Workflows

Find Orthologs for proteins in Ensembl (1)

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Find Orthologs for proteins in Ensembl using biomart.

Created: 2011-10-03 | Last updated: 2011-10-03

Credits: Rafael C. Jimenez

[untitled] (1)

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 æˆ‘的第一个工作流，测试

Created: 2011-10-03 | Last updated: 2011-10-03

Credits: Zhaoyingguang

Comparing Quantities using HyperLEDA (1)

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This workflow receives the name of the property to compare, a file with a list of names of galaxies, and a file with the list of original values of that property. The property name must be typed in the same way used in the HTML returned by HyperLEDA The workflow calls to HyperLEDA using the names of the galaxies as input, and it returns a HTML file with information about the galaxy. This file is parsed by the python tool "ExtractPropertyValues", that extracts the value of the property introdu...

Created: 2011-10-03

Retrieve Molecular Interactions from PSICQ... (1)

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Retrieve Molecular Interactions from PSICQUIC Services for a list of Protein Accessions in PSI-MITAB format

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Rafael C. Jimenez

What's the Season? (1)

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When given a list of astronomical object names, this workflow will check them against a simple Excel spreadsheet and return which season the object is best observed in. It will also compare the distances to the objects in a Google Charts bar chart. A later version of this may switch to a scatter plot, depending on whether or not this works with the Google Chart API. Running this workflow requires Python. Sys and string should be bundled in Python, but the numpy module will need to be downloa...

Created: 2011-10-05 | Last updated: 2011-10-05

Attributions: Spreadsheet Import Example

Extracting Quantities from HyperLEDA (1)

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This workflow receives the name of the property to compare and a file with a list of names of galaxies. The property name must be the same used in the HTML file returned by the HyperLEDA service. The workflow calls to HyperLEda service, using as input the names of the galaxies in order to get a HTML file with information about each galaxy. From each HTML file, it extracts the value of the property selected by the user. The workflow uses a python tool to parse the HTML file (one for each gala...

Created: 2011-10-05 | Last updated: 2011-10-05

HTML Citation Extraction (1)

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 This workflow is a beanshell script that locates and extracts text within an html page.  It was designed to pull citation information from the website http://robjhyndman.com/TSDL/.

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Jeff adamus

Current Date Output (1)

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Returns the Current Date optionally Formatted by input. Free to copy and use by all!.

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Jeff adamus

Time Series Data Graphed and Cited (1)

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This workflow uses time series data from Rob Hyndman's Time Series Data Library (TSDL) and graphs it with Google charts. It also provides the citation information with the current date. The outputs are a Google Chart and the corresponding citation information. The inputs are URL strings for two datasets provided by Rob Hyndman under the subject of Ecology. These datasets include the annual number of lynx pelts and the annual unit price of lynx pelts during the year range 1857 -1911. This...

Created: 2011-10-05 | Last updated: 2011-10-05

Credits: Trisha Adamus Alan Williams Jeff adamus

Attributions: Fetch today's xkcd comic Spreadsheed Data Import Example HTML Citation Extraction Current Date Output

[untitled] (1)

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This workflow ...tbc img, #cubbies-overlay{ -moz-transition-property: margin, box-shadow, z-index; -moz-transition-duration: 0.1s; -webkit-transition-property: margin, box-shadow, z-index; -webkit-transition-duration: 0.1s; } .cubbies-selected{ z-index: 9999; box-shadow: 3px 3px 8px -1px blue !important; cursor: pointer !important; margin: -3px 3px 3px -3px; } .cubbies-selected:active{ box-shadow: 2px 2px 5px -1px darkblue !important; margin: -1px 1px 1px -1px; } #cubbies-overlay{ positio...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Get Element ID from Gzipped GenBank file (1)

