Workflows

Weka Regression from XRFF file. (1)

• Download

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

Substructure filter (1)

• Download

No description

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

QSAR CSV to Weka Regression Dataset (1)

• Download

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

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

• Download

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

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

• Download

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

• Download

Get a PSICQUIC REST URL from a PSICQUIC SOAP URL

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

Credits: Rafael C. Jimenez

EUADR Relationship Extraction Workflow (1)

• Download

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

EUADR - Literature Analysis (1)

• Download

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

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

• Download

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

OpenTox Upload and merge data sets (1)

• Download

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

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

OpenTox Learn and evaluate model (1)

• Download

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

Created: 2011-08-09

OpenTox Get Id (1)

• Download

No description

Created: 2011-08-09

XML-RPC example current time (1)

• Download

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

Difference: Query - Reference (1)

• Download

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

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

• Download

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

BLAST your sequences against the NucleaRDB (1)

• Download

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

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

• Download

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

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

• Download

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

Image metadata extraction (1)

• Download

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

TIFF to PNG (1)

• Download

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

Convert GML to SVG (1)

• Download

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

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

Credits: Harvey

GT: Sample Sheet Generation (7)

• Download

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

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

• Download

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: Database - Master SNP Call Table (1)

• Download

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

Seven day weather by zip code (1)

• Download

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

Fetch today's Johnny Wander Comic (1)

• Download

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

Get Recent Cards From Indexed (1)

• Download

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

Get My Weather (1)

• Download

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

ZipCodeGetWeatherInfo (1)

• Download

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 7 Days Weather by Zip Code (1)

• Download

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

Merge list of errors to string (2)

• Download

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

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

• Download

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

City weather information (1)

• Download

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 cat and girl comic (1)

• Download

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

Fetch today's Girls with Slingshots comic (1)

• Download

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

Seven-Day Forecast (1)

• Download

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

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

• Download

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

Echo (1)

• Download

This does a simple Echo

Created: 2011-09-16

Credits: Christian

Point coordinate projection transformation (1)

• Download

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

Geottif image reprojection (1)

• Download

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

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

• Download

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:

Population histogram in R (1)

• Download

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

Statistics example (1)

• Download

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

Concatenated List of Values (1)

• Download

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

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

• Download

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

Spreadsheet Import Fertilizer Use (1)

• Download

Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet file FertilizerUse.xlsx and generates a graph from the date. The source data is from http://www.myexperiment. org/files/568/download/FertilizerUse.xls and ERS, TVA (Tennessee Valley Authority), AAPFCO (Association of American Plant Food Control Officials), TFI (The Fertilizer Institute).

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

Credits: tpacurtis Alan Williams

Attributions: Spreadsheet Import Example US Fertilizer Use

US Consumption of Plant Nutrients (1)

• Download

This workflow takes data from the ERS, TVA (Tennessee Valley Authority), AAPFCO (Association of American Plant Food Control Officials), and the TFI (The Fertilizer Institute) and represents them in a bar chart.

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

Credits: Kayleigh Ayn Bohémier

Attributions: Spreadsheet Import Example US Fertilizer Use

Broccoli: A State Comparison (1)

• Download

Imports data from NY and NJ to compare broccoli harvest vs. planting rates across the two states. The workflow is currently set to evaluate data from 1960 to 1965. Source: Compiled by ERS from data of USDA, National Agricultural Statistics Service, Vegetables Final Estimates.

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

Credits: Kayleigh Ayn Bohémier

Attributions: Spreadsheet Import Example NJ Broccoli Production NY Broccoli Production

Standard Deviation and Mean Values from a ... (1)

• Download

This incredibly awkward script has another embedded script associated with it. It essentially smashes the output from the other workflows together using a Beanshell script.

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

Credits: Kayleigh Ayn Bohémier

Attributions: Input for PS3 # 2 Part 2

Standard Deviation From a Text File: Neste... (1)

• Download

This workflow takes an input file of a list of numbers and runs it through a simple Python script to produce the standard deviation and average.

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

Credits: Kayleigh Ayn Bohémier

Attributions: Standard Deviation and Mean Values from a Text File Input for PS3 # 2 Part 2

Python Average and Standard Deviation (2)

• Download

This workflow uses a Python script to take a provided filename (or list of filenames) containing numbers (one per line) and return the standard deviation and average (or mean).

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

Credits: Kayleigh Ayn Bohémier

Attributions: Executes Python script Input for PS3 #2 Part 1

New York vs. New Jersey Broccoli Production (1)

• Download

Uses the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports two files and generates a single graph comparing the information from the two spreadsheets.

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

Credits: tpacurtis Alan Williams

Attributions: Spreadsheet Import Example NY Broccoli Production NJ Broccoli Production

Name resolver of galaxies parsing the outp... (1)

• Download

This workflow ask for text file using "Select_file" local services. This file is read by the "read_text_file", using "utf-8" as encoding. The result of "read_text_file" is splitted in lines by "split_string_into_string_list_by_regular_expression" and each of this lines is the input for the Rest_servise. The REST service search for each line (each line contains one name of one galaxy) some information about that galaxy. The string is like: target=cig+1 service=NED(nedwww.ipac.caltech.edu) coo...

