PowerPoint Presentation

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 understood the code you wrote in class, but I cant do the homework problems.

I dont know which parameters are important and which ones Im not supposed to touch.

I dont want to use a tool when I dont entirelyunderstand the math. What if theres some important assumption that Im missing?The toolbox cant find a thing and so it gives an error.The toolbox cant find a thing and so it gives an error.

The toolbox cant find a thing and so it gives an error.I dont know which parameters are important and which ones Im not supposed to touch.I understood the code you showed us in class, but when I go to do the homework problems, I cant figure out what to write.I dont want to use a tool when I dont entirely understand the math. What if theres some important assumption that Im 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.

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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.Immediate gratification can be a helpful motivator.For instructors, modules provide easy exits to move on to other students.

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.

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Fix the axis limits so you can understand the dynamics6

Add tails to see where it is coming from7

Look at the dynamics near the fixed point8

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

Add a label for the counter when looking at the fixed point10

Add transparency to the tails using a function from the file exchange11

Add the quiver plot for the flow field12

Limit the range of the quiver plot and adjust the quiver length13

Switch to a new set of equations15

Add multiple points16

Add points that have an exponential distribution of lifetimes17