diodeproject/mumot

Multiscale Modelling Tool - mathematical modelling without the maths

mumot's Issues

Accept LaTeX arguments in controller building commands

E.g. stream (and all other functions) need to accept as arguments not only
'Psi_{1}'
but also
'\Psi_{1}'
and
'\Psi_1'

Refactor parameter label and value lists as dictionaries

In views, etc.

Intelligently set initial rates and rate limits for views

Controllers can be parameterised with these, so they just need to be chosen appropriately.

error message widget not displaying/updating

The HTML widget for displaying error messages interactively is not always displayed, and is not updated with new error messages

Improve error checking in substitute

In particular, for setting system size check all reactants appear in assignment, with negative sign, and system size parameter sign is positive

Agree consistent error handling mechanism

In places the code uses error classes like SyntaxError, in others custom error classes, in places assert, in other places print and return

View logs lag plots in interactive mode

Parameters reported in logs lag behind latest versions plotted, according to widget values.

Figure download is not working on Chrome

Aggregate the results from the multirun command and visualise them via boxplots

Renaming reactants with substitute without setting system size

Causes strange behaviour, as represented by showODEs()

System-size slider in vector/stream plots to modify graphical illustration of N-dependent noise

Generate multiple plot/figures with one command to visualise various results together

For example, add possibility to visualise network, temporal dynamics and final distribution after a multiagent simulation.
Possible organisation of the figures in tabs.

Replace PyDStool plotting with bespoke routine

This should also enable additional functionality, in particular:

• plotting difference of two state variables
• displaying bifurcation view as part of part of multi view controller (issue #13) - internal PyDStool plotting does not seem well-behaved and does not plot to current axes

Make views completely independent of controllers

Views currently assume presence of a controller to set their parameter values. Expert users should be able to directly instantiate view objects, setting parameter values on creation, without going via a controller.

substitute() changes rules displayed by show() in source model

if model2 is derived from model1 via a call to substitute, then model1.show() can show reactions whose rates reflect the substitution made to create model2

MA and SSA views should use the _getStoichiometry function

At the moment MA and SSA views use a custom _getStoichiometry function.
For consistency, in the project, we should use a single Stoichiometry function.

SSA view outputting to standard output

Should be capturing to log file, or using error widget

Integration with PyDSTool

Too many issues to list at the moment! But the first critical one is to complete a proof-of-concept for interactive bifurcation analysis of a described model using PyDSTool. The widgets update the parameters of the model but the bifurcation analysis raises an exception for reasons that are not currently clear.

Add color selection by user for state

The user can select (through widget) the color to assign to each state (also called reactant).
The color will be used in the plots (e.g., network graph, temporal dynamics)

Intelligently set initial conditions for bifurcation analyses

Either by analytic solution for fixed points, or numerical integration. Trying the former before the latter may introduce unacceptable delays for intractable systems of equations.

Widget order to be sorted

Widgets currently constructed in arbitrary order, which will be confusing for users; sort alphanumerically

LaTeX reactants not rendered correctly

E.g. in showODEs(), showReactants()

Add dynamic plotting while computation is running (especially useful for multiagent simulations)

Add "Play", "Pause", "One-Step" buttons to start, pause and advance 1-step at a time the simulation

Improve format of the exported data files

There is the possibility to download the simulation data file (e.g. through MuMoTmultiagentController.downloadTimeEvolution()), however the current data format is very basic and not properly formatted and should be improved.

Implement empty reactant and constant reactants in model parser

To enable variable-population models, and constant background flows

MA and SSA views/controllers do not handle Figures correctly

MA and SSA views/controllers manage figure with bugs.
For example, running two times
net = model1.multiagent()
will have the widgets interfering between different cells.

The views must use the standard functions: _buildFig and _fig_formatting_2D

Prevent opening of second window when re-plotting bifurcation diagram

Sometimes when moving sliders a second figure window is generated below the first. Moving the slider again the second window is updated correctly. However, this only happens for some examples and not for others.

MA and SSA should have total population slider + proportion sliders

Current implementation does not allow for easy varying of system size while keeping initial condition proportions constant

Render LaTeX labels in 2d and 3d figures

_fig_formatting_2D and _fig_formatting_3D to look up and redner LaTeX variable names correctly

Add bounded arena

At the moment the multiagent particle simulation have periodic boundary conditions (torus).
Add walls and either:

• let the particle bounce on the walls (as molecules do)
• let the particle get stuck to the wall (as simple robots do)

Add final distribution plot for multiagent/network simulations

Data is generated but it is not (yet) visualised.
Possible visualisations (to be decided):

• histograms [+ variance bars when it is result from multiple runs]
• points [+ boxplots when it is result from multiple runs]

Implement 3d stream plot

3d stream plot will need to be implemented by hand, by numerically integrating the equations from selected starting points, as I have not found a library implementation so far

Create joint plots (e.g., multiagent + ODE + SSA)

Overlay results from various description levels in one single plot.

Check system dimension in field plots

Plotting a 3+d system when system size has not been set, but system size is non-constant, requires error handling

Widgets in accordion view flow off edge of screen

Safari issue, or jupyter notebook version issue, possibly? - wanted to check if others see this; e.g. for this command:

mmt.MuMoTdefault.setTimeDefaults(initTime=10, step=1)
net = model1.multiagent()

running at 2560 x 1600 widgets past Particle speed cannot be seen / reached

Vector plots and stream plots system size unset error

Vector and stream plots need to display an error message and exit before constructing widgets, when system size has not been set

Handle divide by zero in fieldplot

Substituting state variables, e.g. U=N-A-B, does not work for van Kampen expansion because original state variable is needed there

however, substituting not by an expression but by another symbol, for example U = X would work

Replot without re-computing all data

When only visualisation options are changed (e.g. "show communication links" in multiagent sim.), MuMoT should replot without re-computing all data

Bifurcation analysis Pais model not working as expected

The PyDStool-based bifurcation function is not analysing the Pais model as expected. To test:

• run notebook MuMoT_PyDStest.ipynb
• in widgets set Delta = 0, mu = +ve
• expected pitchfork bifurcation not detected

Possibility to specify axes length in _fig_formatting_2D

Otherwise, the axes are adapted on data

Bifurcation view does not accept LaTeX arguments

For bifurcation parameter at least - unable to check LaTeX state variables due to issue #36

Seperate views from models

Currently views on models (bifurcation plots are the only current view) are integrated with models; these will be separated out so multiple independent views on the same model are possible

Limit plotting to interior of simplex in field-based plots

2d and 3d field-based plots (stream and vector plots) should not display / compute areas outside the simplex

Add possibility to set all parameters value through command line (without changing widgets)

Add smart parsing of input string.
Add generation of input string from simulation output (to be reused with copy/paste for next command)

Hash LaTeX variables to pure alphabetic variable names in bifurcation

bifurcation view will not work with variable names having underscores, due to _ and {} characters breaking internal PyDS variable naming rules

Suggest a simple function to hash all variable names coming from models to pure alphabetic strings, for passing to PyDS

Enable plotting of time-dependent solution of ODE system

Add bookmark functionality for making standalone plots

Similar to Mathematica Manipulate, print out a string describing the parameterisation of the model, suitable for cut and paste to create a standalone view

Implement proper parser for models

In particular, whitespace should not be required for a valid model specification

Vector length does not change in 3d vector view

Under some Python / Jupyter installations, vector length in 3d vector views appears fixed and uniform.