Building modular tools for visualizing computation

Why are computational tools daunting (for biology graduate students) to use? “I used these four different packages and one of them gave me the result that I think will make my boss happy, so I must have done something wrong on the other ones.” “I don’t want to use a tool when I don’t entirely understand the math. What if there’s some important assumption that I’m missing?” “I don’t know which parameters are important and which ones I’m not supposed to touch.” I understood the code you wrote in class, but I can’t do the homework problems.” “The toolbox can’t find a thing and so it gives an error.” “The toolbox can’t find a thing and so it gives an error.” “The toolbox can’t find a thing and so it gives an error.” “I don’t know which parameters are important and which ones I’m not supposed to touch.” “I understood the code you showed us in class, but when I go to do the homework problems, I can’t figure out what to write.” “I don’t want to use a tool when I don’t entirely understand the math. What if there’s some important assumption that I’m missing?” “I used these four different packages and one of them gave me the result that I think will make my boss happy, so I must have done something wrong on the other ones.”

Benefits of developing in modules Coding involves both hard thinking work and hard doing work so humans need to take breaks while coding. They also need help learning the ”right” time for breaks. For instructors, modules provide easy exits to move on to other students. Immediate gratification can be a helpful motivator. Coding involves both hard thinking work and hard doing work so humans need to take breaks while coding. They also need help learning the ”right” time for breaks. Immediate gratification can be a helpful motivator. For instructors, modules provide easy exits to move on to other students.

Fix the axis limits so you can understand the dynamics

Add tails to see where it is coming from

Look at the dynamics near the fixed point

Start very close to the fixed point, is it stable or unstable?

Add a label for the counter when looking at the fixed point

Add transparency to the tails using a function from the file exchange

Add the quiver plot for the flow field

Limit the range of the quiver plot and adjust the quiver length

Switch to a new set of equations

Add multiple points

Add points that have an exponential distribution of lifetimes