Portfolio
(UNDER CONSTRUCTION)
This analysis portfolio contains some examples of bottom-up and top-down systems biology mini projects and a few other fun projects as well.
Bottom-up systems biology - Agent-based simulations can be a great way to demonstrate how simple rules can lead to emergent behaviors and to build intuition for how changing specific variables can impact outcomes.
Collective Behaviors
Fish and birds school and flock. Let's explore a simple model that can reproduce these fascinating behaviors
Ants modify their environment by depositing pheromones as feedback signals to help drive collective behaviors. Let's create a simple model of this process!
What about collective behaviors when some individuals have a different goal in mind. Let's simulate what happens in a simple predator and prey model where our agents are hunting and trying to avoid being hunted.
Controlling collective behaviors - can we establish a "policy" for a few agents such that they can drive specific collective behaviors? (similar to how dogs herd cattle)
Reaction Network Dynamics
So far, we've looked at collective agents with some intrinsic motivation. Let's explore some less intelligent, but still interesting phenomena where behaviors emerge from collections of interacting molecules.
Geometry and Self-Organization
Many biochemical reactions in cells take place on the plasma membrane, but reaction diffusion simulations are typically simulated on a planar domain. Let's explore what happens when we simulate some reactions on curved surfaces. Not only do these surfaces impact the topology of the domain (i.e. periodic boundaries), but they also impact diffusion itself because curved surfaces have a different metric tensor than flat surfaces.
Top-down systems biology - these mini projects aim to identify possible explanations of phenomena from real data
Collective behaviors
How do cell monolayers move to close wounds?
How do ants work together to move large objects?
Classifying protein staining patterns in single cells
Graph structures in tissues
Other scientific data analysis
Protein structural data
Just for fun
Where do the Lyft e-bikes go in San Francisco?