Computational Biology Resources

Computational (Biology Education)

• High quality 3D animations of the molecular and cellular realm
  
  
  • BioVisions at Harvard is producing some amazing animations
    
    
  • MolecularMovies.org is a portal site where animators share their work and provide tutorials on how they produced some of the amazing animations
    
    
    • DNA replication
      
      
    • ATP synthase
    
    
  • Keep in mind that these 3D animations are different than molecular dynamics animations. In molecular dynamics, the movement of the molecules are calculated based on the energies acting at the atomic (or larger) scale (for example)
    
    
• PhET Interactive Simulations
  
  
  • Eating and Exercise
    
    
  • Reversible Reaction
    
    
  • Gene Machine: The Lac Operon
    
    
• NetLogo Models Library incudes hundreds of simulations of phenomena across disciplines. The NetLogo software is free, and installs with all 450+ models in the models library.
  
  
  • Ants simulates how ants forage food using chemical signals
    
    
  • Flocking simulates bird flocking behavior. Here is a modified version of this model simulating how fish school and avoid predators.
    
    
  • Wolf Sheep Predation
    
    
• AgentSheets is another tool that can produce agent-based simulations, like NetLogo.
  
  
  • Basic enzyme
    
    
  • Bacterial chemotaxis
    
    
  • Wolf Sheep Predation
    
    
• Interactive Anatomy

(Computational Biology) Education

• Teaching your students to use computing to do Biology