may be downloaded from MyExperiment http://www.myexperiment.org/files/911/versions/1/download/SDSS7.vot http://www.myexperiment.org/files/910/versions/1/download/2MASS.vot

Created: 2013-04-12 | Last updated: 2013-04-22

Credits: Jose Enrique Ruiz

Discovery of Brown Dwarfs mining the 2MASS... (1)

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Brown dwarfs are objects occupying the gap between the least massive stars and the most massive planets. They are intrinsically faint objects so their detection is not straighforward and, in fact, was almost impossible until the advent of global surveys at deep optical and near-infrared bands like SDSS, 2MASS or DENIS among others. Here we propose to mine the SDSS and 2MASS databases to identify T-type brown dwarfs through an appropriate combination of colours in the optical and the infra-red...

Created: 2013-04-12

Credits: Jose Enrique Ruiz

Venus: Compare VEX data with HYB model (1)

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It compares data from VEX from a certain date range with what HYB has modeled in the coordinates where VEX spacecraft is at that moment.

Created: 2013-04-07

Credits: David PS Natasha

jpylyzer: Extract width and height (1)

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No description

Created: 2013-04-04

ImageMagick: Convert JPG to TIFF (3)

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Converts a JPG image to a TIFF image

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

EB-eye getAllResultIds and WSDbfetch fetch... (1)

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Get database entries for a query using EB-eye to perform the initial query against the database to get entry identifiers and using the identifiers with WSDbfetch to retrieve the entry data in the desired format. Note: this particular implementation is not suitable for queries which return large numbers of results.

Created: 2013-03-28

Credits: Hamish McWilliam

Comparison of Peptide and Protein Fraction... (1)

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This workflow was used to analyze the data in a manuscript by Mostovenko et al. (2013, submitted), comparing peptide and protein fractionation methods. The workflow identifies proteins by X!Tandem database search and validates the results using PeptideProphet. Additional information such as pI and fraction number is extracted and plotted for IEF and SCX data. For each protein identified in SDS-PAGE derived data sequences are downloaded from UniProt and plotted against the fraction number. Rs...

Created: 2013-03-27

Credits: Kate Mostovenko Yassene Magnus Palmblad

Attributions: Plasma Precipitation Analysis

When do the Fastest type II CME should be ... (1)

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The fastest CME is found from an interval of time, and propagated to Earth, in two steps, first to obtain the Solar wind speed at Earth and then propagated again with a more reasonable CME speed. The output produces Min-Max ETAs for each object in the heliosphere and the plots of the final propagation model. This Workflow was produced as one of the challenges in the HELIO CDAW-IV hosted at TCD

Created: 2013-03-21

Credits: Gab Anja Le Blanc David PS

Attributions: When did the fastest type II CME happened?

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: 2013-03-21

Credits: Nadia Cerezo Anja Le Blanc David PS

Attributions: Monthly counts for event occurences between beginning of year_start and end of year_end

Find data from a list of instruments and a... (1)

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For a certain time range, it looks for flares between a energy range (GOES x-ray flare class), and it provides the observations for such time range for the list of instruments asked. It also provides the table of flares with its properties. Note: This workflow does not look whether the instrument was not looking to the right field of view (eg., CDS)

Created: 2013-03-20

Credits: David PS Anja Le Blanc Nadia Cerezo Gab

Attributions: find events in xray and radio

Untitled (1)

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v2

Created: 2013-03-15

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2

Created: 2013-03-15

Untitled (1)

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Initial version

Created: 2013-03-15