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The ontologies in section 3.3 "The conceptual model" mix glyphs and concepts, which doesn't seem correct.
Indeed, in those ontologies, nodes are classes of glyphs, and arcs _is_a_ relationships share…
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```
Not being able to access node attributes
via "node['A'].property"-like statements is annoying.
I suggest to upgrade from having an array of nodes,
where the id is an attribute of each node,
to a …
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## Description
**Q: What is the name of the feature?**
A: Event metrics service
**Q: What does this feature enable the user to do?**
A: Provide implicit feedback
**Q: What informati…
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```
Not being able to access node attributes
via "node['A'].property"-like statements is annoying.
I suggest to upgrade from having an array of nodes,
where the id is an attribute of each node,
to a …
-
I tried to upload the attached valid SBML file with cy3sbml in Cytoscape 3.7.2. and got the following parsing error
```
Task (org.cy3sbml.SBMLReaderTask@698f9f49) title: cy3sbml reader
Task (…
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At the moment, cola doesn't seem to play nicely with being minified :(
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Currently, we are using [cytoscape-sbgn-stylesheet](https://github.com/PathwayCommons/cytoscape-sbgn-stylesheet), but it only supports PD language, so we cannot show the resulting AF maps as interacti…
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Here is a [Mockup Presentation](https://docs.google.com/presentation/d/1vdwVyMrfj4YdbdJLuzfoTGf3BSWlXlLw4maXR7XtYUU/edit#slide=id.p1) of the workflow
User requirements:
- [ ] creating activity nod…
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pipeline / browser script to transform / precompute layout for all pathways
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We are to define and make /graph and /get web queries optionally generate rich JSON network/graph data (new OutputFormat), such as our web app [uses internally](https://github.com/PathwayCommons/app-u…