Workflows

Single list with statistics values (#2 Par... (1)

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This workflow allows one to produce a single list of statistical output with the list name, average, and standard deviation of the values.  This workflow only produces the average and standard deviation from the input values

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: Wdsnellg

Concatenated List of Values (1)

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This workflow takes multiple lists of values and finds the standard deviation and average of the provided values. It then concatenates each value into a single string.

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: tpacurtis

Statistics example (1)

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This workflow allows one to find the average and standard deviation of a set of values.

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: Wdsnellg

Population histogram in R (1)

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This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: Wdsnellg

Population histogram in R (with Ask Box!) (1)

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This workflow fetches the details of the countries in the world and then uses R to produce a histogram of the log of their population. Prompts the user to enter a title for the histogram.

Created: 2011-09-21 | Last updated: 2011-09-21

Credits: tpacurtis Alan Williams

Attributions:

Geottif image reprojection (1)

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Example of a WPS service that reprojects a geoTIFF by using a EPSG code. THe example image is in EPSG:32119, lcc projection for north caroline and it comes from GRASS-GIS spearfish dataset. The image is reprojected into EPSG:4326 (lat/long): Metadata: http://rsg.pml.ac.uk/wps/generic.cgi?request=describeProcess&service=wps&identifier=reprojectImage&version=1.0.0 Library: gdalwarp

Created: 2011-09-16 | Last updated: 2011-09-16

Credits: Jorgejesus

Point coordinate projection transformation (1)

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Point coordinate transformation. Hard coded example of transformation from 4326 (lat/long) to 32630 (UTM 30N) for 3 points in the UK. The service is called once at the time, just to test the list interactor, since the service could work with a list of points. Metadata: http://rsg.pml.ac.uk/wps/generic.cgi?request=describeProcess&service=wps&identifier=reprojectCoords&version=1.0.0 Library: gdaltransform

Created: 2011-09-16 | Last updated: 2011-09-16

Credits: Jorgejesus

Echo (1)

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This does a simple Echo

Created: 2011-09-16

Credits: Christian

Deformable Organisms Skullstripping (1)

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Overview - Deformable Organisms Skullstripping Pipeline will skull-strip an magnetic resonance (MR) image of the brain using a deformable organisms framework. Problem addressed by this workflow Segment or delineate the brain in whole head MR images. Creates a mask of the brain, separating it from skull, skin, eyes, neck, and cerebro-spinal fluid (CSF). Detailed Workflow Usage & Specifications The module takes ANALYZE or NIFTI magnetic resonance images of the head as input a...

Created: 2011-09-14

Credits: Azamanyan

7 day weather forecast for a list of cities (1)

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This workflow uses an input port to take a list of zipcodes as input. Using the "GetWeatherByZipcode" service ('USA Weather Forecast' web services from WebserviceX.net), the weather forecast is retrieved for each of the zipcodes from the input. These forecasts are output as XML trees.

Created: 2011-09-14 | Last updated: 2011-09-14

Credits: Chrisser

Attributions: Get weather information

Seven-Day Forecast (1)

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This workflow takes a list of zipcodes and generates their seven-day weather reports using the USA Weather Forecast from http://www.webservicex.net/WS/WSDetails.aspx?WSID=68&CATID=12 The output includes maximum and minimum temperatures in both Fahrenheit and Celsius.

Created: 2011-09-14

Credits: Kayleigh Ayn Bohémier

Attributions: Get weather information

Fetch today's Girls with Slingshots comic (1)

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This workflow uses local java plugins and filtering operations to fetch today's comic strip image from http://www.girlswithslingshots.com/. Girls with Slingshots focuses on the lives of a group of women in their twenties. It is one of the few major webcomics to pass the Bechdel test. Based on the workflow "Fetch today's xkcd comic" by Tom Oinn and Stian Soiland-Reyes.

Created: 2011-09-14 | Last updated: 2011-09-14

Credits: Kayleigh Ayn Bohémier

Attributions: Fetch today's xkcd comic Daily Dilbert

Fetch today's cat and girl comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://catandgirl.com/, your major source of essential lead. Based on the Fetch today's xkcd workflow.

