News
Added
- support for using the DuneCopasi simulator with 3d models #937
- 3d volume rendering for voxel visualization #926
- visualization of 3d model geometry meshes #882
- import of geometry image files by drag and drop onto the GUI #933
Added
- initial support for 3d spatial models #850
- support for anisotropic voxels #879
Changed
- disable OK button while selecting geometry image colours #878
- image arrays in sme (Python interface) now include a z dimension #850
Fixed
- lack of geometry image could cause a crash in some cases #872
Added
- support for importing RGBA TIFF image files #862
Fixed
- incorrect function evaluations in some cases #855, #856, #857
Fixed
- incorrect initial concentrations with DUNE simulator for some models #852
Changed
- export format of Image Sampled Field from colors to indices #710 and #830.
Added
- support for importing Combine archives #828
Changed
- offer to use alternative simulator if simulation setup fails #814
Fixed
- crash caused by analytic initial species concentrations involving dividing by zero #805
- disappearing simulation progress bar dialog #752
Added
Changed
- GUI no longer writes logging output to console #771
Fixed
- analytic initial species concentrations were not updated when a parameter value was modified #776
Added
- support for reading compressed sampledFields #709
Changed
- TBB is now used everywhere for multithreading (previously linux Python wheels used OpenMP) #732
Fixed
- improved multi-threading performance #742
- spurious simulation times are no longer appended upon simulation #751
Added
- topology-preserving line simplification option #328
- python interface:
ctrl+c now cancels a currently running simulation #665
Changed
- model reactions with invalid locations can now be seen and removed or relocated #615
Fixed
- functions with zero arguments are now fully supported #674
- python interface: setting
n_threads=1 for simulate takes precedence over n_threads value in model #672 - bug where membrane reactions could disappear when geometry was changed #679
- bug where removing a compartment could result in an invalid model or a crash #685
- SBML export includes any ModifierSpecies in reactions #133
Removed
- incomplete Parametric geometry sbml export support #599
Added
- non-spatial model guided import with automatic reaction rate rescaling #607
- python interface: optional multithreading (via OpenMP) for Pixel simulations on linux #662
Fixed
- bug where loading a model with simulation data and changing model units could cause a crash #666
- show warning message before dune simulation of model with non-spatial species #664
- minimum supported version of MacOS is now 10.14 instead of 10.15 #669
Added
- python interface: access to all built-in example models #637
- python interface: view and edit uniform/analytic/image species initial concentrations #644
Changed
- compartment colour assignments are now preserved when the geometry image is resized #587
Fixed
- python interface: bug where compartment geometry mask was not updated after geometry image changed #630
- slow loading of models with large geometry images #632
- avoid constructing mesh twice on model load #597
- crash when importing geometry image after importing non-spatial model #651
Added
- python interface:
Model.simulation_results() provides access to existing model simulation data #622
Changed
Fixed
- bug where opening a corrupted sme file caused a crash #618
Added
- python interface: add option to simulate without returning the results to reduce RAM usage #610
- more detailed error message when a model cannot be loaded #449
Fixed
- bug where invalid reaction rate expression caused simulation to crash #609
Added
- autocomplete when editing maths #559
- support for all L3 sbml math in reaction rates (with Pixel simulator) #569
- option to invert y-axis of images #568
- option to set size of geometry image in third dimension #582
umol unit of amount added to built-in units #600
Changed
- simulation length/intervals only loaded from model on 'reset' click or new model load #565
- models exported as 3d SBML models (to be consistent with our 3d units for species concentrations and volumes) #588
Fixed
- bug when clicking on simulation results plot selected wrong timepoint #570
- reaction rates involving species from unrelated compartments now displays an error, instead of only giving an error on simulation #552
- simulation crash when species is changed to constant & simulation data are re-loaded #561
- inaccuracy when re-starting a simulation that was stopped early #388
- bug where compartment sizes were not updated when compartment image resolution was altered #583
- bug where invalid mesh could cause a crash #585
- bug where simulating after changing geometry image size could cause a crash #591
- incorrect units used for compartment volumes when referenced in reaction rates #584
- bug where membrane area could be incorrect on model load #595
Added
- COPASI cps file import support (if COPASI is installed and on path) #492
- shift + mouse scroll to zoom in and out of images #532
- support for spatial models with reactions whose compartment is not specified #481
Changed
- mouse scroll no longer changes species stoichiometry in reactions #549
- membrane reaction rates automatically rescaled by membrane area on non-spatial model import #557
