ecell4_base
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ecell
An integrated software environment for multi-algorithm, multi-timescale, multi-spatial-representation simulation of various cellular phenomena
Hi, @kaizu , @ToruNiina , I'd like to report a vulnerability issue in **ecell4-base_2.1.0**. ### Dependency Graph between Python and Shared Libraries  ### Issue Description As shown in the...
```python from ecell4.prelude import * with reaction_rules(): A > B | 0.0 | {"name": "rr1"} m = get_model(is_netfree=True) for rr in m.reaction_rules(): print(rr.as_string(), rr.list_attributes()) # A>B|0 [('name', 'rr1')] for rr...
- [x] Introduce Pyhton APIs (#431) - [x] Remove ParticleVoxel (#435) - [x] Debug Interface voxels and Reactions (#445) - [x] Add tests for OffLattice related to #133
The name `Structure` is confusing because its implementation differs from its name. The major difference between `MoleculePool` and `StructureType` is whether to store coordinates or not. In addition to this,...
The following information may be required when we apply for sponsoring or grant. - Scholarly paper(s) (including preprints) citing or mentioning the software project - Monthly downloads from websites, monthly...
Display the following information after "pip install ecell" - The license document installation PATH of the E-Cell and the bundled binary libs (HDF5 and gsl)
`ecell4-base` has the exceptions which inherit `ecell4::Exception`, and it inherits `std::exception`. However, they have a string member as `std::runtime_error` do. So, we should reconsider the implementation of them and wrap...
Enable the following model: ```python with reaction_rules(): ~X > X | (k * X / (K + X)) run_simulation(t, solver='gillespie') ``` Except for `ode`, no solver supports rate law dependent...