We really liked Yael Lebel and @UriAlonWeizmann's paper on excitability in the immune system, so we reipmlemented it in Poincare, our dynamical systems simulation package. See for yourself how we apply the power of Poincare to cell-cell interction models:
github.com/orgs/dyscolab/dis…
Last week we gave a tutorial at the COMBINE conference about SimBio, our chemichal reactions simulation library. Thanks to the organizers @GokselMisirli, @roberto_galizi and Metehan Unal and to @KeeleLifeSci for hosting! You can check out the material at github.com/dyscolab/simbio-t…
Gambling is everywhere now, so we added it to Jablonski. We just released version 0.3 of the python photochemical systems simulation library with support for stochastic simulations, a revamped excitations api, proper units support in simulation times and more.
For more information see the full announcement on github:
github.com/orgs/dyscolab/dis…
Or go to Jablonski's homepage:
dyscolab.github.io/jablonski…
With @GreccoHernan and @DiNapoli_Tomas we've been working on a python library for photochemical systems simulations which finally released! Jablonski exends poincare with easy binidings for defining energy levels and transitions, and has a suite of analysis tools on top.
It combines poincare's composable models and backend support with tools like simulation of time resolved emission and sweeps for spectra on different excitiation intensities and wavlenghts.
See the full announcemnt on github for more information:
github.com/orgs/dyscolab/dis…
A month ago we released version 1.0 of Poincare and SimBio, python libraries for simulating dynamical systems and chemical reactions. We now released version 1.1 with:
- Reports with a system's equations and variables in Latex.
- Stochastic simulation with Gillespie's algorithm.
The next thing we're working on is Jablonski, a new library for simulationg photochemical systems.
For more information see the full announcemnt on github:
github.com/orgs/dyscolab/dis…
or go directly to the dyscolab page:
dyscolab.github.io/
Poincare and simbio 1.0.0 have released! We've been working with @GreccoHernan, @maurosilber and @DiNapoli_Tomas
to create poincare, a python library for dynamical systems simualtion, and simbio, which adds bindings for chemical reactions.
They provide a layer to separate model declaration and simulation, making model construction easier and allowing different simulation backends, and provide analysis tools for tasks such as parameter sweeps.
To learn more read the announcement on github:
github.com/orgs/dyscolab/dis…
