Workflows

Spreadsheet Import Example (1)

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Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file WaterUse.xlsx and generates a graph from the date. The source data is from http://data.gov.uk/

Created: 2012-04-05

Credits: Alan Williams

Unix tool service using string replacement (1)

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The tool service outputs a message that greets using the names specified on Greet's input ports.

Created: 2012-04-05

Credits: Alan Williams

Create and execute a simulation on the RIS... (1)

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Create and execute a simulation on the RISE server. This workflow take 3 inputs: the XML to configure the RISE framework, the URL of the ZIP file model (a zipped directory containing the model files), and the new framework name. This workflow produce on the output the simulation LOG file.

Created: 2012-04-09

Pathways and Gene annotations forQTL region (1)

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This workflow searches for genes which reside in a QTL (Quantitative Trait Loci) region in the mouse, Mus musculus. The workflow requires an input of: a chromosome name or number; a QTL start base pair position; QTL end base pair position. Data is then extracted from BioMart to annotate each of the genes found in this region. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to searcg for pathways in the KEGG path...

Created: 2012-01-20 | Last updated: 2012-01-20

Credits: Bonilla

A heuristic measure for detecting undesire... (2)

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The workflow takes TIFF image instances as input, applies a list of JP2 compression parameter values, executes OCR using an open source OCR engine, evaluates the results, and creates a diagram visualising the results. Dependencies on external tools for the tool service components: Tesseract ImageMagick Kakadu Gnuplot Dependencies on external Java libraries of beanshells: Apache commons lang

Created: 2012-02-06 | Last updated: 2012-03-09

Credits: Sven

Explain concept scores (7)

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Purpose of workflow: This workflow takes two concept ids as input and returns the top ranking "B" concepts according to Swanson's ABC model of discovery, where the relationships AB and BC are known and reported in the literature, and the implicit relationship AC is a putative new discovery. It might also be the case that AC is already known. In that case AC does not represent a new discovery but will still be returned (see workflow example values). The B concepts are returned sorted on the pe...

Created: 2012-02-07 | Last updated: 2014-07-14

Credits: Reinout van Schouwen

Define Associated Regions and Genes (2)

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Defines regions and genes from associated SNPs A JAVA MySQL connector is required to run the workflow and must be placed in the $TAVERNA_HOME/lib directory.

Created: 2012-02-08 | Last updated: 2012-05-09

Credits: Paul martin

Migration Imagemagick convert no compression (2)

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Converts an image using imagemagick convert -compress None

Created: 2013-02-25 | Last updated: 2013-02-26

Credits: Kraxner Markus Plangg

Attributions:

Test RShell (1)

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workflow hacked to include empty username and password elements

Created: 2013-02-27

Credits: Reinout van Schouwen Eleni

Attributions: workflow to test Rshell (for internal purposes)

Calculate_Isotopic_Distribution (1)

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This small workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Calculate_Isotopic_Distribution, that calculates the (integer mass) isotopic distribution using the FFT method. To shift to approximate real masses (or m/z values), transpose the distribution with the difference between the integer and real monoisotopic masses (both easily calculated using ...

Created: 2013-03-05

Credits: Magnus Palmblad

Visualize PAV provenance as SVG (2)

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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: 2013-03-05 | Last updated: 2013-04-05

Credits: Stian Soiland-Reyes

First Taverna workflow (1)

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No description

Created: 2013-03-06

Credits: Prasundutta87

imagemagick-convert-tiff2tiff-compression (1)

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Migration of tiff2tiff with compression action

Created: 2013-03-06 | Last updated: 2013-03-06

Three Microbase responders used for the Id... (1)

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Three microbase responders are used to take .sff data from IonTorrent and report on the organisms present within the data. It also takes three JSON input messages. The first calls sff_extract python script, the next calls MIRA or Ray and the final responder calls BLAST. For more information including a user manual visit www.bioinformatix.co.uk

Created: 2013-03-07

Credits: Team A

Metabolic profiling from NCBI GIs (1)

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This workflow will take NCBI GIs and produce the following output: KEGG identifier corresponding to the NCBI GI Information about the gene corresponding to the NCBI GI Pathway IDs corresponding to the the KEGG identifier Images of the pathways that the proteins defined by the NCBI GIs are involved in.

Created: 2013-03-08

Credits: Team A

Identification of Virulence Factors from a... (1)

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 This workflow takes a user specified genomic sequence and, via BLAST, queries a database containing genomic sequences of virulence factors. The database and genome sequence must be held locally. A python script is associated with this workflow and should be downloaded from www.bioinformatix.co.uk. A user and maintenance manual relating to this workflow can be found at www.bioinformatix.co.uk and should be consulted before this workflow is utilised.