- reactions moved between compartments and membranes rescaled by ratio of area to volume #558
Fixed
- bug loading simulation settings depending on system locale setting #535
- slow loading of simulation data #504
- bug where simulation doesn't run again after being stopped #545
- bug where selected reaction sometimes changes when reaction location is changed #548
- ensure species involved in a reaction are valid when reaction location is changed #551
- bug where loading existing simulation uses initial concentrations instead of latest simulation concentrations #541
Added
- sme file format, contains model, simulation settings and simulation results #482
- support multiple simulation lengths as comma delimited lists #464
- support for simulating models with empty compartments with the Dune-Copasi simulator #435
- option to resize the number of pixels in the geometry image #462
- option to reduce the number of colours in the geometry image #280
- support for non-integer stoichiometries in reactions #495
- optional grid and scale to geometry image #497
- python interface: DUNE simulator can now be used #276
- python interface: existing simulations can be continued #514
- zoom option to geometry image #516
Changed
- use v1.1.0 of Dune-Copasi simulator
Fixed
- python interface: revert change in default simulate() behaviour when doing a second simulation of a model #475
- multiple event related simulation bugs #484, #485, #486
- incorrect compartment name displayed in simulate display options #487
- simulation image intervals changing length of simulation #492
- bug where removing compartment could cause a crash #506
- artefacts in import of species concentrations into simulation #508
- DUNE maximum iteraction count simulation error #490
Added
- open/save as
.sme filetype: contains both the model and the simulation results #461 - support for time-based events: parameters and species concentrations can be set at specified times in the simulation
- diagnostic info & image when a simulation fails #432
- zoom option for Boundary and Mesh images in the Geometry Tab
- new option in Simulation Tab to export concentrations to model as initial concentrations
Changed
- simulation is no longer reset when the Simulate tab is left in the GUI
- simulations can be continued using a different simulator
- use v1.0.0 of Dune-Copasi simulator
- GUI warns before closing a model with unsaved changes #346
- Membrane names can now be edited in the GUI and in the python interface
Fixed
- diffusion constant bug in the Pixel simulator #468
- bug in dune-copasi mesh generation that could cause a crash #434
- bug where unused diffusion constant parameter was sometimes not removed from sbml document
- data race in generating simulation concentration images #434
Removed
- incomplete Parametric geometry sbml import support #452
Added
- python library can now import a new geometry image using
sme.Model.import_geometry_from_image()
Changed
- mesh generation is now done using the CGAL library
Removed
- dependence on Triangle mesh library removed due to its non-free license
Fixed
- illegal instruction crash on old CPUs #422
Added
- python library
sme.Model.simulate: - simulation results now also contain rate of change of concentrations
- option to return partial results instead of throwing on simulation timeout
Changed
- more accurate initial concentration interpolation for dune-copasi simulations
- applies to both GUI simulations and exported TIFF files for stand-alone dune-copasi simulation
- improved performance of interior point determination in mesh construction
Fixed
- meshing bug where invalid 2-point boundary line could cause crash
Added
- user can edit dune-copasi Newton solver parameters
- Pixel simulator supports reactions that explicitly depend on t, x, y
Changed
- dune-copasi simulations now support membrane flux terms
- rectangular membrane compartments no longer required
- simpler mesh generation
- faster and more accurate simulations
- improved boundary construction
- use pixel edges as boundary edges instead of pixels
- shared boundaries and their end points now unambiguously determined
- improved line simplification
Fixed
- bug in scaling of membrane reactions in Pixel simulations
- added missing
1/a factor, where a is the width of a pixel in model units
Removed
- inconsistent
RateRule support in SBML import
Added
- simulation display options are now saved
Changed
- python library API
- lists now have name-based look-up, old name-based look-up functions removed
- examples of old -> new change required in user code:
model.compartment("name") -> model.compartments["name"]model.specie("name") -> model.species["name"]
Fixed
Added
- python library example notebooks
Changed
- python library performance improvements
Fixed
- python library segfault / missing data issue on some linux platforms
Added
- python library documentation and example notebooks
- support for import of geometry image with alpha channel / transparency
- display compartment size and membrane length
Changed
- python library performance improvements
Fixed
- normalisation of simulation concentration images
- geometry imported from another model not saved bug
- python library segfault / missing data issue on linux
- reaction removal bug
Added
- membranes to python library
- compartment pixel mask to python library
- timeout parameter to simulate function in python library