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Commit a3f3ae62 authored by Dhruva Gowda Storz's avatar Dhruva Gowda Storz
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Improved Bistables and Oscillators section on solvers using harshas write up in cookbook

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......@@ -21,9 +21,18 @@ In chemical bistable models that use solvers, there are optional arguments that
python filename.py [gsl | gssa | ee]
Where ``gsl`` is Gnu Scientific Library's deterministic solver, ``gssa`` stands for Gillespie stochastic simulation algorithm, and ``ee`` is the exponential euler algorithm.
Where:
All the following examples can be run with either of the three solvers, which in some cases produces a different outcome. However, simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
- gsl: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.
- gssl: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.
- Exponential Euler:This methods computes the solution of partial and ordinary differential equations.
All the following examples can be run with either of the three solvers, each of which has different advantages and disadvantages and each of which might produce a slightly different outcome.
Simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
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Simple Bistables
================
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......@@ -23,9 +23,15 @@ In chemical models that use solvers, there are optional arguments that allow you
python filename.py [gsl | gssa | ee]
Where ``gsl`` is Gnu Scientific Library's deterministic solver, ``gssa`` stands for Gillespie stochastic simulation algorithm, and ``ee`` is the exponential euler algorithm.
Where:
All the following examples can be run with either of the three solvers, which in some cases produces a different outcome. However, simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
- gsl: This is the Runge-Kutta-Fehlberg implementation from the GNU Scientific Library (GSL). It is a fifth order variable timestep explicit method. Works well for most reaction systems except if they have very stiff reactions.
- gssl: Optimized Gillespie stochastic systems algorithm, custom implementation. This uses variable timesteps internally. Note that it slows down with increasing numbers of molecules in each pool. It also slows down, but not so badly, if the number of reactions goes up.
- Exponential Euler:This methods computes the solution of partial and ordinary differential equations.
All the following examples can be run with either of the three solvers, each of which has different advantages and disadvantages and each of which might produce a slightly different outcome.
Simply running the file without the optional argument will by default use the ``gsl`` solver. These ``gsl`` outputs are the ones shown below.
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