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Add explanations and references for each algorithm #23

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kaizu opened this issue Apr 29, 2020 · 0 comments

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kaizu commented Apr 29, 2020

ode

Ordinary Differential Equations. "Explicit Euler", "Cash-Karp", or "Controlled Rosenbrock 4". See Boost.Numeric.Odeint
https://www.boost.org/doc/libs/release/libs/numeric/odeint/

gillespie

The Gillespie algorithm. The direct method.
https://doi.org/10.1021/j100540a008

meso

The spatial Gillespie algorithm. The mesoscopic cubic-lattice-based algorithm. The next subvolume method.

bd

The Reaction Brownian Dynamics (RBD) method.

spatiocyte

The microscopic HCP-lattice-based algorithm. The Spatiocyte algorithm.

egfrd, sgfrd

The enhanced Green's Function Reaction Dynamics (eGFRD) method.

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kaizu mentioned this issue

Add references for algorithms in docstring ecell/ecell4_base#330

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kaizu changed the title ~~Add references for algorithms in docstring~~ Add explanations and references for each algorithm

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