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This workflow gunzips a *.gbk.gz file, converts it to XML (via agavewriter) and finds the Element ID. Does not work on *.gz files larger than 10MB. I upped the JVM settings on Taverna to:         <key>VMOptions</key>         <string>-Xmx4096m -XX:MaxPermSize=1024m</string> Created my own agave.dtd to get the XPath service to work the XML file generated from the Read_GenBank_File service. You will need to ...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Mutanthumb Alan Williams

Elevation plot v.2 (2)

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Functionally identical to the original. I tried to upload a version with annotation, but somehow the notes didn't make it to myExperiment. From the prior verion: This workflow accepts city and country names as user-supplied input. These value are supplied to the GetWeather webservice (http://www.webservicex.net/globalweather.asmx?WSDL), which returns an XML record of location and weather info for each recognized city. (See the uploaded photo "weather example") The XML returned fr...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Latitude with beanshell (1)

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This workflow takes in a string value or list of values and pulls out latitude coordinates formatted as ##-##(N or S) using the following regular expression: \d\d-\d\d(N|S). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow contains primarily string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatting I requi...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Longitude with beanshell (1)

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This workflow takes in a string value or list of values and pulls out longitude coordinates formatted as ###-##(N or S) using the following regular expression: \d\d\d-\d\d(E|W). The coordinates are processed and formatted to be in the form required by the web service used in my "Elevation plot" workflow. This workflow primarily contains string manipulation. For many of the text and list services used, the beanshell script needed to be modified in order to produce the formatti...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Chrisser

Mapping Workflow - Attempt (1)

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PLEASE NOTE: This is an early variation of http://www.myexperiment.org/workflows/2474.html. This workflow was abandoned as the above mentioned workflow is more streamlined. This workflow may or may not work successfully.

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: tpacurtis

Mapping Service (2)

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This service generates a google map of a group of place names and coordinates. The workflow will accept both coordinates and place names. This workflow takes place names/coordinates from both a spreadsheet, as well as on-the-fly input of a list of coordinates or place names (please note, if no supplemental data is desired, an empty link will allow the workflow to function). The Mapping Service workflow was created to assist in generating a map of where a series of interviews took p...

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: tpacurtis

Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2011-10-06 | Last updated: 2011-10-06

Credits: Alan Williams

Average and Standard Deviation (1)

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This workflow takes in a list of values and a list name, and returns the list name, average, and standard deviation of the values.

Created: 2011-10-07 | Last updated: 2011-10-07

Credits: Atminer

Population Plot with R (1)

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This script pulls the population of every country and creates a plot of them. This is based on the script at http://www.myexperiment.org/workflows/1728.html , with a few modifications for labelling axes and the title.

Created: 2011-10-08

Credits: Atminer

Broccoli Production New York State, 1960-1965 (1)

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This workflow takes data about agricultural production in New Jersey and New York from 1960 -1965, to compare productivity in broccoli growing.

Created: 2011-10-09 | Last updated: 2011-10-09

Credits: Atminer Alan Williams

Attributions: Spreadsheet Import Example

Spreadsheet Import - Fertilizer Use (1)

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This workflow takes data from a spreadsheet and creates a graph of fertilizer use in NY state from 1960-1965.

Created: 2011-10-09 | Last updated: 2011-10-09

Credits: Atminer

Attributions: Spreadsheet Import Example

WPS-GRASS-Bridge r.los example (1)

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r.los generates a raster output map in which the cells that are visible from a user-specified observer position are marked with the vertical angle (in degrees) required to see those cells (viewshed). A value of 0 is directly below the specified viewing position, 90 is due horizontal, and 180 is directly above the observer. The angle to the cell containing the viewing position is undefined and set to 180. http://grass.fbk.eu/grass62/manuals/html62_user/r.los.html

Created: 2011-10-13

Credits: Jorgejesus

Get homologous from NCBI homoloGene (1)

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Get homologous from NCBI homoloGene for a list of Refseq protein accessions. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Created: 2011-10-13 | Last updated: 2011-10-13

Credits: Rafael C. Jimenez

Find orthologs using a uniprot accession (1)

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Find orthologs based on ensembl information using as input/output uniprot accession