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

New Population Histogram (1)

• Download

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 Based on Population histogram in R by Alan R Williams

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

Credits: Mutanthumb

Mean Rshell (1)

• Download

Used the Rshell to find the MEAN and standard deviation of a list of values.

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

Credits: Mutanthumb

Name resolver of galaxies parsing the outp... (1)

• Download

This workflow ask for text file using "Select_file" local services. This file is read by the "read_text_file", using "utf-8" as encoding. The result of "read_text_file" is splitted in lines by "split_string_into_string_list_by_regular_expression" and each of this lines is the input for the Rest_servise. The REST service search for each line (each line contains one name of one galaxy) some information about that galaxy. The string is like: target=cig+1 service=NED(nedwww.ipac.caltech.edu) coo...

Created: 2011-09-21

Nested Mean Rshell (1)

• Download

This workflow uses a nested workflow. The nested workflow takes a list of values and finds the mean and standard deviation for each list. The result of the nested workflow is then concatenated with a list of names using Dot Product for list handling.

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

Credits: Mutanthumb

Ag Spreadsheet Import (1)

• Download

Based on Spreadsheet Import Example by David WithersSusan 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: 2011-09-21 | Last updated: 2011-09-21

Credits: Mutanthumb Alan Williams

Population histogram in R (1)

• Download

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: Chrisser

Attributions:

Failed 2 Chart Attempt (1)

• Download

Tried to show 2 charts simulatneously.

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

Credits: Mutanthumb Alan Williams

IST600 - Spreadsheet Import Example (1)

• Download

Example using the SpreadsheetImport service to import data from an Excel spreadsheet. The workflow imports the file spreadsheet FertilizerUse.xls and generates a graph from the date. The spreadsheet is available at http://www.myexperiment. org/files/568/download/FertilizerUse.xlsimg, #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-s...

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

Credits: Chrisser

slightly more complicated Spreadsheet Impo... (1)

• Download

Example using two instances of the SpreadsheetImport service to import data from  Excel spreadsheets. The workflow imports these file spreadsheets f and generates a graph comparing the data.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 ...

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

Credits: Chrisser Wdsnellg tpacurtis

Attributions: Spreadsheet Import Example

input list example (1)

• Download

This workflow is a simple example of how to input a list of numeric values and perform some ultra-basic calculations using Rserve. The output is two separate numbers, the mean and standard deviation of the list of input values. 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...

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

Credits: Chrisser

Pad numeral with leading 0s - specified ta... (1)

• Download

The pad numeral with leading 0s takes the input '12' and pads it to the specified target length of 4, yielding the output '0012'.

Created: 2010-10-29 | Last updated: 2010-10-29

Pad numeral with leading 0s - too short ta... (1)

• Download

The pad numeral with leading 0s takes the input '12' and because the specified target length of 1 is too short, yields the output '12'.

Created: 2010-10-29

Split string into string list by regular e... (1)

• Download

The split string into string list by regular expression takes the string 'a,b,c' and using the default regular expression ',' splits it into the list ['a','b','c']

Created: 2010-10-29

Split string into string list by regular e... (1)

• Download

The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression ':' splits it into the list ['boo','and','foo']

Created: 2010-10-29

Split string into string list by regular e... (2)

• Download

The split string into string list by regular expression takes the string 'boo:and:foo' and using the specified regular expression 'o.*n' splits it into the list ['b','d:foo']

Created: 2010-10-29 | Last updated: 2010-10-29

String list difference - yielding non-empt... (1)

• Download

The string list difference service takes in ['a','b','c'] and ['a','e','c'] and returns the list ['b','e'].

Created: 2010-10-29

String list difference - yielding empty list (1)

• Download

The string list difference service takes in ['a','b','c'] and ['a','c','b'] and returns the empty list [].

Created: 2010-10-29

String list intersection - yielding non em... (1)

• Download

The string list intersection service takes in ['a','b','c'] and ['a','e','c] and returns the list ['a','c'].

Created: 2010-10-29

String list intersection - yielding empty ... (1)

• Download

The string list intersection service takes in ['a','b','c'] and ['x','y','z'] and returns the empty list [].

Created: 2010-10-29

String list union - yielding non-empty list (1)

• Download

The string list union service takes in ['a','b','c'] and ['a','e','c'] and returns a list equivalent to ['a','b','c','e'].

Created: 2010-10-29

String list union - yielding empty list (1)

• Download

The string list union service takes in two empty lists [] and [] and returns an empty list [].

Created: 2010-10-29 | Last updated: 2010-10-29

Ask - no parameters (1)

• Download

The ask service displays a prompt with no title and no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29

Ask - just message parameter (1)

• Download

The ask service displays a prompt with no title but with the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29

Ask - just title parameter (1)

• Download

The ask service displays a prompt with the title 'Some title' but no prompt message. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29 | Last updated: 2010-10-29

Ask - title and message parameters (1)

• Download

The ask service displays a prompt with 'Some title' and the prompt message 'Some message'. If the user presses cancel, then a service failure is generated. If the user presses OK then their input, even if it is empty, is passed to the answer port of the ask service and so to the output of the workflow.