Created: 2011-09-14 | Last updated: 2011-09-14

Credits: Atminer

Attributions: Fetch today's xkcd comic

City weather information (1)

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Get the weather forcast of the day for you city. Info display: wind, visibility, temperature, sky conditions and pressure. The default value is my home town. To find out any supported city run the 'Get cities by country name' workflow

Created: 2011-09-14 | Last updated: 2011-09-14

Credits: Wdsnellg

Fetch today's Dinosaur Comic (http://qwant... (1)

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This workflow retrieves the newest comic from http://qwantz.com. Using a string constant to input the URL, the workflow then copies the HTML code from the location indicated by the URL. A list of links to images is then taken from the HTML code. Using a regluar expression supplied by another string constant, this list is then search for the URL specificallyt for the comic. The image file for the comic is then retrieved and the comic is displayed as the workflow output.img, #cubbies-overlay{ -...

Created: 2011-09-13 | Last updated: 2011-09-14

Attributions: Fetch today's xkcd comic

Merge list of errors to string (2)

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Based on http://myexperiment.elda.org/workflows/27/ The beanshell scripts collectively builds a temporary file of the merged string (by default using newline as separator). As each item is appended to the file separately by Write_text_append, this means it can handle occassional errors in the list, such as in the output from Sometimes_fails. Such items are not included in the merged string. To use, merge with your workflow and delete "Create_Lots_if_Strings", "Sometimes_Fai...

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

Get 7 Days Weather by Zip Code (1)

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This workflow allows for the input of a list of zipcodes and outputs the weather for the zip codes.

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

Credits: tpacurtis

ZipCodeGetWeatherInfo (1)

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Gives the 7 day weather forecast by Zip Code Info display: wind, visibility, temperature, sky conditions and pressure. Based on "Get Weather Info" by Franck Tanoh

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

Credits: Mutanthumb

Get My Weather (1)

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Gets a variety weather info for "Cleveland" and "Indianapolis" Based on "Get weather information" by Franck Tanoh

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

Credits: Mutanthumb

Get Recent Cards From Indexed (1)

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This gets the jpgs from the "This is Indexed" URL: http://thisisindexed.com/page/2/ using the regular expression .*/uploads/*. pull everything in the "uploads" directory. Based on "Fetch today's xkcd comic" by Tom Oinn, Stian Soiland-Reyes Use the local java plugins and some filtering operations to fetch the comic strip image from http://xkcd.com/

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

Fetch today's Johnny Wander Comic (1)

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Use the local java plugins and some filtering operations to fetch the comic strip image from http://www.johnnywander.com/ Based on the FetchDailyDilbert workflow & Fetch today's XKDC comic

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

Credits: tpacurtis Franck Tanoh

Attributions: Fetch today's xkcd comic

Seven day weather by zip code (1)

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Get the seven day weather forcast for your zip code. Info display: wind, visibility, temperature, sky conditions and pressure.  Add zip code values to get weather information.

Created: 2011-09-10 | Last updated: 2011-09-14

Credits: Wdsnellg

GT: Database - Master SNP Call Table (1)

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Either load new Master SNP call data into the database (from an Excel file) or export the master SNP data from the database into an Excel file. NOTE: Running this workflow will take a couple of minutes. If loading excel data into database, make sure the file is located in the correct directory: /gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/

Created: 2011-09-10

Credits: Chengc

The NOTCH2 workflow (1)

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Analysis of the exome sequencing data for the following article: Nat Genet. 2011 Mar 6;43(4):306-8. Truncating mutations in the last exon of NOTCH2 cause a rare skeletal disorder with osteoporosis. Isidor B, Lindenbaum P, Pichon O, Bézieau S, Dina C, Jacquemont S, Martin-Coignard D, Thauvin-Robinet C, Le Merrer M, Mandel JL, David A, Faivre L, Cormier-Daire V, Redon R, Le Caignec C. using knime4bio

Created: 2011-09-06 | Last updated: 2011-09-06

Credits: PL

GT: Genotyping Comparison Analysis and Clu... (7)

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Creates a genotyping comparison analysis Excel file and heatmap image given final report and gender call input files. User provides either plate numbers, CLID/BIOIDs, cNames, etc. and can choose to either load the data into the database or not. Note that if user chooses to load data into database, script may take longer (few minutes) to run. Before running, make sure the final report and gender call text files are correctly named and that they are in the correct directory under: /gne/researc...