Created: 2011-10-14 | Last updated: 2011-10-14

Credits: Rafael C. Jimenez

Find orthologs using a list of uniprot acc... (2)

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Find orthologs based on ensembl information using as input/output uniprot accessions

Created: 2011-10-14 | Last updated: 2014-06-03

Credits: Rafael C. Jimenez

Get homologous from NCBI homoloGene using ... (1)

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Get homologous from NCBI homoloGene for one UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Created: 2011-10-14 | Last updated: 2011-10-14

Credits: Rafael C. Jimenez

Get homologous from NCBI homoloGene using ... (1)

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Get homologous from NCBI homoloGene for a lsit of UniProt protein accession. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Created: 2011-10-14 | Last updated: 2011-10-27

Credits: Rafael C. Jimenez

KEGG pathway to proteins (2)

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Get various information about the proteins in a KEGG pathway. Demonstrates integrating SADI services with non-SADI services.

Created: 2011-10-17 | Last updated: 2011-10-18

Revisión Sistemática de Software (4)

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 Workflow for sistematic software revision.

Created: 2011-10-18 | Last updated: 2011-12-12

Credits: E3matheus

Get homologous from an NCBI homoloGene.dat... (1)

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Get homologous from NCBI homoloGene for a lsit of UniProt protein accession. This workflow is useful if you have a long list of protein accessions. Use PICR to convert UniProt to RefSeq, get homologous from homoloGene and convert RefSeq results to UniProt. Be patient, the workflows has to bring a file around 11Mb. ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/README

Created: 2011-10-20 | Last updated: 2011-10-27

Credits: Rafael C. Jimenez

BLASTP with simplified results returned (1)

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Perform a blastp search on protein sequence and extract information based on the user input, e.g. a list of GI numbers.

Created: 2011-10-25 | Last updated: 2011-10-25

Credits: Halima alshabani

r.stats workflow for pixel statistics (1)

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r.stats operation for image. Output will group pixels by: DN, total area, relative %. This worflow is used inside the ice Class exampel as a nested workflow

Created: 2011-11-02 | Last updated: 2011-11-02

Credits: Jorgejesus

date filter for ice Class Map service (NERSC) (1)

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Workflow to filter available dates with ice classification images. Service provided by NERCS. Dates are filtered using a simple regular expression

Created: 2011-11-02 | Last updated: 2011-11-04

Credits: Jorgejesus

Ice Class Map pixel analysis (NERSC) (1)

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NERSC ice classification workflow. Avaible images for a specific date will be fecthed from the WPS service, and their color table changed to allow for a user to easly identify specific areas. Statistical analysis also run using the r.stats module. Worflow uses a list of image, the list will flow thru the workflow for process resulting in mutiple outputs

Created: 2011-11-02 | Last updated: 2011-11-02

Credits: Jorgejesus

Propagation of physical quantities in the ... (3)

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This workflow takes as input a file for each of this properties: J2000 Coordinates, velocity, galactic extinction, log of axis ratio, and the Total B-magnitude. With this properties it calculates the distance of the galaxy and, in other hand, the total apparent corrected B-magnitude. It takes account if the velocity of the galaxy is lower than a threshold (1000km/s), it can not be possible to calculate the distance so, in those cases the distance will be "NaN". At the end, it calculates the ...

Created: 2011-11-30 | Last updated: 2013-04-22

Gathering galaxy properties using HyperLEDA (2)

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The user provides an ASCII text file with a list of galaxy names, and the workflow queries the HyperLEDA database and parses the response with the help of regular expressions included in simple Python scripts. The result of the workflow is a series of ASCII text files with the values of the equatorial coordinates in J2000 epoch, the velocities in km/s, the dust extinction coefficient Ag, the axis ratio of the isophote 25 mag/arcsec2 logr25 and the apparent total B magnitude BT. The performanc...

