Workflows

Python Average and Standard Deviation (2)

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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)

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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)

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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)

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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 Based on Population histogram in R by Alan R Williams

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

Credits: Mutanthumb

Mean Rshell (1)

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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)

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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)

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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)

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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)

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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: Chrisser

Attributions:

Failed 2 Chart Attempt (1)

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Tried to show 2 charts simulatneously.

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

Credits: Mutanthumb Alan Williams

IST600 - 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 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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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A tutorial workflow of Taverna.

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

Credits: Sukhdeep Singh

BiomartAndEMBOSSAnalysis (1)

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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)

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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)

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

Created: 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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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)

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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