Created: 2011-09-01 | Last updated: 2011-09-10

Credits: Chengc

GT: Sample Sheet Generation (7)

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Creates a sample sheet from a SAMid exported file. User provides a plate number. Before running, make sure the SAMid exported file is in the correct directory under: /gne/research/data/lab-shares/gCell/_gCell/Baseline_Profiling_Cells/Genotyping/Plate_# Results will be stored under this directory: /gne/research/data/bioinfo/gcell/genotype/prd/Plate_#

Created: 2011-08-31 | Last updated: 2011-09-08

Credits: Chengc

Convert GML to SVG (1)

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This workflow can convert the GML (Geography Markup Language) file to SVG image.

Created: 2011-08-31 | Last updated: 2011-08-31

Credits: Harvey

TIFF to PNG (1)

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This workflow can convert Image format from TIFF to PNG. This workflow is one of the example for GENESI-DEC ontology.

Created: 2011-08-31 | Last updated: 2011-08-31

Credits: Harvey

Image metadata extraction (1)

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This workflow invokes the gdalinfo service and will list various information about a GDAL supported raster dataset of the image ( GeoTIFF, PNG, JPEG and GIF.).

Created: 2011-08-31 | Last updated: 2011-08-31

Credits: Harvey

BATWING (1)

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Batwing reads in multi-locus haplotype data, and model and prior distri- bution specifications, and uses a Markov chain Monte Carlo (MCMC) method based on coalescent theory to generate approximate random samples from the posterior distributions of parameters such as mutation rates, effective population sizes and growth rates, and times of population splitting events. It also generates approximate posterior samples of the entire genealogical tree underly- ing the sample, including the tree hei...

Created: 2011-08-25 | Last updated: 2011-08-25

Credits: Pipeline

Find instruments of a special type in a se... (1)

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This workflow takes a type of isnstrument as input and the minimum and maxium coordinates in HCI as input. Cadence for the location service is for defining the 'continues' presence. Output is a VOTable based on the ICS return where two columns are added for the time this instrument has entered and exited the Region of Interest.

Created: 2011-08-24 | Last updated: 2011-08-24

Credits: Anja Le Blanc

Attributions: Find instruments of a special type in a section of space described in HCI coordinates

Find instruments of a special type in a se... (1)

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This workflow takes a type of isnstrument as input and the minimum and maxium coordinates in HCI as input. Cadence for the location service is for defining the 'continues' presence. Output is a VOTable based on the ICS return where two columns are added for the time this instrument has entered and exited the Region of Interest.

Created: 2011-08-24 | Last updated: 2011-08-24

Credits: Anja Le Blanc

BLAST your sequences against the NucleaRDB (1)

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BLAST your sequences against the NucleaRDB. Input requires a sequence with amino acids only (no fasta format etc)

Created: 2011-08-19 | Last updated: 2011-08-19

Credits: Bas Vroling

Rave Usability Lab Workflow (1)

Created: 2011-08-16 | Last updated: 2011-11-10

Credits: Liz Masterman

Split string into string list, new line se... (1)

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Split string into string list using new line as separator. Should work in Linux, Mac and Windows.

Created: 2011-08-15 | Last updated: 2014-02-26

Credits: Rafael C. Jimenez

Difference: Query - Reference (1)

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Difference bettwen the query list and the reference list. Things that are in the query and not in the reference.

Created: 2011-08-15 | Last updated: 2011-08-15

Credits: Rafael C. Jimenez

Plotting Training vs Testing Error (Loop +... (1)

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This process increases the parameter C of a support vector machine and hence also the risk for overfitting. It uses an outer loop operator for increasing the parameter value and an inner log operator for storing the current number of applications together with the current errors on the training and the testing data set. At the end of the process, the log data can be plotted (for example with the plotter "Scatter Multiple" with "Count" on the x-axis and both "Training Error" and "Testing Error...

Created: 2011-08-15

XML-RPC example current time (1)

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Using Apache ws-xmlrpc from Beanshell scripts to call time.xmlrpc.com - see http://www.xmlrpc.com/currentTime To use, download the JARs from http://ws.apache.org/xmlrpc/download.html (ie. http://apache.mirror.anlx.net//ws/xmlrpc/apache-xmlrpc-current-bin.zip ) - unzip and put into Taverna's home directory lib/ folder. Right-click on the Beanshell script and check the "Dependencies" tab to check that all JARs have been ticked off (minimum required: ws-common-util.jar, xmlrpc-client.jar and x...

