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Items tagged with "list" (22)

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Files (2)

Blob filter a sdfile by a list of ids

Created: 2010-10-05 11:17:35 | Last updated: 2010-10-05 11:18:37

Credits: User De maas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Used an array to hold the ids but I'm curious if there is a better way like a (sorted) list or an index file.

File type: JavaScript

Comments: 0 | Viewed: 25 times | Downloaded: 18 times



Blob filter a sdfile by a list of ids, keep in memory

Created: 2010-10-05 14:40:24 | Last updated: 2010-10-05 14:40:26

Credits: User De maas

License: Creative Commons Attribution-Share Alike 3.0 Unported License

In order to speedup a second run keep the sd-file in memory. So use a list in stead of a iterator which reads from disk.

File type: JavaScript

Comments: 0 | Viewed: 22 times | Downloaded: 17 times


Workflows (20)

Workflow CountListElements (5)

Very simple workflow to count the number of items in a list (top level only in case of nested lists). Does no more than count = list.size();

Created: 2007-10-17 | Last updated: 2007-10-17

Workflow CloneItemsInList (1)

Utility workflow that clones an item copy_number times. You can use this to work around standard iteration strategies, e.g. in combination with the CountListItems workflow. Workflow examples: TestIterationStrategy_withClones. For an alternative approach see TestIterationStrategy_withNesting. Example I/O: input: A copy_number: 3 result: [A,A,A] input: [A,B,C] copy_number: 3 result: [[A,A,A][B,B,B][C,C,C]] input: [A,B,C] copy_number: [3,2] result: [[[A,A,A],[A,A]][[B,B,B],[B,B]],[[C,C,C],...

Created: 2007-11-29

Credits: User Marco Roos

Workflow TestIteratorStrategy_withCloning (2)

This workflow implements a strategy for this problem: > I would like to perform an iteration including a dot product between > a list and a list of lists; example: > Input: > > [1] (1) > [A,B,C] (2) > [[a,b],[c,d],[e,f]] (3) > > Desired output: > > [1Aa, 1Ab, 1Bc, 1Bd, 1Ce, 1Cf] In this implementation a java beanshell is used to clone the items in list 2 as many times per item as there are items in the sublists of list 3. The iteration stra...

Created: 2007-11-29 | Last updated: 2007-11-29

Credits: User Marco Roos

Workflow fetch_fasta (1)

This work flow is designed to take an EMBL file containing the genomic data for an identified bacterium. From this information the workflow can determine whether or not that this strain is an MRSA type of bug. This can be determined based on the MecA profile of the given strain. Blast is utilised to find a relationship with given proteins and that of know S. aureus strains. This phylogenic output is generated from a ClustalW algorithm that plots a phylogenic tree. The output is prese...

Created: 2009-03-20 | Last updated: 2009-03-20

Credits: User Jumblejumble

Workflow Search InChI in ChemSpider (1)

This workflows queries ChemSpider for compound information and compound images. Note that a Chemspider security token is needed in order to access some of the ChemSpider services (receive one by registering at ChemSpider). Possible search terms might be InChI codes, ChemSpider identifiers or names.

Created: 2009-03-30 | Last updated: 2009-03-30

Credits: User Michael Gerlich

Workflow Pipelined list iteration (1)

Perform multiple iterations of services in order to show pipelining

Created: 2009-07-03

Credits: User Stian Soiland-Reyes User Ian Dunlop


Workflow Select items from list (1)

This workflow pops up a window containing an input list of strings. The user is invited to select one or more strings for downstream processing.

Created: 2010-03-30

Credits: User Peter Li

Workflow Using a Create_List script with a dot-prod... (1)

Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which you now want to keep in a list [a,b]. The shim Create_list takes two single inputs, and returns a list of [in1, in2]. Configured with the Dot product list strategy it means that it will pipeline out [a1,b1], [a2,b2], [a3,b3] etc.Create_lots_of_strings gives implicit iteration over the service add_a_and_b - assume this is a service that returns two values which...

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

Credits: User Stian Soiland-Reyes


Workflow Download Structures from PubChem given che... (1)

This workflow takes the input file containing chemical names and returns a single SDF file of structures. The names are searched against pubchem compounds via e-search. If the compound name is found an XML file containing PubChem ID is returned.The max return compound_ID is set to 1 which could be increased. If the compound name is not found then no ID is returned.  The pubchem compound_ID is then used to download structures from PubChem.  

Created: 2011-05-24 | Last updated: 2011-05-24

Credits: User Kalai User Michael Gerlich

Attributions: Workflow Download Entries from PubChem

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

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: User Rafael C. Jimenez

Workflow Merge list of errors to string (2)

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


Workflow Longitude with beanshell (1)

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

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

Credits: User Chrisser

Workflow getFirstElementDFS (2)

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

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

Workflow Get image mimetype (1)

Returns the mimetype of an image.

Created: 2012-02-21 | Last updated: 2012-02-21

Credits: User Markus Plangg

Workflow Query EVS by chromosomal position (1)

The workflow takes a list of chromosomal positions (in the format chr:pos e.g. 2:139574) and returns a selection of data in the Exome Variant Server (http://evs.gs.washington.edu/EVS/).

Created: 2013-07-26 | Last updated: 2013-07-26

Credits: User Sirisha Hesketh

Workflow Empty list output and a value (1)

Simply returns a port, depth 1, with nothing in it and a port, depth 0, with a constant.

Created: 2014-01-24

Credits: User Robert Haines User Alan Williams

Workflow Empty list output (1)

Simply returns a single port, depth 1, with nothing in it.

Created: 2014-01-24

Credits: User Robert Haines User Alan Williams

Workflow Get Concept IDs (5)

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

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

Credits: User Kristina Hettne User Reinout van Schouwen User Martijn Schuemie User Marco Roos Network-member BioSemantics

Workflow ImportConvertEnsembl (1)

This workflow accepts a spreadsheet file as input and extracts a list of ENSEMBL Gene IDs from column A. The hsapiens_gene_ensembl service converts these IDs to Entrez_geneIds

Created: 2014-09-05

Credits: User Katy Wolstencroft

Workflow chebi2keggID (1)

This workflow converts a (list of) chebi identifiers to kegg compound identifiers.

Created: 2016-06-21

Credits: User Kristina Hettne

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Linked Data

Non-Information Resource URI: https://www.myexperiment.org/tags/541

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