1. Building modular tools for visualizing computation

2. 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.”

3. 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.

6. Fix the axis limits so you can understand the dynamics

7. Add tails to see where it is coming from

8. Look at the dynamics near the fixed point

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

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

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

12. Add the quiver plot for the flow field

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

15. Switch to a new set of equations

16. Add multiple points

17. Add points that have an exponential distribution of lifetimes