Created: 2011-08-11 | Last updated: 2011-08-11

Credits: Stian Soiland-Reyes

OpenTox Learn and evaluate model (1)

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Learns a LoMoGraph model on the TUM servers and evaluates it using 10 fold cross validation.

Created: 2011-08-09

OpenTox Upload and merge data sets (1)

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Uploads 2 data sets to OpenTox, merges them and returns the merged data set.

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

Example of a conditional execution workflow (1)

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If the input is true then the string 'foo' is emited, if false then 'bar'. Just a simple example to show how the monster works, so to speak.

Created: 2011-08-04

Credits: Taverna 1.7.1 workflow workbench examples

sampleDistribution Web service operation (1)

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Probabilistic distribution sampling operation which uses Mathematica software (http://www.wolfram.com/mathematica/).

Created: 2011-08-03 | Last updated: 2011-08-04

Credits: trybik

Find common events in HEC tables which use... (5)

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Use only tables which provide lat_hg and long_hg. Inputs: table names of two HEC tables; time interval in which the search is being conducted; delta for time and location to enlarge the search space. Output: VOTable which combines the resultset of the HEC by the common event.

Created: 2011-08-03 | Last updated: 2012-02-03

Credits: Anja Le Blanc

EUADR - Literature Analysis (1)

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The aim of the "Literature Analysis" workflow is to automate the search of publications related to ADRs corresponding to a given drug/adverse event association. To do so, we defined an approach based on the MeSH thesaurus, using the subheadings «chemically induced» and «adverse effects» with the “Pharmacological Action” knowledge.

Created: 2011-07-27 | Last updated: 2011-07-27

Credits: Avillach

EUADR Relationship Extraction Workflow (1)

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The workflow offers the ability to automatically determine if an ADR and a Drug are co-mentioned in any of the indexed resources. However the actual relationship between a Drug and an ADR can only be determined by referring to the actual resource The co-occurance relationship workflow seeks to automate the search for resources (publications, drug labels) related to ADRs corresponding to a given drug/ adverse event association. To enable this concept profiles for drugs and adverse effects wer...

Created: 2011-07-27 | Last updated: 2012-09-07

Credits: Bharat Singh

Get a PSICQUIC REST URL from a PSICQUIC SO... (1)

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Get a PSICQUIC REST URL from a PSICQUIC SOAP URL

Created: 2011-07-22 | Last updated: 2011-07-22

Credits: Rafael C. Jimenez

Genetic Algorithm for Input Component Anal... (1)

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This workflow uses a genetic algorithm to optimize the given molecular descriptor set. Afterwards the workflow splits the data into a training set and test set and evaluates the results which are stored as PDF files.

Created: 2011-07-22

Get Molecular Interactions from a PSICQUIC... (3)

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Check the different iput parameter you could use for this workflow in ... http://code.google.com/p/psicquic/wiki/RestAccess Check available PSICQUIC Services in ... http://www.ebi.ac.uk/Tools/webservices/psicquic/registry/registry?action=STATUS More about PSICQUIC ... http://code.google.com/p/psicquic/

Created: 2011-07-22 | Last updated: 2013-07-10

Credits: Rafael C. Jimenez

QSAR CSV to Weka Regression Dataset (1)

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This workflow converts the molecular descriptor data from a CSV file to a Weka XRFF file. The workflow merges the retention time values from IN IDRT CSV with the molecular descriptor values from IN QSAR CSV to create a valid Weka regression set.

Created: 2011-07-21

Weka Regression from XRFF file. (1)

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The here shown workflow splits the given data into a training set and a test set. Afterwards a machine learning model is created by the Weka Regression worker which is evaluated by the Evaluate Regression Results as PDF worker. The resulting sets are stored as XRFF files in the folder determined by the OUT TRAIN XRFF and OUT TEST XRFF input ports. The calcualted machine learning models and the evaluation results are saved in the folder of OUT MODEL input port

Created: 2011-07-21 | Last updated: 2011-07-21

ELM Database Retrieval Workflow (1)

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This workflow retrieves all the current entries stored in the Eukaryotic Linear Motif (ELM) Database and returns all entries in a collated readable format. This requires the ELM Database retrieval WSDL file: http://elm.eu.org/webservice/ELMdb.wsdl

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: Kieren Lythgow

Probabilistic Model Checking (PMC): plot r... (1)

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) Mathematica plotting Web service operation. This is a second-part for the computationaly exhaustive PMC: compute results workflow (http://www.myexperiment.org/workflows/2266).

