pensimpy 1.2.5

The Python implementation of IndPenSim

Development Status: As of 08/2020 PenSimPy is under active maintenance (expect bug fixes and updates). Please follow, star, and fork to get the latest functions.

PenSimPy

PenSimPy is a Python version of IndPenSim, which simulates the industrial-scale Penicillium chrysogenum fermentation. This simulator is based on c++ solving the ODE functions so as to achieve a faster performance than the MATLAB version.

PenSimPy aims for recording those key features such as pH, temperature, vessel volume, vessel weight, penicillin concentration, dissolved oxygen concentration, sugar feed rate, soil bean feed rate, aeration rate, back pressure, water, acid, phenylacetic acid flow-rate, Oxygen in percent in off-gas, and the Raman spectroscopy data throughout the whole process. A conventionally used Sequential Batch Control strategy with PID control is presented with example codes and all the recipe's feed can be manually updated.

Furthermore, we incorporate Reinforcement Learning to improve the penicillin gain and present them as example codes. A web application based on PenSimPy can be found here.

Installation

PenSimPy relies on fastodeint, a python bindings for an ODE solver implemented in C++. Unfortunely, it's not available as a PyPI package at this point, so you need to follow the installation instruction here to build it yourself. Once fastodeint is installed, you can install PenSimPy by the following command

pip install pensimpy

Examples

See the examples directory

• see examples/batch_generation.py to generate batch and Raman data with self-designed recipes
• see examples/reinforcement_learning_boilerplate.py to simulate penicillin yield process with reinforcement learning