Created: 2011-11-30 | Last updated: 2013-03-08

Comparison and update values (1)

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This workflow receives two files, the name of a table and the name of a field as input. One of the file should be contain a list of old values (name galaxy and value), and the other one should be a list of new values (name galaxy,value) The workflow makes a comparison between the two files. This comparison will be a list of 7 columns: name of the galaxy, old value, old error, new value, new error, difference of value, difference of error. In other hand, this workflow makes a sql script with ...

Created: 2011-11-30 | Last updated: 2011-11-30

Match concept profiles (6)

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Purpose of workflow: The workflow can be used to match a set of concept profiles with another set of concept profiles. Result: A list of concepts ordered by their match to the query concept profiles.

Created: 2011-12-02 | Last updated: 2014-07-14

Credits: Marco Roos Kristina Hettne Martijn Schuemie Reinout van Schouwen

dcraw (NoConversion, NoInterpretation, Fix... (4)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

dcraw (sRGB, ColorInterpolated, FixedWhite... (2)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

dcraw (sRGB, ColorInterpolated, FixedWhite... (2)

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Reads a RAW image with these parameters using dcraw and returns the image data as byte array.

Created: 2011-12-08 | Last updated: 2011-12-16

Connect flare events with proton events on... (2)

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This workflow uses flares listed in any HELIO HEC flare catalogue (using the semantic mapping service), checks whether these flares are connected to Earth via the Parker spiral, and looks for proton events at earth listed in the goes_proton_event list. The flare listing and the proton listing are combinded into a list of VOTable outputs (one VOTable per flare catalogue with results).

Created: 2011-12-09 | Last updated: 2011-12-13

Credits: Anja Le Blanc

Attributions: Connect flare events with proton events on Earth via propagation model

Propagation of the Co-roationg interaction... (2)

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use of the processing service to calculate time delays to the planets Inputs: time when propagation should start longitude of starting point on the sun speed of the solar wind error speed of the solar wind

Created: 2011-12-13 | Last updated: 2012-02-03

Credits: Anja Le Blanc

Propagation of the Solar Energetic Particl... (2)

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use of the processing service to calculate time delays to the planets Inputs: time when propagation should start longitude of starting point on the sun speed of the solar wind error value of solar wind speed traveling speed of energetic particals as percentage of the speed of light

Created: 2011-12-13 | Last updated: 2012-02-03

Credits: Anja Le Blanc HELIO

[untitled] (1)

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 A KUP domain image segmentation workflow that identifies ans annotates important regions on microscopic Kidney biopsy images (vessels and glomerulus)

Created: 2012-01-03 | Last updated: 2012-01-03

Credits: Charalampos

Hello World (1)

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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: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-01-03 | Last updated: 2014-03-03

Credits: Stian Soiland-Reyes

Attributions: Hello World

Calculation of distances, magnitutes and l... (2)

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Calculation of distances, corrected apparent B magnitude mB-corr and luminosities with values gathered from the HyperLEDA database. This workflow receives a list of galaxy names (hyperLEDA names. ie: KIG0001) and a file with the morphological types of those galaxies Using the name of a galaxy, the workflow querys Hyperleda to extract some properties of this galaxy (J2000 Coordinates, velocity, galactic extinction,log of axis ratio, and the Total B-magnitude ). With this properties it calcula...

Created: 2012-01-10 | Last updated: 2012-01-16

Credits: Stian Soiland-Reyes

Attributions: Calculation of distances, magnitutes and luminosities using HyperLEDA Data involved in RO Propagation of quantities Scripts in RO Propagation of quantites

NCBI Gi to Kegg Pathway Descriptions (5)

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This workflow accepts a list of NCBI 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: 2012-01-12 | Last updated: 2013-01-30

Credits: Katy Wolstencroft

Attributions: NCBI Gi to Kegg Pathways

getFirstElementDFS (2)

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Returns the first element of a nested list using depth first search. The maximum depth of the input is set to 2. You can savely increase this by increasing the depth of the workflow input port and the beanshell input port. Taverna will wrap the input into a list with correct depth. However this will create a little overhead.

