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User: Stian Soiland-Reyes

Workflow Example dbfetch (2)

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Run EBI's dbfetch

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

Credits: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions:

Blob Bonn 2014 Agenda

Created: 2014-09-01 09:08:17 | Last updated: 2014-09-03 08:10:40

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Agenda Bonn “in silico experimentation” course 2014-09-01 / 2014-09-03Please sign up and join the myExperiment group: Bonn Workshop Sep 2014For each tutorial and presentation, there is an accompanying slideset in this group. For your convenience, this Agenda PDF has links to each of these as [T-xxx.pdf].  

File type: Adobe PDF

Comments: 0 | Viewed: 96 times | Downloaded: 93 times

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Blob TEST file

Created: 2014-04-29 13:21:44

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Why is this so tiny?

File type: Trident (Package)

Comments: 0 | Viewed: 8 times | Downloaded: 5 times

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Pack Test pack


Created: 2014-04-29 13:16:38 | Last updated: 2014-04-29 13:17:26

Pack for blab lblahttp://example.com/

2 items in this pack

Comments: 0 | Viewed: 74 times | Downloaded: 6 times

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Workflow 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: User Stian Soiland-Reyes

Attributions: Workflow Find compounds pharmacology and align against target sequences

Workflow 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: User Stian Soiland-Reyes User Katy Wolstencroft

Attributions: Workflow Blast_Align_and_Tree

Workflow 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: User Stian Soiland-Reyes

Blob Workflow run: Pav2Svg using ChemSpider VoID

Created: 2013-04-05 09:28:31

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Taverna provenance of workflow run on PAV2SVG using the ChemSpider VoID descriptor as input. See Pack 418.

File type: ZIP archive

Comments: 0 | Viewed: 11 times | Downloaded: 5 times

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Blob Visualization of ChemSpider VoiD provenance

Created: 2013-04-05 09:23:22 | Last updated: 2013-04-05 10:40:18

Credits: User Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

SVG visualization of the PAV provenance from the ChemSpider VoID descriptor example. See Pack 418.Note that this file has been made with PROV Toolbox 0.1.2 as 0.1.3 does not show shortened labels as here.

File type: image/svg+xml

Comments: 0 | Viewed: 36 times | Downloaded: 12 times

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Workflow Visualize PAV provenance as SVG (2)

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VoID descriptions are fetched as Turtle, cleaned up to be valid OWL ontology and include useful labels, processed through the OWL reasoner Pellet; this adds inferred PROV statements to the RDF, which is then fed to the PROV Toolbox, generating an SVG visualization of the provenance. Note that this workflow downloads CWM, Pellet and ProvToolbox on demand, and uses UNIX command line tools like wget and md5 which are unlikely to work in Windows. This workflow has been tested on Ubuntu 12.10 wit...

Created: 2013-03-05 | Last updated: 2013-04-05

Credits: User Stian Soiland-Reyes

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