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View Code? Open in Web Editor NEWThe Sphinx source for https://ecell4.e-cell.org/
Home Page: https://ecell4.e-cell.org/
License: GNU General Public License v2.0
The Sphinx source for https://ecell4.e-cell.org/
Home Page: https://ecell4.e-cell.org/
License: GNU General Public License v2.0
This combination is useful not only for metabolic profile but also for expression profile.
The pathway networks to combine the profiles are
https://github.com/opencobra/COBRA.papers/blob/master/2019_efmviz/efmviz_rcy3_ecoli.Rmd
could be used for this purpose.
Create a Binder link for Zenodo DOI following this link
https://blog.jupyter.org/binder-with-zenodo-af68ed6648a6
For example
Q&A forum (self-hosted, on Stack Exchange etc.)
Add some examples explaining how to use ecell4.extra.ensemble
.
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.
Modify tutorial3.ipynb.
https://github.com/ecell/ecell4-notebooks/blob/4-1-stable/tutorial3.ipynb
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