Created: 2012-01-13 | Last updated: 2012-02-13

Import and convert gene list (1)

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This workflow extracts a column of RefSeq gene IDs from a CSV file and then converts them to Unigene identifiers

Created: 2012-01-15 | Last updated: 2012-03-12

Credits: Katy Wolstencroft

UnigeneID to KEGG Pathways (3)

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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: 2012-01-16 | Last updated: 2012-12-17

Credits: Katy Wolstencroft Paul Fisher

Attributions: NCBI Gi to Kegg Pathways

Reactome pathways (1)

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This workflow returns a list of pathways gene products are involved in, along with their descriptions and Gene Ontology annotations

Created: 2012-01-16

Credits: Katy Wolstencroft

FFmpeg convert audio2aac (REST) (1)

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Converts supported audio files to AAC using FFmpeg through a REST webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

ImageMagick convert image2jp2 (REST) (1)

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Converts supported image files to JPEG2000 using ImageMagick through a REST webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

ImageMagick convert image2jp2 (SOAP) (1)

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Converts supported image files to JPEG2000 using ImageMagick through a SOAP webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

FFmpeg convert audio2aac (SOAP) (1)

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Converts supported audio files to AAC using FFmpeg through a SOAP webservice.

Created: 2012-01-16 | Last updated: 2012-01-16

Credits: Rui Castro

SNPs to Concept Set through Concept Profil... (6)

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Purpose: Currently, this workflow takes one SNP and a concept set as input, calculates the matching score between these, finds co-occuring documents between the query concept and the match concept, finds the concept that contributes the most to the match, and the documents that support this finding. Author comments: The workflow is in Beta stage. It runs, but needs more testing with different parameter settings. This workflow can be used together with other workflows in this pack: http://www...

Created: 2012-06-26 | Last updated: 2013-02-05

Credits: Kristina Hettne Eleni Harish Dharuri Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

Attributions: Find Supporting Documents SNP_ID2EntrezGene_ID DatabaseID to ConceptID Match gene lists based on information in literature Match concept profiles Explain concept scores

VOTables from NED Web Services (1)

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Extraction of a sample of VOTables from all the NED Web Services present in paper 2007ASPC..382..165M Web-based Tools - NED VO Services (Mazzarella, J. M.; NED Team). The National Virtual Observatory: Tools and Techniques for Astronomical Research. ASP Conference Series, Vol. 382. Edited by M.J. Graham, M.J. Fitzpatrick, and T.A. McGlynn. San Francisco: Astronomical Society of the Pacific, 2007., p.165

Created: 2012-06-28 | Last updated: 2013-04-12

Credits: Jose Enrique Ruiz

Simple executable plan example (1)

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A simple executable plan containing a migration action component and a QA component. The migration action uses imagemagick convert. The QA component consists of two characterisation components (fits) and another QA components (imagemagick compare).

Created: 2012-06-29

Credits: Markus Plangg

Astronomical object name to equatorial coo... (1)

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 Resolve equatorial coordinates of a list of objects (names) with AstroTaverna plugin

Created: 2012-06-30 | Last updated: 2012-07-01

Credits: Jose Enrique Ruiz

VOTable of NED Images from a List of Objects (1)

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Extraction of metadata using NED Image Virtual Observatory Service into a single VOTable, providing a list of objects and the width for each field in arcmin. Among the most relevant metadata are the URL link to the FITS images. This Wf makes use of a Tool developed as an internal pyhton script file.

Created: 2012-07-01 | Last updated: 2012-07-01

Credits: Jose Enrique Ruiz

Attributions: Astronomical object name to equatorial coordinates Resolver

Get all applications available on the HPS (1)

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This workflow requests all available applications on the HPS which do not require authentication to run. No inputs. Outputs contain all information to execute the application on the HPS such as the ID of the application and the names of all parameters.

