James Marshall

icon indicating a website link http://staffwww.dcs.shef.ac.uk/people/J.Marshall/james.html

icon company Opteran Technologies icon location Chief Scientific Officer at Opteran Technologies / Professor of Theoretical and Computational Biology at University of Sheffield

Results 39 comments of James Marshall

Clean exceptions

PS some warnings should go to the log, some should probably be displayed. Most probably should go to the log - so need to pay attention to this...

Replace global var figcounter with matplotlib.pyplot.get_fignums()?

Doing this may be part of resolving issue #231

remove MuMoTcontroller._plotLimitsWidget and use the self._widgetsExtraParams['plotLimits']

Does that make sense? plot limits can be seen on views that don't have extra advanced widgets... e.g. field views.

remove MuMoTcontroller._plotLimitsWidget and use the self._widgetsExtraParams['plotLimits']

In my opinion, since field plots currently have no advanced widgets to my knowledge, and since this is fairly basic functionality, it may be better to have this `showNoise` and...

Allow for creating models from Python strings

If this is necessary to close issue #157 I should be able to do something quick in a few days - the existing functionality is probably nicer for a user...

Allow for creating models from Python strings

You mean it already works as described @willfurnass (I'd be surprised unless you changed something) or it would be straightforward to make it work (I agree, was thinking the same,...

Allow for creating models from Python strings

Great, on reflection I can see why this would work - since this is a satisfactory workaround for testing purposes I can focus now on #158

Allow for creating models from Python strings

Feel free to add some pre-processing to the input string within the `parseModel(...)` method though, and close

Bifurcation() fails to find all branches

Thanks @renapagli - neat workaround! What happens if you choose `initBifParam = 1` by the way? ;) @tbose1 we know this kind of functionality is hard to implement in general...

Feature request: support for 2-simplex (ternary) plot

@renapagli just to clarify, I think field-based plots (vector and stream) can be plotted for this system using a system-size substitution via `substitute()` - are you particularly asking for integration...