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: trybik

Probabilistic Model Checking (PMC): comput... (1)

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) PRISM model translation and model checking Web service operations.

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: trybik

List of PSICQUIC services (names and URLs)... (1)

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PSICQUIC provides access to molecular interaction databases. This workflow queries the registry and gets a list of available PSICQUIC services (names and URLs).

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

Simulate SBML-derived ODEs (2)

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Exemplary experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) ODEs simulation and plotting Web service operations.

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: trybik

PSICQUIC Registry (Molecular Interactions ... (1)

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Query the PSICQUIC registry to retrieve information about services providing molecular interactions

Created: 2011-07-20 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

Isoelectric Point (1)

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Calculates the Isoelectric Point for a protein sequence using a protein accession as input

Created: 2011-07-19 | Last updated: 2011-07-20

Credits: Rafael C. Jimenez

EBI NCBI BLAST Multi FASTA (2)

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This workflow performs multiple sequence similarity searches using the NCBI blast at the EBI. It 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. If you want to make a blast search for more than 10 sequences I would recommend you to run the workflow using the comm...

Created: 2011-07-16 | Last updated: 2011-07-16

Credits: Rafael C. Jimenez

NOR Service (2)

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Workflow for an automatic orthorectification of raw images service, using the NOR service developed by JRC under the GENESI-DEC and GENESI-DR projects. It takes as input a URL of a zipped SPOT4|SPOT5 raw image, and generates a new URL of a zipped file of the orthorectified image.

Created: 2011-07-15 | Last updated: 2011-07-15

Credits: Panos Thomas

Secure Web service call example (1)

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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.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: Alex Nenadic

Secure REST service call example (1)

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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: 2011-07-14 | Last updated: 2011-07-14

Credits: Alex Nenadic

Fast Correlation Based Filter (FCBF) (1)

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Runs FCBF feature selector and accuracy is estimated using Naive Bayes. Grid Search Optimization is used for parameter optimization.

Created: 2011-07-14 | Last updated: 2011-07-14

Plot error surface (1)

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Exemplary workflow for plotting error surface using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) mahtPlot WS operation. Data input format is compatibile with Tav4SB MPSA workflows.

Created: 2011-07-14 | Last updated: 2011-07-14

Credits: trybik

Multi-parameter sensitivity analysis (MPSA... (2)

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Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA PRISM probabilistic model checking is basis of analysis of SBML model parameters space.

Created: 2011-07-14 | Last updated: 2011-07-21

Credits: trybik

Multi-parameter sensitivity analysis (MPSA) (2)

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Exemplary multi-parameter sensitivity analysis (MPSA) experiment using Tav4SB (http://bioputer.mimuw.edu.pl/tav4sb/) WS operations. In this version of MPSA, ODEs simulations are basis of analysis of SBML model parameters space.

Created: 2011-07-14 | Last updated: 2011-07-21

Credits: trybik

Unix tool for 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: 2011-07-13 | Last updated: 2011-07-13

Credits: Alan Williams Steffen Möller

Unix tools with zip, unzip and diff (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: 2011-07-13 | Last updated: 2011-07-13

Credits: Alan Williams Steffen Möller

Attributions: Example for external tools with gzip and gunzip

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: 2011-07-13 | Last updated: 2011-07-13

Credits: Alan Williams

A workflow version of the EMBOSS tutorial (1)

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Designed to show the use of EMBOSS based Soaplab services from Taverna, this workflow has no inputs as all initial values are specified as string constants. A sequence set is fetched using the seqret tool, then simultaneously scanned for predicted transmembrane regions and subjected to a multiple alignment using emma. This alignment is then plotted to a set of PNG images and also used to build a profile using the prophecy and prophet tools.

