{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Biochemical Engineering (CBI 310)\n", "\n", "### 1. Introduction and bio basics\n", "\n", "* [Introduction and bio basics](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/Introduction%20and%20bio%20background/Intro%20and%20bio%20background.ipynb)\n", "\n", "### 2. Basic biochemistry and python\n", "\n", "* [2.1 Basic biochemistry](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/2%20Basic%20biochemistry/Basic%20Biochemistry.ipynb) \n", "\n", "* [2.2 Basic python](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/2%20Basic%20biochemistry/Chapter%202.2.ipynb)\n", "\n", "### 3. Stoichiometry without internal reactions\n", "\n", "* [3.1 Defining rates and yields and balancing equations](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/3%20Stoichiometry%20without%20internal%20reactions/Defining%20rates%20and%20yields%20and%20balancing%20equations.ipynb)\n", "\n", "* [3.2 The cmol balance and biomass as molecule](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/3%20Stoichiometry%20without%20internal%20reactions/The%20cmol%20balance%20and%20biomass%20as%20molecule%20.ipynb)\n", "\n", "* [3.3 Degree of reduction balances](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/3%20Stoichiometry%20without%20internal%20reactions/Degree%20of%20reduction%20balances.ipynb)\n", "\n", "\n", "### 4. Stoichiometry that includes internal reactions \n", "\n", "* [4.1 Modelling the anabolism](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/4%20Stoichiometry%20that%20includes%20internal%20reactions/Modelling%20the%20anabolism.ipynb)\n", "\n", "* [4.2 Main fermentative pathways](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/4%20Stoichiometry%20that%20includes%20internal%20reactions/Main%20fermentative%20pathways.ipynb)\n", "\n", "* [4.3 TCA cycle and oxidative phosphorylation](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/4%20Stoichiometry%20that%20includes%20internal%20reactions/TCA%20cycle%20and%20oxidative%20phosphorylation.ipynb)\n", "\n", "### 5. Basic fermenter modeling\n", "\n", "* [5.1 Real life fermenters](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/5%20Basic%20bioreactor%20modeling/Real%20life%20fermenters.ipynb)\n", "\n", "* [5.2 Solving differential equations](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/5%20Basic%20bioreactor%20modeling/Solving%20differential%20equations.ipynb)\n", "\n", "* [5.3 The fermenter equation](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/5%20Basic%20bioreactor%20modeling/The%20fermenter%20equation.ipynb)\n", "\n", "* [5.4 Understanding growth](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/5%20Basic%20bioreactor%20modeling/Understanding%20growth.ipynb)\n", "\n", "### 6. Modeling stoichiometry variations\n", "\n", "* [6.1 Altering rates](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/6%20Modeling%20stoichiometry%20variations/Altering%20rates.ipynb)\n", "\n", "* [6.2 Example on growth and maintenance variation](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/6%20Modeling%20stoichiometry%20variations/Example%20on%20growth%20and%20maintenance%20variation.ipynb)\n", "\n", "* [6.3 Oxygen starvation in batch fermenters](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/6%20Modeling%20stoichiometry%20variations/Oxygen%20starvation%20in%20batch%20fermenters.ipynb)\n", "\n", "* [6.4 Facultative anaerobes](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/Tutorials/Tut%206.3.ipynb)\n", "\n", "### 7. Fed-batch fermentation and more\n", "\n", "* [7.1 Fed-batch fermentation](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/7%20Fed-batch%20and%20continuous%20fermenters/Fed-batch%20fermenters.ipynb)\n", "\n", "\n", "\n", "\n", "\n", "\n", "\n", "### [Tutorials](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/Tutorials/All%20tutorials.ipynb)\n", "\n", "### [Practical (CLB321)](https://nbviewer.jupyter.org/github/willienicol/Biochemical-engineering-notes/blob/master/CBI310%20practical/CLB321%20Biokinetics%20manual.ipynb)\n", "\n", "\n" ] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.13" } }, "nbformat": 4, "nbformat_minor": 4 }