Workflows

LASCO_CME_QUERY (2)

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This workflows queries the LASCO CME list and returns a VOTable with the following fields pa, pa_width, v_final and v_diff which is abs(v_init-v_final)/2

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

Credits: Baptiste Cecconi

Attributions: Extract content of columns from VOTables

Get SecchiRH composites images (1)

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 This workflow extracts the composite image from the http://secchirh.obspm.fr survey page.

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

Credits: Baptiste Cecconi

LASCO_CME_QUERY (1)

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This workflows queries the LASCO CME list and returns a VOTable with the following fields pa, pa_width, v_final and v_diff which is abs(v_init-v_final)/2

Created: 2012-09-05

Credits: Gab Eoincar Anja Le Blanc

SNP Workflow (1)

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This workflow extracts information about the position of SNPs and the genes they are associated with

Created: 2012-09-05

Credits: Vishalkpp

SNP Workflow (1)

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This workflow extracts information about the position of SNPs and the genes they are associated with

Created: 2012-09-05

Credits: Aishualex

[untitled] (1)

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complete part one of assignment

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

Credits: Mcasfrox

READ_MULTI_FASTA_FILE (1)

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Read multi fasta file and split into a list of fasta sequences

Created: 2012-09-04 | Last updated: 2012-09-04

Credits: Mcasfrox

RCOMM 2012 Sudoku Challenge: 4 - Solve Sudoku (1)

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Process from the http://rcomm2012.org live data mining challenge. The task was to partially solve a Sudoku puzzle by solving three subtasks. Processes 1-3 in this pack are the actual solutions to the tasks, process 0 loads the required data into your repository and process 4 is the bonus that solves the entire puzzle. Finally, this process solves the entire Sudoku. It uses process 3 to add inferred cell values to the set of predefined values. It does so repeatedly until 81 values are defined...

Created: 2012-09-04

RCOMM 2012 Sudoku Challenge: 3 - Drop impo... (1)

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Process from the http://rcomm2012.org live data mining challenge. The task was to partially solve a Sudoku puzzle by solving three subtasks. Processes 1-3 in this pack are the actual solutions to the tasks, process 0 loads the required data into your repository and process 4 is the bonus that solves the entire puzzle. IMPORTANT: Save this process as "RCOMM 2012 Sudoku Challenge: 3 - Drop impossible values (loop)" since it is included from process 4. This process uses process 2 repeatedly to ...

Created: 2012-09-04

RCOMM 2012 Sudoku Challenge: 2 - Drop impo... (1)

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Process from the http://rcomm2012.org live data mining challenge. The task was to partially solve a Sudoku puzzle by solving three subtasks. Processes 1-3 in this pack are the actual solutions to the tasks, process 0 loads the required data into your repository and process 4 is the bonus that solves the entire puzzle. IMPORTANT: Save this process as "RCOMM 2012 Sudoku Challenge: 2 - Drop impossible values" since it is included from process 3. This process eliminates impossible rows from the...

Created: 2012-09-04

RCOMM 2012 Sudoku Challenge: 1 - Generate ... (1)

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Process from the http://rcomm2012.org live data mining challenge. The task was to partially solve a Sudoku puzzle by solving three subtasks. Processes 1-3 in this pack are the actual solutions to the tasks, process 0 loads the required data into your repository and process 4 is the bonus that solves the entire puzzle. This process loads the numbers 1..9 and uses two Cartesian Product operators to compute the set of all combinations x, y, v. Finally we compute the index of the 3x3 sub-field a...

Created: 2012-09-04

RCOMM 2012 Sudoku Challenge: 0 - Get Data (1)

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Process from the http://rcomm2012.org live data mining challenge. The task was to partially solve a Sudoku puzzle by solving three subtasks. Processes 1-3 in this pack are the solutions to the actual tasks, process 0 loads the required data into your repository and process 4 is the bonus that solves the entire puzzle. This process loads the two required data sets from rapid-i.com and stores them in your repository. The first data set contains the numbers 1 to 9 and the second contains the pr...

Created: 2012-09-04

Associate Active Regions and Filaments to ... (1)

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This workflow is querying the HEC for the fastest 100 CME of a given list (input parameter); it calculates the latitude from the postion angle; last step is to query the HFC for Active Regions and Filaments for the given time where the bounding box of the feature contains the longitude (feature must be on the correct side of the Sun.) Inputs: HEC list name (must contain fields: v, time_start, pa_width, pa) Outputs: v, time_start, pa_width, pa of the 100 fastest CME, VOTables for associated A...

Created: 2012-09-03

Credits: Anja Le Blanc

Retention Time Prediction with X!Tandem (1)

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This workflow identifies peptides from tandem mass spectra using X!Tandem as in a standard installation of the Trans-Proteomic Pipeline (TPP, version 4.6, but earlier versions should also work). The peptide-spectrum matches are validates using PeptideProphet (also from a standard installation of TPP) and peptides with at least a probability 0.95 are used to train a linear retention time predictor (Palmblad et al., 2002), whereby retention coefficients are also derived. These indirectly provid...

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

Credits: Magnus Palmblad Yassene Eleni

Attributions: rt3.c

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

NCBI Protein Clustal Omega Alignment (1)

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Searches NCBI Proteins for a given organism and protein. User VMatch (xmknr) Vmatch, a versatile software tool for efficiently solving large scale sequence matching tasks to remove possible dubplcate and clustal omega to generate a multiple sequence alignment. Clustal Omega is the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. It will also make u...

