Team:USP-Brazil/OnlineLectures

Online Courses in Synthetic Biology

In addition to the course in mathematical modelling, our team also prepared an online course on mathematical modelling in synthetic biology, as well as an online course on molecular biology. The courses are in portuguese, with their english translation in preparation. The videos are being hosted at our team's youtube channel.

Mathematical Modeling in Synthetic Biology

This course aims at those with basic undergraduate molecular biology knowledge, i.e., knowing roughly what do enzymes, promoters and DNA do, and with high school level mathematics—essentially knowing what are functions, and some elementary examples, namely power functions, trigonometric functions and logarithms. The goal of part A is to teach the basics of differential and integral calculus, focusing on explaining differential equations. Part B turns to Mathematical Modeling, explaining how to use differential equations to model the behavior of a biological system—focusing then on the most common examples in synthetic biology. Part C is made of special extra topics, for those who are familiar with parts A and B and want to deal with more complicated problems.

Part A - Mathematical Concepts

• Lesson 1 - Derivatives, rules of derivation
• Lesson 2 - Integrals
• Lesson 3 - Applications of calculus
• Lesson 4 - Differential equations
• Lesson 5 - Numerical solution of differential equations: Euler method, implemented in python

Parte B - Modeling

• Lesson 1 - What is modeling
• Lesson 2 - Mathematical modeling of a population. Exponential and Logistic growth
• Lesson 3 - Interacting species: Lotka-Volterra and Law of Massa Action - examples: promoters, activation, inhibition
• Lesson 4 - Common models in Synbio: Michaelis Menten Enzime Kinetics, Hill coefficient
• Lesson 5 - Complete example: Detecthol

Part C - Extra Topics

• Lesson 1 - Linear stability analysis
• Lesson 2 - Phase plane analysis
• Lesson 3 - Spatial dynamics: diffusion, advection, saturation
• Lesson 4 - Stochastic simulations: Gillespie algorithm
• Lesson 5 - Difference equations and logistic maps

Molecular Biology

This course is turned to those with little or no undergraduate molecular biology knowledge - essentially, knowing what is DNA. The goal of part A is to teach the mechanisms behind what happens to DNA, RNA and proteins in replication, transcription and translation, while part B focuses on some basic lab techniques used during the iGEM competition.

Part A - Basic Concepts

• Lesson 1 - Central dogma of molecular biology
• Lesson 2 - DNA Replication
• Lesson 3 - Transcription
• Lesson 4 - Translation

Part B - Laboratory Techniques:

• Lesson 1 - PCR
• Lesson 2 - Gel
• Lesson 3 - Bacterial transformation
• Lesson 4 - BLAST

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