Created: 2013-03-08

Credits: Team A

Antibiotic resistance profiling (1)

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 A workflow that takes a user defined genomic sequence and queries a third party database of genes encoding antibiotic resistance through a BLAST search for matching sequences. The accession IDs from the matches are extracted and the Entrez webservice is used to retrieve genbank records for the antibiotic resistance genes found. A python script is essential in the functioning of this workflow and this can be found at www.bioinformatix.co.uk along with a user and maintenance manual whic...

Created: 2013-03-08

Credits: Team A

Microbase S3CMD and AWS Workflow to Analys... (1)

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 This workflow is designed to interact with the aws and a specific VM, to carry out commands and analsye next gen sequence data (SFF FASTQ)

Created: 2013-03-08

Credits: ROBSeq Tech. Ltd.

Extract a column from a VOTable into a List (3)

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Snippet showing how to use AstroTaverna tool for extracting a column from a VOTable into a single List.

Created: 2013-03-08 | Last updated: 2013-04-22

Credits: Julian Garrido Susana

Simulate_Mass_Spectrum (1)

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This workflow takes as input a peptide sequence and calculates the elemental composition of the peptide (Calculate_Elemental_Composition). This is then transferred as a numerical vector to the Rshell Simulate_Mass_Spectrum, that calculates the isotopic distribution using the FFT method and convolutes the theoretical (infinite resolution) distribution with a Gaussian peak shape. The building blocks can be used in any other workflows using the isotopic distribution of peptides or other molecul...

Created: 2013-03-12

Credits: Magnus Palmblad

Untitled (1)

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Initial version

Created: 2013-03-15

Untitled (1)

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Initial version

Created: 2013-03-15

Untitled (1)

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2

Created: 2013-03-15

Untitled (1)

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v2

Created: 2013-03-15

retrive dpas data for all ics instruments ... (2)

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No description

Created: 2013-03-20 | Last updated: 2013-03-21

Credits: Nadia Cerezo

Attributions: retrive dpas data for all ics instruments for HEC event data

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

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

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?

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

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

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

jpylyzer: Extract width and height (1)

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No description

Created: 2013-04-04

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

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

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

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

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

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

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

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

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:

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

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

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

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

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

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

When do the Fastest type II CME should be ... (2)

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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: 2012-10-21 | Last updated: 2013-03-20

Credits: David PS Eoincar Gab Baptiste Cecconi Shanem Jbyrne Florian Mayer Natasha A lynnyk

Attributions: LASCO_CME_QUERY LASCO_CME_QUERY MDES simple execution timeToTimeRange Forward CME propagation model (SHEBA) - defined outputs When did the fastest type II CME happened? Goes Flare Check WF 100CME_task1 Extract average Solar wind speed from ACE data

Back CIR-CME propagation model (1)

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With a observing time at an object and the type of PM that you want to run executes it and provides the plots and the time and longitude where it should be seen the origin of the event.

Created: 2012-10-24

Credits: David PS Anja Le Blanc

Attributions: CME backwards propagation Co-rotating Interaction Regions backwards propagation

Solar Wind properties and plot (1)

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Using HELIO-MDES this workflow provides some properties of the solar wind from an input date and a mission and the plot +/-1 day for context.

Created: 2012-10-25

Credits: David PS

Attributions: MDES simple execution

Extract average Solar wind speed from ACE ... (1)

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It reads the data coming from a MDES (HELIO) query and calculates the average Solar Wind speed. Notice that it just works for ACE as other missions could have the columns in different order.

Created: 2012-10-30

Credits: Eoincar

Number of bonds/atoms generator from Chemi... (1)

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No description

Created: 2012-10-30 | Last updated: 2012-10-30

Credits: Michael Smith

Matching flare events to active regions (1)

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No description

Created: 2012-11-01

Credits: Anja Le Blanc

Mp3 To Wav Migrate QA CLI List Test (4)

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Migrates Mp3 files from input List to Wav files and performs QA. The QA steps include File Format Validation, Significant Property Comparison and migrationQA file content comparison (all CLI). As this is a Test workflow, the (very large) Wav files are deleted, and only the QA results and log files are saved for analysis. This workflow matches solution SO4 on the SCAPE opf wiki, see http://wiki.opf-labs.org/display/SP/SO4+Audio+mp3+to+wav+Migration+and+QA+Workflow

Created: 2012-11-05 | Last updated: 2012-11-13

Credits: Bolette Jurik

HFC Synoptic map from date (1)

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query the HELIO Feature Catalogue, and retrieves the image with all the features catalgued for certain date.