Created: 2012-07-03

Credits: Anja Le Blanc

Task Data Pattern (BeanShell) (1)

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This is a sample implementation of "Task Data" pattern intoduced workflowPatterns.com It defines a variable inside a Beanshell and uses the passed value through the processors input. Details: http://www.workflowpatterns.com/patterns/data/visibility/wdp1.php

Created: 2012-07-06

Get Concept IDs (5)

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Purpose: The workflow retrieves the concepts within a concept set. The Web service/workflow currently returns no values (bug).

Created: 2012-07-06 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Martijn Schuemie Marco Roos BioSemantics

Get concept information (5)

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The workflow takes a (list of) concept ID(s) as input and returns the profile, ID, definition and name of the concept.

Created: 2012-07-06 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

List Concept Sets (3)

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Pupose: The workflow returns a list of all Concept Set IDs currently available in the database. The Concept Sets have an hierarchical structure that can be inferred by referring to the parent Concept Set ID.

Created: 2012-07-06 | Last updated: 2014-07-14

Credits: Kristina Hettne Marco Roos Reinout van Schouwen Martijn Schuemie BioSemantics

Gene to Pathways (1)

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This is a Taverna workflow that given a gene ID fetches the corespondondings pathways. To do so, the workflow make use of two KEGG web services.

Created: 2012-07-09 | Last updated: 2012-07-10

Credits: Khalid Belhajjame

Find co-occurring documents (6)

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Purpose: This workflow search an indexed literature database for documents mentioning both of the input concepts. Author comments: Currently, PubMed is the underlying data source.

Created: 2012-07-13 | Last updated: 2014-07-14

Credits: Kristina Hettne Reinout van Schouwen Marco Roos Martijn Schuemie BioSemantics

Example of how to use Sesame service and V... (1)

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This workflow needs as input a list of names of galaxies. Then it queries Sesame services to get the coordinates of this galaxies, and finally with this coordinates queries a Virtual Observatory Services (a cone service).

Created: 2012-07-14

Example of Execute_SQL_Query with parameters (1)

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This workflow connects to a mysql on localhost, queries the "world" database which is one of the test databases on MySQL 5.5, queries it about which countries have Dutch as a language, and emits answers in both Lists and in xml. This workflow is intended as an example to help you see the syntax for the various inputs to this local service beanshell. see: http://www.mygrid.org.uk/dev/wiki/display/taverna/Execute+SQL+Query for instructions on jars, dependencies etc. The jar used he...

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: Helen Hulme

Available instruments through DPAS which a... (1)

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This workflow uses a DPAS servlet to obtain all available intrument keys in the DPAS (Data Provider Access Service) and formats the return as VOTable.

Created: 2012-03-16 | Last updated: 2012-03-16

Credits: Anja Le Blanc

Attributions: Available instruments through DPAS Split VOTable into its values

(Updated)Retrieve sequence in EMBL format. (1)

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This workflow retrieves a sequence associated with its features in embl format.

Created: 2012-03-19 | Last updated: 2012-04-02

Credits: Ankit upadhyay

DemoWorkflow (1)

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 Demo Workflow

Created: 2012-03-22 | Last updated: 2012-03-22

Credits: Jribault

Get Pathway-Genes and gene description by ... (2)

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Given a specific entrez gene id, returns the pathways that this gene participates in and for each of those pathways which genes (including their description) are associated with.

Created: 2012-03-27 | Last updated: 2012-04-03

Credits: Eleni

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Katy Wolstencroft

BiomartAndEMBOSSMouseRat (1)

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This workflow retrieves all genes on human chromosome 22 that are associated with a disease and aligns the upstream regions of the mouse and rat homologues. The alignments are plotted and corresponding sequence ids are also returned.

Created: 2012-04-05

Credits: Alan Williams

BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Demonstration of configurable iteration (1)

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This workflow shows the use of the iteration strategy editor to ensure that only relevant combinations of inputs are used during an implicit iteration.

