Kazunari Kaizu

```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...

Rate law dependent synthesis

2

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...

Version identification

7

Determine the style of version naming. The following documents gives the style for Python packages though it seems too complicated. https://www.python.org/dev/peps/pep-0440/ The version style affects the following part: https://github.com/ecell/ecell4-base/blob/master/ecell4/core/extras.hpp#L90-L101 https://github.com/ecell/ecell4-base/blob/master/ecell4/core/extras.cpp#L103-L168

new_particle has variety

1

`SpatioctyeWorld::new_particle` returns `boost::optional` and other worlds does `std::pair`.

Simulators should support infinite reaction rates.

1

```python import numpy with reaction_rules(): A + B > C | 0.01 C > D | numpy.inf ``` The second reaction must occur immediately after the first reaction.

Anaconda is popular on the Windows platform, isn't it?

Copy constructor of Species is too slow

1

This would be due to attributes. https://github.com/ecell/ecell4/blob/master/ecell4/core/Species.hpp#L52-L61 Species should be lightweight and handy.

In gillespie, each ReactionRuleEvent caches the number of molecules specified with Species rules (e.g. the following link). This should be done rather in Space. https://github.com/ecell/ecell4/blob/master/ecell4/gillespie/GillespieSimulator.hpp#L226-L306