ecell4_base

• Update hdf5 version for Windows
• Adding pickle support for ODENetworkModel #128
• Adding longer serial support for Species in HDF5 #146

• Adding the datasource module to
• Adding Python3 64bit support for Windows
• Adding ensemble_simulations to run_simulation
• Fix CellList index
• Fix Integer3 operators
• Improvement in CMake build script

Changes

• We started to upload the E-Cell wheel files to PyPI. Now you can install E-Cell4 with pip install ecell !
• #132

Bug fix

• #127
• #130

Enhancement

• Progressbar on Jupyter Notebook #105
• Better styles for visualization especially for matplotlib #79
• A member function to distinguish Species for molecules and structures #102
• Enable user-defined macros for Python decorators #59
• Enable to save a movie as mp4 #85
• Enable to set tolerances for ODE through a Factory class #97
• 2D visualization of 3D world for animation #95
• getVelocity for ODE simulation #96
• Implicit dissolution of bindings in the rule-based modeling #113
• Higher resolution for plot_movie #110
• Enable to save time course data of NumberObservers #109
• FixedIntervalTrajectoryObserver should have its small interval to check the periodic boundary effect separately from logging interval #93
• Convenient functions for declaring fundamental objects #90
• Enable to set ranges to show trajectories on viz.plot_trajectory #82

Bug fix

• Fixed kernel death that would occur when there is no species in the viz.plot_movie_with_matplotlib(..., species_list) #104
• Implement egfrd::World::list_species() #118
• Spatiocyte doesn't accept the second-order reaction with translocation #124
• Wrong absorption rate for mesoscopic simulations #103

Features added

• Spatial Gillespie simulator
• Spatiocyte simulator
• eGFRD simulator
• Python-valid rule-based modeling
• Jupyter Notebook inline visualization

HDF5 is optional in beta2.
(Attached binaries do NOT require HDF5 lib.)

• Add simulators for the enhanced Green's Function Reaction Dynamics and spatial Gillespie methods.
• new build system (moved from waf to CMake and Python wheel).
• new tutorial IPython notebooks.
• inline javascript particle visualizer in IPython notebook.
• Support a network-frees simulation using C++ rulebased modeling engine.