DiODeProject/MuMoT

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Multiscale Modelling Tool - mathematical modelling without the maths

Stars: 24
Forks: 5
Open beginner issues: 0
Indexed issues: 59

Dominant language: Python
License: GPL-3.0
Last GitHub push: Mar 18, 2022
Latest indexed: Sep 15, 2026
Contributing guide: No contributing guide
Code of conduct: No code of conduct
Beginner labels: help wanted good first issue
PR merge metrics: No merged PRs in 30d

Open All

59 issues indexed so far

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

enhancement

DiODeProject/MuMoT#7 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add color selection by user for state Open

enhancement

DiODeProject/MuMoT#11 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add bounded arena Open

enhancement

DiODeProject/MuMoT#15 · 3 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Figure download is not working on Chrome Open

wontfix

DiODeProject/MuMoT#21 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
View logs lag plots in interactive mode Open

bug

DiODeProject/MuMoT#26 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
An error in Jupyter cell stops the plotting of previous figures Open

wontfix

DiODeProject/MuMoT#55 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Vector and stream could have first parameters as optional (and set through widgets) Open

enhancement

DiODeProject/MuMoT#95 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Improve quality of visualise images and LaTeX rendering Open

DiODeProject/MuMoT#130 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Refactor code moving members into base classes where possible Open

DiODeProject/MuMoT#132 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
The dropdown widget of MuMoTstochasticSimulationController for the Final distribution visualisation does not render latex correctly Open

wontfix

DiODeProject/MuMoT#136 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Allow multicontrollers to encapsulate multiple models Open

enhancement

DiODeProject/MuMoT#141 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Allow for creating models from Python strings Open

enhancement good first issue

DiODeProject/MuMoT#156 · 6 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
LaTeX in output cells slow to render Open

bug

DiODeProject/MuMoT#162 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add plot of noise spectrum from noise solutions Open

enhancement

DiODeProject/MuMoT#165 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Use nbval to perform regression testing on MuMoTtest.ipynb Open

enhancement testing

DiODeProject/MuMoT#187 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Readthedocs should open external sites in new browser windows Open

documentation enhancement

DiODeProject/MuMoT#198 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use parser library in parseModel Open

enhancement

DiODeProject/MuMoT#199 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add figures based on parameter sweeps of numerical simulations Open

enhancement

DiODeProject/MuMoT#212 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Stream lines shading should be scaled to avoid barely visible stream lines Open

enhancement

DiODeProject/MuMoT#218 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Allow substitute() to perform simple reactants scaling and time scaling Open

enhancement

DiODeProject/MuMoT#222 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Feature request: create and save animated gif of multiagent or SSA runtime plots Open

enhancement

DiODeProject/MuMoT#224 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Feature request: support for 2-simplex (ternary) plot Open

enhancement

DiODeProject/MuMoT#225 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Expand options for types of graphs in multiagent() network topology Open

enhancement

DiODeProject/MuMoT#226 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
SSA multiple runs plots: change box plots for shaded confidence intervals Open

enhancement

DiODeProject/MuMoT#227 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Bifurcation() fails to find all branches Open

help wanted question

DiODeProject/MuMoT#228 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Implement model cell bookmarking Open

enhancement

DiODeProject/MuMoT#244 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Implement more sophisticated analytic and numerical noise solutions / approximations Open

enhancement help wanted

DiODeProject/MuMoT#251 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
remove MuMoTcontroller._plotLimitsWidget and use the self._widgetsExtraParams['plotLimits'] Open

enhancement

DiODeProject/MuMoT#281 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
showNoise in MuMoTfieldControllers should be treated as all other parameters and a widget created accordingly Open

enhancement

DiODeProject/MuMoT#282 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
MuMoTfieldController should include the toggle 'plotProportions' as most other controllers do Open

enhancement

DiODeProject/MuMoT#283 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
aggregateResults toggle in MuMoTfieldController should only trigger replotting without re-computing all data Open

enhancement

DiODeProject/MuMoT#284 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Check advanced multicontroller bookmarks Open

bug

DiODeProject/MuMoT#292 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Enable result download for non-stochastic simulation views Open

enhancement

DiODeProject/MuMoT#305 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Implement custom download results widget Open

enhancement

DiODeProject/MuMoT#308 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Consider DOI release assignment strategy Open

documentation question

DiODeProject/MuMoT#319 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Consider pointing binder icon to latest release branch Open

documentation enhancement question

DiODeProject/MuMoT#320 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Greek letters should be used consistently in all functions Open

DiODeProject/MuMoT#324 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Test suite: run all notebooks in one or more dirs rather than explicitly named notebooks Open

enhancement testing

DiODeProject/MuMoT#325 · 9 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Enhance random walk computation Open

enhancement

DiODeProject/MuMoT#326 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Update contributors Open

documentation

DiODeProject/MuMoT#327 · 2 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Add type hints Open

enhancement

DiODeProject/MuMoT#328 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
1d stream plot does not appear in full after re-generation using sliders Open

bug help wanted

DiODeProject/MuMoT#329 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Replace global var figcounter with matplotlib.pyplot.get_fignums()? Open

DiODeProject/MuMoT#333 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Document 1d and 3d stream plots Open

documentation

DiODeProject/MuMoT#335 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Visualise noise in 3d stream plot Open

enhancement

DiODeProject/MuMoT#336 · 0 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
Add unit tests Open

testing

DiODeProject/MuMoT#339 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Clean exceptions Open

DiODeProject/MuMoT#352 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Multicontrollers missing some advanced options Open

bug

DiODeProject/MuMoT#353 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Muticontroller plot warning Open

warning

DiODeProject/MuMoT#355 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Reduce runtime of CI jobs? Open

enhancement question

DiODeProject/MuMoT#366 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

DiODeProject/MuMoT

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