Projects

bayesian-inference

This package is a collection of useful classes for basic Bayesian inference. Currently, its main goal is to be a tool for learning and exploration of Bayesian probabilistic calculations. Currently it also includes subpackages for stochastic simulation tools which are not strictly related to ... [More] Bayesian inference, but are currently being developed within BIP. One such package is the BIP.SDE which contains a parallelized solver for stochastic differential equations, an implementation of the Gillespie direct algorithm. The Subpackage Bayes also offers a tool for parameter estimation of Deterministic and Stochastic Dynamical Models. This tool will be fully described briefly in a scientific paper currently submitted for publication. I hope that in time it will mature into an useful tool for general use. [Less]

dsmts

NEWS26/3/09: SBML L2v4 version of the DSMTS is released MotivationStochastic simulation is a very important tool for Systems Biology modelling. However, it is difficult to check the correctness of a stochastic simulator, since any two realizations from a single model will typically be different. ... [More] AboutThis is a test suite of stochastic models encoded in the Systems Biology Markup Language (SBML) that have been solved either analytically or using numerical methods. This allows the accuracy of stochastic simulators to be tested against known results. The test suite is already being used by a number of stochastic simulator developers. [Less]

pysbml

This project describes some python tools for that are (hopefully) useful in systems biology. pysbmlUnfortunately due time constraints, I could no long maintain this package. So I've I separated out some the components as stand alone libraries (see below). VisualiseSBMLVisualiseSBML is a ... [More] python script for visualising SBML using the graphviz library. Moment ClosureThe Momentclosure package applies the moment closure approximation to mass-action kinetic models. See MomentClosure for more information. In the near future, this package will be merged into pysbml. [Less]

python-ising

Paquete pyhon para crear simulaciones de la dinámica de Glauber y de Kawasaki para el modelo de Ising en 2D. En el segundo caso, se enfatiza la observación de la emergencia de la gota de Wulff para un rango adecuado de parámetros del sistema.

pmarkets

Piggy Market Squeak is a stocks and shares financial quote trend alert Trading System and technical analysis software. Piggy Market Squeak is an Open Source software edited under GNU General Public License. Piggy Market Squeak provides advice to buy or sell stocks and shares using financial quote ... [More] technical analysis. The tool is quite versatile, and made to programmaticaly integrate any Trading Indicator as long as it is based on open, closed, high, low prices, as well as trade volumes. [Less]

optimalpython

Methods for specifying and solving stochastic dynamic optimization problems in Python using methods such as dynamic programming (DP) and reinforcement learning (RL).

kiefer

Simulates a functional of a Kiefer random field

pyeoq

This project aims to provide a set of Python modules for solving problems in inventory theory.

pythonpso

The developer was very bored in his high school Java class, so he started playing around with particle swarm optimization. The name similarity to pypso is accidental, and in fact pypso was the first choice name for this. Currently has big problems with local optima. Will be adding some features ... [More] such as neighborhood swarms, perhaps a grim reaper / regenerator, and maybe throw some PID or similar controls into the mix. This is just fun and games for me, but if someone else finds it interesting, I am more than happy to give and receive help on the project. [Less]

quadrinomialtree

This project builds a quadrinomial tree that incorporate stochastic rates.