Created: 2010-10-29

Async WPS example (2)

• Download

Example on how to work with an async service, where the statusURL is used to check for Example on how to work with an async service, where the statusURL is used to check for if the process has finished or not

Created: 2010-11-04 | Last updated: 2011-04-27

Credits: Jorgejesus

retry-example (1)

• Download

This workflow executes a local beanshell script that has been programmed to fail on some iterations. It demonstrates the advantages of setting retries in your workflows to make them more robust

Created: 2010-11-08 | Last updated: 2010-11-08

Credits: Alan Williams

[untitled] (1)

• Download

A tutorial workflow of Taverna.

Created: 2010-11-12 | Last updated: 2010-11-12

Credits: Sukhdeep Singh

BiomartAndEMBOSSAnalysis (1)

• Download

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2010-11-12 | Last updated: 2010-11-12

Credits: Krisztina

BiomartAndEMBOSSAnalysis (1)

• Download

Using Biomart and EMBOSS soaplab services, This workflow retrieves a number of sequences from 3 species: mouse, human, rat; align them, and returns a plot of the alignment result. Corresponding sequence ids are also returned.

Created: 2010-11-12

Credits: Krisztina

Pathways and Gene annotations for QTL region (1)

• Download

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

Created: 2010-11-15 | Last updated: 2010-11-16

Credits: Paul Fisher

Attributions: Pathways and Gene annotations for QTL region

Pathways and Gene annotations for RefSeq ids (1)

• Download

This workflow searches for genes which were found to be differentially expressed from a microarray study in the mouse, Mus musculus. The workflow requires an input of gene ref_seq identifiers. Data is then extracted from BioMart to annotate each of the genes found for each ref_seq id. The Entrez and UniProt identifiers are then sent to KEGG to obtain KEGG gene identifiers. The KEGG gene identifiers are then used to search for pathways in the KEGG pathway database.

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

KEGG pathways common to both QTL and micro... (1)

• Download

This workflow takes in two lists of KEGG pathway ids. These are designed to come from pathways found from genes in a QTL (Quantitative Trait Loci) region, and from pathways found from genes differentially expressed in a microarray study. By identifying the intersecting pathways from both studies, a more informative picture is obtained of the candidate processes involved in the expression of a phenotype

Created: 2010-11-15 | Last updated: 2010-11-15

Credits: Paul Fisher

A Basic example R workflow (3)

• Download

This workflow uses an R service running on localhost to calculate sin(0.45)

Created: 2010-11-26 | Last updated: 2014-08-20

Credits: Alan Williams

R logical workflow (1)

• Download

Checks what the logical_input is in R. For an logical_input of TRUE - is_false should be FALSE and is_true TRUE FALSE - is_false should be TRUE and is_true FALSE For any other input values, is_false and is_true should both be NA

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R numeric workflow (1)

• Download

This workflow uses an Rshell service to calculate the square of a numeric inputThis workflow uses an

Created: 2010-11-26

Credits: Alan Williams

R string workflow (1)

• Download

This workflow determines the lower case version of the input string.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R logical vector workflow (1)

• Download

The workflow returns a list containing the logical inversion of the logical vector input

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R integer vector example (1)

• Download

This workflow takes a list of integer values and returns a list containing the square of the input list's elements, and the sum of the input list's elements.

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R string vector example (1)

• Download

The workflow takes a list of strings and outputs a list contains the lower-cased versions of the input elements, and also a concatenation of the input elements

Created: 2010-11-26 | Last updated: 2010-11-26

Credits: Alan Williams

R integer workflow (1)

• Download

This workflow uses an Rshell service to calculate 100 modulus the integer input

Created: 2010-11-29

Credits: Alan Williams

R integer vector example (1)

• Download

This workflow takes a list of integer values and returns a list containing 100 modulus the list's elements, and the sum of the input list's elements.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

R PNG-value example (2)

• Download

This workflow produces a PNG plot on the figure port.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

R Text-file example (1)

• Download

This workflow contains two services. The file_writer uses a File in R to output a string. The file_reader uses a File in R to input a string, the contents of which are output.

Created: 2010-11-29 | Last updated: 2010-11-29

Credits: Alan Williams

R generic example (1)

• Download

This workflow shows how string vectors can be used to transfer a complex R object (in this case a matrix) between Rshell services

Created: 2010-11-29

Credits: Alan Williams

NCBI BLAST (SOAP) (1)

• Download

Perform a BLAST search using the EMBL-EBI’s NCBI BLAST (SOAP) service (see http://www.ebi.ac.uk/Tools/webservices/services/sss/ncbi_blast_soap). The query sequence, database to search and BLAST program to use are inputs, the other parameters for the search are allowed to default.

Created: 2010-11-29 | Last updated: 2013-03-28

Attributions: EBI_NCBI_BLAST NCBI BLAST (SOAP)

Phylogenetic Tree (1)

• Download

Workflow compose by 2 services that goal buid a Phylogenetic Tree using ClusltalW and Phylip services.

Created: 2010-11-30 | Last updated: 2010-11-30

Credits: Caiocb