All content

Example dbfetch (2)

• Download

Run EBI's dbfetch

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

Credits: Stian Soiland-Reyes Katy Wolstencroft

Attributions:

View Download

Bonn 2014 Agenda

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

Credits: Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Adobe PDF

Comments: 0 | Viewed: 112 times | Downloaded: 104 times

This File has no tags!

View Download

TEST file

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

Credits: Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: Trident (Package)

Comments: 0 | Viewed: 14 times | Downloaded: 7 times

This File has no tags!

View Download

Test pack

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

2 items in this pack

Comments: 0 | Viewed: 76 times | Downloaded: 7 times

This Pack has no tags!

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

• Download

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)

• Download

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)

• Download

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

View Download

Workflow run: Pav2Svg using ChemSpider VoID

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

Credits: Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: ZIP archive

Comments: 0 | Viewed: 17 times | Downloaded: 7 times

This File has no tags!

View Download

Visualization of ChemSpider VoiD provenance

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

Credits: Stian Soiland-Reyes

License: Creative Commons Attribution-Share Alike 3.0 Unported License

File type: image/svg+xml

Comments: 0 | Viewed: 54 times | Downloaded: 18 times

Visualize PAV provenance as SVG (2)

• Download

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: Stian Soiland-Reyes