Computational and mathematical modules for incoming students in the Mathematical, Computational and Systems Biology graduate program.
- Module 1: Coding practices, git, version control, collaboration, Continuous Integration/Continuous Deployment
- Module 2: Dynamical models, parameters, simulation, prediction
- Module 3: High-level programming languages (Matlab, Python, Julia, R), numerical calculus, differential equations
- Module 4: Classical mathematical biology models, emergent phenomena, excitability, bifurcations, ultrasensitivity, spatially-distributed systems.
- Module 5: Data and parameter learning from real data, bacterial growth rates
- Module 6: Gene regulatory networks, feedback, adaptation, bistability
- Module 7: Language zoo, low-level languages, C++
- Module 8: Scientific visualization, 3D modeling with blender
- Make a GitHub account if you don't already have one
- Install git:
- macOS
- Install GitHub Desktop (easier) or
- install git (if you install GitHub Desktop, git will automatically be installed)
- You can also use git from the terminal but you might run into password authentication issues.
- Installing command line tools in MacOS says it will take 5 hours but is actualy much faster.
- Windows
- Install GitHub Desktop (easier but less full-featured) and/or
- Install Windows Linux Subsystem, and then install git in the WLS (note unlike macOS, installing git in Windows is not the same as installing git inside the WLS.)
- Note if you have another git client, besides GitHub Desktop, you are free to use that instead!
- macOS
- Install Matlab
- Recommended but not required:
- Install Blender
- Bring an external mouse (we have extras if you need one)
- Install Mathematica
- Intro to git from Software carpentry
- Matlab basics
- ODE/dynamical systems:
- Steven Strogatz "Nonlinear Dynamics and Chaos"
- Leah Edelstein-Keshet "Mathematical Modeling in Biology"
- Assorted skills including command line basics from BU bioinformatics