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Tomoinn

Attributions: A workflow version of the EMBOSS tutorial

BioMoby tutorial workflow (1)

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A workflow from part of the BioMoby tutorial

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: EdwardKawas

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: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams Tomoinn

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: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams Tomoinn

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: 2011-07-12 | Last updated: 2011-07-12

Credits: Tomoinn Stian Soiland-Reyes

Attributions: Fetch today's xkcd comic

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: 2011-07-12 | Last updated: 2011-07-12

Credits: Franck Tanoh

Attributions: GBSeq test

Pipelined list iteration (1)

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Perform multiple iterations of services in order to show pipelining

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Ian Dunlop Stian Soiland-Reyes

Attributions: Pipelined list iteration

Retrieve sequence in EMBL format (1)

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

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Franck Tanoh

Attributions: Retrieve sequence in EMBL format

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: 2011-07-12 | Last updated: 2011-07-12

Credits: David Withers

Attributions: Spreadsheed Data Import Example

Fetch Dragon images from BioMoby (1)

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Fetch images and annotations of snapdragons

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Tomoinn

Multiple choice quiz (1)

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A fun example workflow showing user-interaction and service looping

Created: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams George

Attributions: Multiple choice quiz

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: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams

EBI_InterproScan_NewServices (1)

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This workflow performs an interproscan at the EBI on sequences provided as input. The output is provided as text, xml or png. 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: 2011-07-12 | Last updated: 2011-07-12

Credits: Alan Williams Katy Wolstencroft

Attributions: EBI_InterproScan_NewServices

BiomartAndEMBOSSDisease (2)

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

Created: 2011-07-12 | Last updated: 2012-03-19

Credits: Katy Wolstencroft

Attributions: BiomartAndEMBOSSDisease

Iterate over Attribute Subsets and Store A... (1)

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This process iterates over all possible feature subsets and stores a) the names of all attribute subsets, b) the number of used features, and c) the achieved performance in a log table which can then be further analyzed.

Created: 2011-07-07

Trim and Replace White Space (1)

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This process removed leading and trailing white spaces from an attribute and replaces inner white spaces of any type by a single space. Might be useful for text processing (if you are not using tokenization anyway...)

Created: 2011-07-07

Common SCAPE QA command line tool RESTful ... (1)

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The QA REST package enables creation of RESTful web service that wraps any QA command line tools. The main element of this workflow is a RESTful service designed in the SCAPE QA command line tools RESTful package https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper-rest. The Github project https://github.com/openplanets/scape/tree/master/xa-rester from Andy Jackson is a basis implementation for pc-qa-toolwrapper-rest package. The workflow comprises path to the RESTful servi...

Created: 2011-07-01 | Last updated: 2012-04-04

Credits: Roman

Extract histogram features from image file... (1)

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The main element of this workflow is a RESTful service designed in the SCAPE QA command line tools RESTful package https://github.com/openplanets/scape/tree/master/pc-qa-toolwrapper-rest. The Github project https://github.com/openplanets/scape/tree/master/xa-rester from Andy Jackson is a basis implementation for pc-qa-toolwrapper-rest package. The QA REST package enables creation of RESTful web service that wraps QA command line tool like ‘extractfeatures’ or ‘create’...

Created: 2011-07-01 | Last updated: 2012-04-04

Credits: Roman

tblastx non-redundant alignment (1)

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This workflow carries out alignments using TCoffee and ClustalW2 for a set of non-redundant proteins where the starting point is a particular genomic coding sequence representing only one member of the gene family in a given species.   For the BioExtract Server implementation, the necessary steps for accomplishing this task involve: 1.   Selecting the NCBI tblastx tool and providing the accession number of the known nucleotide sequence record as input. 2.   The output from ...

Created: 2011-06-30 | Last updated: 2011-07-04

Credits: Carol Lushbough

Sequence Format Conversion (1)

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Demonstrate the use of the format conversion tool. Converts a DNA sequence in fasta format into plain, genbank, and phylip formats.

Created: 2011-06-28 | Last updated: 2011-06-28

Credits: Carol Lushbough

Mining Semantic Web data using Corresponde... (1)

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This workflow will explain that how an example set can be extracted from an RDF resource using the provided SPARQL query. This example set is then divided into training and test parts. These sub-example sets are used by the Correspondencce Analysis operators (encapsulate the Correspondencce Analysis data transformation technique) which processes each feature at a time and transform the data into a different space. This transformed data is more meaningful and helps the learner to improve clas...