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

EBI_InterproScan_NewServices (2)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text and xml. This workflow uses the new EBI services, which are asynchronous and require looping over the nested workflow (Status) until the workflow has finished. Many of the EBI services now work in this way, so you can use this workflow as an example of the invocation pattern and looping configuration.

Created: 2012-04-05 | Last updated: 2014-04-09

Credits: Alan Williams

Example for external tools with zip and unzip (1)

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This workflow only works on a Unix machine. This workflow takes a fixed URL from which a text file is downloaded (output as Original_file). That file is zipped (output as Zipped_File) and then unzipped again (output as Unzipped_File). The orginal file and the unzipped version are then diff'd/

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Example of conditional invocation (1)

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This workflow demonstrates how nested workflows can be conditionally invoked

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Example of explicit looping (1)

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This workflow demonstrates how a nested workflow can be called an explicit number of times. Note that the loop iterator does not need to be used in the logic of the loop contents. It can be used as a sentinel (see the conditional workflow)

Created: 2012-04-05

Credits: Alan Williams

Example workflow for REST and XPath activi... (1)

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This workflow fetches weather forecast for the user-specified location. First of all it uses the provided location name to obtain a WOEID ("Where On Earth ID") of that location, then uses that unique identifier to fetch the weather forecast from Yahoo server. Multiple results may be obtained in case there is no unique translation of the location to a WOEID. REST activity is used to perform HTTP requests and fetch data from remote servers; XPath activity is then used to parse the XML data a...

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Fetch PDB flatfile from RCSB server (1)

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Given an identifier such as '1crn' fetches the PDB format flatfile from the RCSB

Created: 2012-04-05

Credits: Alan Williams

Fetch today's xkcd comic (1)

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Use the local services and some filtering operations to fetch the comic strip image from http://xkcd.com/ Based on the FetchDailyDilbert workflow.

Created: 2012-04-05

Credits: Alan Williams

Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

GBSeq test (1)

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This workflow retrieves nucleotide and protein sequences with the literature and references associated to them given a protein and a nucleotide id.

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Hello Anyone (1)

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An extension to helloworld.t2flow - this workflow takes a workflow input "name" which is combined with the string constant "Hello, " using the local worker "Concatenate two strings", and outputs the produced string to the workflow output "greeting".

Created: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

Hello World (1)

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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: 2012-04-05 | Last updated: 2014-03-03

Credits: Alan Williams

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Numerically adding two values. (1)

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This workflow relies on a Unix system. It wraps the "bc" command line calculator. It downloads the calculation script from a URL.

Created: 2012-04-05

Credits: Alan Williams

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2012-04-05

Credits: Alan Williams

Render gene via BioGPS (3)

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This workflow uses the REST API of BioGPS to list the plugins and then allow the user to select which plugin to use to display the input gene id

Created: 2012-04-05 | Last updated: 2012-05-23

Credits: Alan Williams

Retrieve sequence in EMBL format (1)

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This workflow retrieves a sequence associated with its features in embl format

Created: 2012-04-05 | Last updated: 2012-04-05

Credits: Alan Williams

Secure REST service call example (2)

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This is an example of a workflow that contains a call to a secure REST service that requires user to authenticate with HTTP Basic Authentication. You can use testuser/testpasswd as username and password for authentication when running the workflow.

Created: 2012-04-05 | Last updated: 2014-01-16

Credits: Alan Williams

Secure Web service call example (2)

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This is an example of a workflow that contains a call to a secure Web service that runs behind HTTPS and requires user to authenticate. The first thing you can expect to see is a pop up dialog asking if you trust the Web service to be invoked over HTTPS. You can use testuser/testpasswd as username and password for authentication when running the workflow. To see where the security is being configured, right-click the service in the diagram and select "Configure security" from the menu. You ...

Created: 2012-04-05 | Last updated: 2013-06-11

Credits: Alan Williams

Simple Python example (1)

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This workflow generates a random number within the range 0 to 100. The generation is done by a python script. The workflow assumes that python is in the path.

Created: 2012-04-05

Credits: Alan Williams