Created: 2012-11-05

Credits: David PS

CDAW CME movie from date (1)

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generates the url for the input date to visualize CMEs and GOES xray light curve produced by CDAW at GSFC

Created: 2012-11-05

Credits: David PS

Attributions: HFC Synoptic map from date

ImportRefSeqtoKegg (3)

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Kegg gene identifiers. This workflow uses the new KEGG REST service, which replaces the old SOAP interface from 31st December 2012

Created: 2012-11-12 | Last updated: 2013-01-08

Credits: Katy Wolstencroft

Finding the origins of Solar Wind events a... (6)

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This gives a comprenhensive overview of high speed solar wind events (CME or CIR) seen at Eart, by obtaining the maximum in-situ measure velocity from the data evaluation service (DES), propagating the even backwards to Earth using the HELIO processing service (HPS) and SHEBA propagation model, and search whether halo CMEs or CHs were observed on that time, and retrieves, besides all the previous information, a context solar wind plot (+/- 1 day) and a URL linking to a context movie for CMEs...

Created: 2012-11-16 | Last updated: 2013-03-21

Credits: David PS

Attributions: CME backwards propagation Co-rotating Interaction Regions backwards propagation HFC Synoptic map from date CDAW CME movie from date Solar Wind properties and plot Back CIR-CME propagation model LASCO_CME_QUERY

AIT Matchbox Scenario All (1)

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In this scenario matchbox will find duplicates in passed digital collection. All matchbox workflow steps are executed automatically in one turn. User will get a list of duplicates in result. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24 | Last updated: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Professional (3)

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In this scenario matchbox will find duplicates in passed digital collection. Each matchbox workflow step can be executed separately. User will get a list of duplicates in result. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine. This workflow starts duplicate finding process using the FindDuplicates python script of the matchbox tool. Matchbox tool support python in version 2.7. Execution starts from the directory where python scripts ...

Created: 2012-11-24 | Last updated: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Find Duplicates usin... (1)

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In this scenario matchbox will find duplicates in passed digital collection. All matchbox workflow steps are defined separately using input parameter sequence: clean, extract, train, bowhist and compare. User will get a list of duplicates in result. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Check Duplicate Pair... (1)

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In this scenario matchbox will check duplicate pair of previously found duplicates in passed digital collection if output information was lost. The pair check does not require the time consumpting whole analysis and is very fast. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24

Credits: Roman SCAPE

AIT Matchbox Scenario Compare Image Pair b... (1)

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In this scenario matchbox will compare given image pair based on extracted profile information. User will get a histogram intersection distance value in result. Small value means high similarity, high value means different images. Matchbox in this scenario is installed on remote Linux VM. Digital collection is stored on Windows machine.

Created: 2012-11-24

Credits: Roman

Ingest.t2flow (1)

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 characterisation of NeXus files

Created: 2012-12-19

Credits: Arifshaon

Microbial Metagenomic Trait Statistical An... (9)

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This workflow retrieves the following microbial metagenomic traits from the Microbial Metagenomic Trait Database: -GC content -Variance of GC content -Dinucleotides -Number of rRNA -Codon usage -Amino acid composition -Acidic to basic amino acids ratio -% of Transcriptional factors -% of classified reads -Functional content -Functional diversity -Taxonomic content -Taxonomic diversity After the retrieval performs the ecological analyses described in Barberan et al. 2012 (http://dx.doi.or...

Created: 2012-12-19 | Last updated: 2014-11-12

Credits: Antonio Fernandez-Guerra Renzo Peliny BioVeL

Intialize Sample (2)

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This workflow saves a tabular *.pckl Python pickle dataset in the local file system, containing values calculated on physical parameters associated to potential companions of a sample of target galaxies. These original physical parameters are extracted from a postgreSQL database, containing information of all galaxies covered by the SDSS spectroscopic survey. The workflow first access the external database located in the AMIGA server and selects the target galaxies from the sample (those havi...

Created: 2013-01-04 | Last updated: 2013-01-05

Credits: Juandesant Jsm

Environment (2)

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From a previously selected cube of galaxies residing in a remote database, we provide extragalactic environment parameters for all galaxies sample. This workflow takes as input the path of the tabular *.pckl Python pickle dataset created in the previous workflow, as well as the database connection settings and several criteria on how to filter the potential companions of the target galaxies. It provides a file with the SDSS identifiers of each target galaxy of the sample, environmental estim...

Created: 2013-01-04 | Last updated: 2013-01-14

Credits: Juandesant Jsm

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

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

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

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

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

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

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

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

GWAS to biomedical concept (3)

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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: 2013-04-15 | Last updated: 2014-07-14

Credits: Kristina Hettne Harish Dharuri Marco Roos Reinout van Schouwen

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