Created: 2011-06-25 | Last updated: 2011-06-25

Mining Semantic Web data using Corresponde... (1)

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This workflow describes how to learn from the Semantic Web's data using a data transformation algorithm 'Correspondence Analysis'. The input to the workflow is a feature vector developed from a RDF resource. The loaded example set is divided into training and test parts. These sub-example sets are used by the Correspondence Analysis operators (encapsulate the Correspondence Analysis data transformation technique) which processes each feature at a time and transform the data into a different...

Created: 2011-06-25 | Last updated: 2011-06-25

Mining Semantic Web data using FastMap - R... (1)

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This workflow will explain that how an example set can be extracted from an RDF resource using the provided SPARQL query. This example set is then divided into training and test parts. These sub-example sets are used by the FastMap operators (encapsulate the FastMap data transformation technique), which processes each feature at a time and transform the data into a different space. This transformed data is more meaningful and helps the learner to improve classfication peformance. The tranfo...

Created: 2011-06-25 | Last updated: 2011-06-25

Mining Semantic Web data using FastMap - E... (1)

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This workflow describes how to learn from the Semantic Web's data. The input to the workflow is a feature vector developed from a RDF resource. The loaded example set is then divided into training and test parts. These sub-example sets are used by the FastMap operators (encapsulate the FastMap data transformation technique), which processes each feature at a time and transform the data into a different space. This transformed data is more meaningful and helps the learner to improve classfica...

Created: 2011-06-25 | Last updated: 2011-06-25

NGS sample workflow with data (1)

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 Sample workflow for NGS data analysis This worklfow relies on community contributions that can be installed through the following update site: http://tech.knime.org/update/community-contributions/nightly specifically the  KNIME NGS tools and the KNIME R Scripting extensions.    

Created: 2011-06-24 | Last updated: 2011-06-24

Credits: Baj

Biomart SNP (1)

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Normal 0 false false false EN-US X-NONE AR-SA /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyl...

Created: 2011-06-20 | Last updated: 2011-07-05

Credits: Yosr Bouhlal

[untitled] (1)

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This is simly a test fortest

Created: 2011-06-19 | Last updated: 2011-06-19

Credits: Merdmann

Compare histogram features of image files (1)

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As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This project enables creation of WSDL web service that wraps command line tool like ‘extractFeatures’ or ‘create’. The workflow for ‘compare’ tool has three input parameters. These are two URLs to the XML histogram files that comprise information about image features. These files are acquired us...

Created: 2011-06-16 | Last updated: 2012-04-04

Credits: Roman

Extract histogram features from image file (1)

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As a template for creation of image workflows was used xa-toolwrapper project from Sven Schlarb (https://github.com/openplanets/scape/tree/master/xa-toolwrapper). This project enables creation of WSDL web service that wraps command line tool like ‘extractFeatures’ or ‘create’. The workflow for ‘extractFeatures’ tool has two input parameters. The URL to the input image file and the number of histogram bins as integer. This workflow extracts histogram feature...

Created: 2011-06-16 | Last updated: 2012-04-04

Credits: Roman

Detect compressed TIFF files and remove th... (3)

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The workflow takes a list of TIFF images as input, identifies the "Group 4 Fax" comressed TIFF images and converts them to uncompressed TIFF images using convert. Finally it characterises the converted image. This version of the workflow replaces the web services of the original workflow with tool services.

Created: 2011-06-15 | Last updated: 2012-03-08

Credits: Sven

Attributions:

Cataloguing Workflow 2 (1)

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Workflow example. Not to be used. Only for OJAX++ synchronisation.

Created: 2011-06-11 | Last updated: 2011-06-11

Credits: Fbracken

Retrieval of molecular interactions within... (1)

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Description of the flow steps: 1. split the list of identifiers using allows separators, 2. build a MIQL query with these identifier in preparation of running a PSICQUIC request, 3. Retrieve molecular interaction from IntAct's PSICQUIC service using the generated MIQL statement, 4. filter the list of returned MITAB using the list of identifiers and only keep those lines where both participating molecules are members of the input list, 5. return the count and list of filtered MITAB lines.

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

Credits: Skerrien