Cytoscape WikiInterviewed by: Chris Workman and Mike Smoot
What things would you like to see improved in Cytoscape?
- Edge labels overlap each other, this is bad. Makes labels unreadable for anything remotely large.
- There is no single file format. A single format would facilitate scripting.
- GO mapping is useless. Map attributes to node, but because it's a list attribute, it can't be displayed.
- Filtering interface is insane. It is possible to figure out how it works, but it's not intuitive. Some names imply regular expression use, but don't. The interface is very general, but isn't useful for non-experts.
- Vizmapper not quite as bad.
- The design of these features (vizmap+filter) show a developer-centric view of the features rather than a user-centric view.
- These features tend to be very jargony, meaning they use words and phrases that mean something to the developers, but not to inexperienced users. A good example is the PassThroughMapper.
- GUI should be very simple. Hard code top 10 things into GUI. Alternatively have a beginner/expert interface.
- You can't use all maps on some attribute types. For example, text labels can only have a pass-through mapper applied to them so it shouldn't be an option to do anything besides that.
- Users shouldn't have to read the manual to apply color to nodes.
What additional features would make your work with Cytoscape easier?
A command line interface from within the GUI, possibly just a text field somewhere that would take a command and execute it. PyMOL is a good example. Syntax is tricky for PyMOL but the general usage is to select a group of atoms and apply something to that set. This is basically what Cytoscape does with networks.
- Beyond a certain level of complexity, it is impossible to anticipate expert use.
Real time bug report...
- Closed cytoPanel 2 and found it hard to reopen.