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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: 2009-07-03

Credits: Stian Soiland-Reyes

Attributions: GBSeq test

Pattern: Return errors instead of null (1)

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 As Taverna can't (currently) handle null (see http://www.mygrid.org.uk/dev/issues/browse/TAV-653) - in Taverna 2 one can instead return exceptions on individual ports and inside lists. Exceptions are registered as error documents by Taverna, and are passed along. The ErrorBounce layer of processors downstream will prevent execution if they see this 'null'-exception - as showed in this example that the string concatination is just run for the two list elements that are not exceptio...

Created: 2010-01-04 | Last updated: 2010-01-04

Credits: Stian Soiland-Reyes

Example dbfetch (2)

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Run EBI's dbfetch

Created: 2014-09-03 | Last updated: 2014-09-03

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

Find compounds pharmacology targets in Ope... (2)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTS API https://dev.openphacts.org/docs/1.5. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this means this workflow would be propagating 404 Not Found errors. Until there is a Local worker to filter out...

Created: 2013-10-16 | Last updated: 2015-11-19

Credits: Stian Soiland-Reyes

Attributions: Find compounds pharmacology and align against target sequences

Find compounds pharmacology and align agai... (1)

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Look up concept URI from freetext, e.g. "aspirin", find compound pharmacology and their target info. For each target, blast+tree on its sequence - if any. Uses the Open PHACTs API https://dev.openphacts.org/docs/alpha and the myExperiment workflow 3369 "Blast_Align_and_Tree" http://www.myexperiment.org/workflows/3369. Notice that in tihs workflow, most concepts won't have compounds, and most compounds won't have targets, and most targets won't have a sequence - Open PHACT API wise this mean...

Created: 2013-10-16

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions: Blast_Align_and_Tree

Refresh SPI after plugin installation (1)

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This workflow hacks into Taverna's plugin system to force update the net.sf.taverna.t2.workbench.views.results.saveactions.SaveAllResultsSPIRegistry SPI, which means it is possible to install/update the Taverna PROV plugin without restarting. This is needed to enable live update of this plugin, because there is a bug in Taverna 2.4 and below where the SPI registries are not updated correctly after installation of a plugin.

Created: 2013-09-10

Credits: Stian Soiland-Reyes

The title (1)

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The description. This could be quite long.

Created: 2012-09-26

Credits: Stian Soiland-Reyes

WCP-04 Exclusive choice - if/else branching (1)

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The choice of executing choiceA or choiceB is determined by using String_List_Intersection and String_List_Difference. If in="true" then the intersection will yield a non-empty list, triggering execution of choiceA. This list will however not differ from the input, and so choiceB will iterate over an empty list (ie. not execute). Note how using 'difference' for the else-case here means that if you run the workflow with in="bob", choiceB would still run. Some early if/el...

Created: 2012-02-20 | Last updated: 2012-02-20

Credits: Stian Soiland-Reyes

Attributions: Example of a conditional execution workflow Example of conditional invocation

Calculation of distances, magnitutes and l... (2)

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Calculation of distances, corrected apparent B magnitude mB-corr and luminosities with values gathered from the HyperLEDA database. This workflow receives a list of galaxy names (hyperLEDA names. ie: KIG0001) and a file with the morphological types of those galaxies Using the name of a galaxy, the workflow querys Hyperleda to extract some properties of this galaxy (J2000 Coordinates, velocity, galactic extinction,log of axis ratio, and the Total B-magnitude ). With this properties it calcula...

Created: 2012-01-10 | Last updated: 2012-01-16

Credits: Stian Soiland-Reyes

Attributions: Calculation of distances, magnitutes and luminosities using HyperLEDA Data involved in RO Propagation of quantities Scripts in RO Propagation of quantites

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