Created: 2012-08-31

Credits: Carol Lushbough

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

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

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

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

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

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

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

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 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

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

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

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

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

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

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

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

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

Hadoop Large Document Collection Data Prep... (1)

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Workflow for preparing large document collections for data analysis. Different types of hadoop jobs (Hadoop-Streaming-API, Hadoop Map/Reduce, and Hive) are used for specific purposes. The *PathCreator components create text files with absolute file paths using the unix command 'find'. The workflow then uses 1) a Hadoop Streaming API component (HadoopStreamingExiftoolRead) based on a bash script for reading image metadata using Exiftool, 2) the Map/Reduce component (HadoopHocrAvBlockWidthMapR...

Created: 2012-08-17 | Last updated: 2012-08-18

Credits: Sven

KEGG:Pathway Scheme (2)

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The purpose of the workflow is to determine all the genes operating in the 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: 2012-08-14 | Last updated: 2013-08-27

Credits: Harish Dharuri

Gathering info from SDSS into a VOTable to... (4)

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This workflow joins two main nested workflows: - "Extract SDSS field information and PSF" workflow, which gathers information from SDSS VO service and from the header image in several VOtable. It also generates the psf files. - "Joining VOtables with information to execute Sextractor, Galfit and Ellipse" workflow, which joins the VOtables generated by the previous workflow to get only one VOtable with all the information

Created: 2012-08-13 | Last updated: 2013-03-08

Credits: Susana

Joining VOtables with information to execu... (3)

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This workflow join 13 votables, obtained from the workflow "Extract SDSS field information and PSF" in order to get a only one votable with all the information. Also it adds the columns "zp", "magzeropoint", xconvsize, yconvsize that are calculated from values provided in the inputs. The zp is -( aa + kk * airmass ), the magzeropoint is zp + 2.5 * log10(53.907456), the xconvsize is roundUp(nx/10) and the yconvsize is roundUp(ny/10)

Created: 2012-08-13 | Last updated: 2013-03-08

Credits: Susana

Convert a list into a VO Column (2)

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This workflow converts a list of values into a VO table with only one column. It receives two inputs: the list of values and the header name of the column to be built.

Created: 2012-08-13 | Last updated: 2013-03-08

Credits: Susana

Oryza Sativa QTLs and genes retrieval from... (2)

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For a given trait and QTL maximum size, retrieve accession numbers of the QTLs along with their mapping positions in Oryza sativa and retrieve genes present in the mapping genomic interval of a given QTL. Data integration from TropGene, Gramene and Ensembl relational databases. Semi-automatic creation of 7 Semantic Web Services for TropGene and Gramene with BioSemantic Use of BioMart Web Services for Ensembl interrogation

Created: 2012-08-08 | Last updated: 2012-09-28

Credits: Julien wollbrett

Hadoop hOCR parser (1)

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Big data processing: chaining Hadoop jobs using Taverna. This workflow demonstrates a simple way of linking different hadoop job components using the standard output of the hadoop jobs. It is not for thought for productive use, but for demonstration using small data sets. The code for the hadoop jobs is available on Github: tb-lsdr-hocrparser and tb-lsdr-seqfilecreator.

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

Credits: Sven

Calculate ellipses that describe a galaxy ... (2)

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This workflow calculates the ellipses that better match a galaxy by doing two iterations. In the first one the center and the outer ellipse are aproximated because there might be bars that affect to the inner ellipses. In the second one, files with the ellipse data are built. It creates ellipse scripts using data from a votable, it runs ellipse, its results are added to the votable, it creates new scripts for ellipse using the previous results, it runs ellipse a second time and it finally in...

Created: 2012-08-07 | Last updated: 2012-09-11

Credits: Julian Garrido

Attributions: Create configuration files from a template and a votable Run scripts from a column in a votable Create votable from ellipse results Detect ellipse failures and get votable without ellipse failures

Create votable from ellipse results (2)

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The workflow takes from a votable the names of files where the ellipse result is stored. These files contain data for several ellipses and the workflow takes the center from the inner ellipse and the ellipticitiy from one of the outter ones. It uses astrotaverna plugin (http://wf4ever.github.com/astrotaverna/).

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

Credits: Julian Garrido

Run scripts from a column in a votable (2)

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It runs scripts whose pathname are values of a column in a votable

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

Credits: Julian Garrido

Gene_To_Pathways (Vistrails) (1)

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This workflow retrieves the pathways that are associated with given Kegg gene identifiers.

Created: 2012-08-06 | Last updated: 2012-08-08

Credits: Khalid Belhajjame

Gene_To_Pathways (Vistrails) (1)

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This workflow retrieves the pathways that are associated with given Kegg gene identifiers.

Created: 2012-08-06 | Last updated: 2012-08-08

Credits: Khalid Belhajjame

Gene_To_Pathways (Vistrails) (1)

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This workflow retrieves the pathways that are associated with given Kegg gene identifiers.

Created: 2012-08-06 | Last updated: 2012-08-08

Credits: Khalid Belhajjame

Gene_To_Pathways (1)

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 This workflow identifier the pathways that are associated with given Kegg gene identifiers. Example inputs that can be used to run the workflow are eco:b0002, eco:b0078

Created: 2012-08-06 | Last updated: 2012-09-07

Credits: Khalid Belhajjame Stian Soiland-Reyes

Attributions: Hello Anyone

de Bruin et al. Workflow 4 (1)

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This is "Workflow 4" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 3 (1)

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This is "Workflow 3" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad

de Bruin et al. Workflow 2 (1)

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This is "Workflow 2" from de Bruin et al., Mol. Cell. Proteomics 2012.

Created: 2012-08-01 | Last updated: 2012-08-01

Credits: Magnus Palmblad