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Dynamical Simulation Collaboration

Building open-source tools for modeling, simulation, and analysis across mathematics, physics, chemistry, and biology.

  • Example 
    import numpy as np
from poincare import *

class BiasedDouble(System):
    x: Variable = initial(default=-2)
    v: Derivative = x.derive(initial=0)
    c: Parameter = assign(default=1)

    eq = v.derive() << -v - x**3 + 2 * x + c

sim_2 = Simulator(BiasedDouble)
steady = SteadyState(t_end=1000)
uad = steady.sweep_up_and_down(sim_2, variable=BiasedDouble.c, 
                               values=np.linspace(-3, 3, 30))

uad.sel(direction="up")["x"].plot(label = "Up")
uad.sel(direction="down")["x"].plot(label - "Down")
Bistability plot for the biased double well implemented in Poincare.

Libraries

  • Poincare

    General dynamical system simulation in python. Learn more.

  • SimBio

    Simulation of chemical reaction networks in python. Learn more.

  • Jablonski

    Simulation of photochemical systems in python. Learn more.

About

Dyscolab is an organization dedicated to the creation of open source tools for modeling, simulation, and analysis of dynamical systems. It maintains 3 main python libraries, as well as a number of other utilities:

  • Poincare: general dynamical systems simulation. It's the basis on which the others are built.
  • SimBio: chemical reaction networks simulation. Built on Poincare, it adds a number of bindings specific to chemical reactions, such as Species, MassAction or Synthesis.
  • Jablonski: photochemical systems simulation. Similarly to SimBio, it builds on Poincare by adding specific bindings such as SingletState, Absortion or Fluoresence. It is still in development.
  • Other libraries: Dyscolab also maintains other libraries which are auxiliary or related to the main user facing ones.

Contact

The dyscolab discussion forums on github are the main form of communication for dyscolab related topics.

Dyscolab projects are maintained by:

  • Tomás Di Napoli: tomas.dina98@gmail.com.
  • Hernán E. Grecco: hgrecco@df.uba.ar.
  • Mauro Silberberg: maurosilber@gmail.com.
  • Oliverio Starosta: oliveriostarosta@gmail.com.