Workflows

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

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

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

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

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

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 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

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 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

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 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 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

ref (2)

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ref

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

Fundamental matrix (1)

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This component calculates the fundamental matrix from a stage matrix

Created: 2013-05-28

Clustering of Molecular Compounds with Bio... (4)

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This workflow downloads an input set of molecular compounds in SMILES format, using Chemspider service. The most frequent molecular fragments are extracted by means of MoSS tool (see http://www.borgelt.net/moss.html) , in order to obtain a set of features for each compound. Then a clustering and a visual exploration of the input dataset is performed by BioDICE service (see http://biolab.pa.icar.cnr.it/biodice.html), implementing Fast Learning Self-Organized Map (FLSOM) algorithm. Finally the ...

Created: 2013-05-29 | Last updated: 2014-01-09

Credits: Antonino Fiannaca Massimo La Rosa

Attributions: Get compound information Simple search

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

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

MusicClassificationExperiment (1)

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Performs a scientific experiment of classifying music into genres

Created: 2013-06-20

Credits: Rudolf Mayer

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

Test for Taverna Server + multiple R compo... (1)

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No description

Created: 2013-06-27

Test Taverna Server with coupled R components (1)

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No description

Created: 2013-06-27

maps genes to chromosomal location with co... (1)

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No description

Created: 2013-06-27

Simple WikiPathways SPARQL query (1)

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No description

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

Check HEC instances for diverging content (2)

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This workflow check all tables in HEC on festung1 and festung3 for diverging content by comparing the last 1000 entries in each table. Output is a list of tabel names with different content.

Created: 2012-08-20 | Last updated: 2012-08-20

Credits: Anja Le Blanc

Kegg:Reactions Scheme (2)

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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: 2012-08-20 | Last updated: 2013-08-27

Credits: Harish Dharuri

Create_SNP_Set (1)

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The purpose of the workflow is to determine SNPs in the vicinity of the genes and create a SNP set for a given set of genes. The user has the freedom to choose the flanking width around the gene for determining the SNPs. The input is in the form of entrez gene ids. Biomart services are used to determine the chromosome and position of the gene as well as determining Affy gene chip 6k ids. The final report is stored as a tab-delimited text file with Affy 6 gene chip ids for the SNP and Kegg inf...

Created: 2012-08-21

Credits: Harish Dharuri

Create votable from different galfit param... (2)

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The workflow creates a votable from the results provided by galfit. 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 galfit and such files must be accesible from taverna. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/) and it has a dependency on stil library (http://www.star.bris.ac.uk/~mbt/stil/). The galfit files may come from adjusting 'disk, bulb, ba...

Created: 2012-08-21 | Last updated: 2012-09-07

Credits: Julian Garrido

Number of features in a month in a year (1)

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Returns the number of features in a HFC catalogue which occured in a month in a year given as inputs.

Created: 2012-08-21

Credits: Anja Le Blanc

Get models from BioModels including the in... (3)

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A service to look for models in BioModels using a UniProt accession as input. If the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Created: 2012-08-22 | Last updated: 2012-08-24

Credits: Rafael C. Jimenez

Get a list of proteins annotated with an O... (3)

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A service to look for models in BioModels using an Ontology Id as input. First the workflow will look in QuickGO for UniProt accessions annotated with the provided Ontology Id. Then it will look for models using the list of proteins. If one of the input protein is found in one model the workflow will provide the BioModels Id, the SBML and a link to the BioModels database. Please use taverna 2.4 or above.

Created: 2012-08-22 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

Number of recorded features in catalogue p... (1)

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The number of features of the specified catalogue are counted per month between beginning of the year_start und the end of the year_end. Return format is VOTable

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

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 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

Read file from S3 bucket (1)

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This workflow simply loads a text file that is stored in an AWS S3 bucket. It is provided as an example of how to do this, rather than be a complete, reusable solution. You need to have s3fs installed and configured with your AWS credentials to use this workflow (see http://code.google.com/p/s3fs/).

Created: 2012-08-23

Credits: Robert Haines

Write file to S3 bucket (1)

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This workflow simply writes a text file to an AWS S3 bucket. It is provided as an example of how to do this, rather than be a complete, reusable solution. You need to have s3fs installed and configured with your AWS credentials to use this workflow (see http://code.google.com/p/s3fs/).

Created: 2012-08-23

Credits: Robert Haines

Attributions: Read file from S3 bucket

Mining the Kegg pathway database with the ... (2)

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Genome-Wide Association studies (GWAS) with metabolomic phenotypes yield several statistically significant SNP-metabolite associations. To understand the biological basis of the association, scientists typically dwell on identifying genes in the vicinity of the SNP and the possible pathways that the gene participates in. The information needed to arrive at an understanding of the mechanistic basis of the association requires integration of disparate data sources. The purpose of this workflow ...

Created: 2012-08-29 | Last updated: 2013-05-15

Credits: Harish Dharuri

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

Add columns to a votable resulting from ex... (1)

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Addcolumns that are needed to run galfit and ellipse. it requires columns coming from sextractor and the astrotaverna plugin.

Created: 2012-08-30

Credits: Julian Garrido

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: Julian Garrido

Cocatenates several VOTables into one (3)

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

Created: 2012-08-30 | Last updated: 2013-04-22

Credits: Julian Garrido

Get completion function V / Vm using the a... (1)

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Get completion function V / Vm using the apparent magnitude list of a set of galaxies

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

Credits: Julian Garrido