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wf4ever slides

Created: 2010-12-02 09:52:26 | Last updated: 2010-12-02 10:16:34

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new workflow data entry

Created: 2010-12-01 16:02:28 | Last updated: 2010-12-01 16:02:29

Credits: Richard Crane

License: Creative Commons Attribution-Share Alike 3.0 Unported License

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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

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

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 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

Transform XML with parameters (1)

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Similar to Transform_XML local widget but accepts transformation parameters and skips the part with writing to the output file. The essence, i.e. Transform_XML beanshell works with Strings representing file contents, not with file URLs. The XML transfomation parameters are given as a list of strings in the "param_name = param_value" format.

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

Credits: trybik

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 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 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 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 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 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 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 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

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My Pack

Created: 2010-11-23 05:04:05 | Last updated: 2010-11-23 05:04:06

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Association of HLA Profiles

Created: 2010-11-17 18:33:50 | Last updated: 2010-11-17 18:33:51

Credits: Pqmarkdev

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

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grid

Created: 2010-11-16 07:04:22

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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

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

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

Search OpenTox data sets by title. (1)

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 Use of an OpenTox ontology server to find data sets with a particular string in the title, such as 'EPA' as in this case.

Created: 2010-11-14 | Last updated: 2010-11-14

Credits: Egon Willighagen

Run OpenTox models on local data. (1)

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 Runs a remote OpenTox model to predict properties for local data which is uploaded on the fly.

Created: 2010-11-13 | Last updated: 2010-11-13

Credits: Egon Willighagen

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

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

[untitled] (1)

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A tutorial workflow of Taverna.

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

Credits: Sukhdeep Singh

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

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

Sacs Gene Muation Analysis (1)

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This workflow was created to predict the effect of the mutation on the primary and the secondary structure of a mutated sacsin protein. The genomic sequence bearing the mutation should be pasted on FASTA format as input for the Transeq tool. This sequence will be translated to protein and compared to the wild type protein, already extracted from NCBI database, through the Supermatcher tool. Variation(s) will be verified by multiple alignment using Blastp and ClustalW tools. Prediction of th...

Created: 2010-11-03 | Last updated: 2010-11-03

Credits: Yosr Bouhlal

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Uniqueness, Self belonging and Intercourse in Nature...

Created: 2010-10-30 18:39:41 | Last updated: 2010-10-30 18:39:42

Credits: M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

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Mind Matter and Contour : A Two Timing Ether or a Wh...

Created: 2010-10-30 18:33:46 | Last updated: 2010-10-30 18:34:57

Credits: M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

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Evolution at the Surface of Euclid:Elements of a Lon...

Created: 2010-10-30 18:30:51 | Last updated: 2014-02-23 01:03:48

Credits: M. Kirsh

License: Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 Unported License

File type: Adobe PDF

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Calculate molecular descriptors with OpenT... (1)

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 Queries an OpenTox ontology server for available molecular descriptor, picks one, and calculates the descriptor value for a few molecules.

Created: 2010-10-30 | Last updated: 2010-10-30

Credits: Egon Willighagen

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

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 - 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 - 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

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

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 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 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 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 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

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

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... (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

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

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 - default targ... (1)

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The pad numeral with leading 0s takes the input '12' and pads it to the default target length of 7, yielding the output '0000012'.

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

FIlter list of strings by regex extracting... (1)

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The workflow examines the five element list split from the first service. For each element, if it contains an 'a' followed by two characters, then that triple is included in the output. Thus, for the input ['a','b','abcde','cdef','axy'], only 'abcde' and 'axy' contain a match and so ['abc', 'axy'] is output.

Created: 2010-10-29