Workflows

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

Untitled (1)

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2

Created: 2013-03-15

Untitled (1)

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Initial version

Created: 2013-03-15