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Biocomplexity Institute

Indiana University

Bloomington, IN 47405

USA

�Generous funding by:�NIH U24 EB028887, NIH R01 GM122424, NIH R01 GM123032, NIH P41 GM109824, NSF 1720625

The workshop will begin at 10:00 EDT

Screensharing and microphones have been disabled

Please submit questions / concerns vis zoom chat

User support will be done in zoom breakout rooms.

CompuCell3D User Training Workshop�Introduction to Python Programming

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CompuCell3D User Training Workshop�Introduction to Python Programming

Biocomplexity Institute

Indiana University

Bloomington, IN 47405

USA

�Generous funding by:�NIH U24 EB028887, NIH R01 GM122424, NIH R01 GM123032, NIH P41 GM109824, NSF 1720625

Instructor: Dr. Bobby Madamanchi,

Moderator: Mr. Hayden Fennell

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Why Learn Python?

Reaction-Network design and analysis
Adding behaviors to model biological cells
Analyzing data from experiments

Python is a convenient, widely used language that works well at these tasks
Will use ‘programming’ a bit differently in reaction/network analysis vs. biological cell model construction

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Topics

Learn the necessary programming concepts to build, study, and analyze advanced models in CompuCell3D

Model and simulate biochemical networks such as chemical, gene regulatory, signaling, etc..
Analyze results
Create decision-making algorithms, functions and data types
Implement behaviors in biological cell models

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Keys to Success

No one (including me) knows everything about everything related to a programming language

In software, there is always something new to learn

At least once today, we’ll come across something that I don’t know… and that’s ok!

Don’t know something? Look it up!

A coder’s best friends: manuals, other coders (e.g., Stack Overflow, open source software), and a trusty debugger

Solutions in programming are almost never unique

Focus on what you want to do

Experiment with different ways of how you do it

#1 key to success: perseverance

Feeling overwhelmed? Stop, take a breath, and then break up a task into a set of simpler, more manageable sub-tasks

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nanoHUB Environment

Creating a nanoHUB account
Logging in
Finding Jupyter Notebook App
Running cells

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Logging in to nanoHUB

Go to nanohub.org

Hit Login

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Create a nanoHUB Account

Go to https://nanohub.org

From ‘Menu’, select ‘sign up’

Choose to sign up with your university of choice (if it is a US university) or sign in with Google.

Choose an appropriate username / password / user info

If its your first time signing up you will need to provide some biographical information

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Logging in to nanoHUB

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Launch The Jupyter Notebook App on nanoHUB

https://nanohub.org/tools/jupyter70

Click the Collect button to add Jupyter to your favorites & then click Launch Tool

Jupyter Notebook (202105)

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Opening a New Notebooks

Click New and select Python3 to launch a new notebook

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Using Jupyter in nanoHUB

Native language is Python
Boxes are interactive ‘cells’
Cells are interactive edit boxes where you will type Python code
Type “shift+enter” to evaluate (execute code in) selected cells

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Saving Notebooks

To save use “Save as” in the File Pulldown Menu
nanoHUB saves Notebooks in the session subdirectory by default
For safety always download your work to your local computer before you end a session using “Download as”. Use .pynb as the file type

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Exercise: calculating distance

Type expressions in the cell, see the output
You can type expressions in each cell.
Type shift-enter to evaluate
Type some mathematical expressions…
Operators: +, -, /, *, **

��Problem

Given: Two positive integers a and b,

Return: The integer corresponding to the sum of a and b.

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You’ve just used Scalar Types

programs manipulate objects
objects have a type that defines the kinds of things programs can do to them

Ana is a human so she can walk, speak English, etc.

objects are

scalar (cannot be subdivided)
non-scalar (have internal structure that can be accessed)

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Scalar Types

int – represents integers e.g., 3
float – represents real numbers e.g., 5.1
bool – represents Boolean values e.g. True
NoneType – special; has one value: None
To get the type of an object: “type()”

x = 5.1
type(x)
>>> float

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Type Conversion

A.k.a., “cast”
Convert an object from one type to another

E.g., truncate a float to an integer

int(5.1)

>>> 5

E.g., convert an integer to float

float(5)

>>> 5.0

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EXPRESSIONS

combine objects and operators to form expressions
an expression has a value, which has a type
syntax for a simple expression

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OPERATORS ON ints and floats

→ the sum

→ the difference

→ the product

→ division

→ the remainder when i is divided by j

i**j → i to the power of j

if both are ints, result is int

if either or both are floats, result is float

result is float

Exercises

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How to do math calculations

Ordinary order of operations applies
operator precedence without parentheses ()

**
*
/
+ and –
executed left to right, as appear in expression

Exercises

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Assigning values to variables

equal sign is an assignment of a value to a variable name

pi =

3.14159

pi_approx = 22/7

value stored in computer memory
an assignment binds name to value
retrieve value associated with name or variable by invoking the name, by typing pi

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Can change the values stored in variables

value for area does not change until you tell the computer to do the calculation again

radius

area

3.14

2.2

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3.2

pi = 3.14

radius = 2.2

area = pi*(radius**2) radius = radius+1

Exercises

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STRINGS

letters, special characters, spaces, digits
enclose in quotation marks or single quotes

hi = "hello there"

concatenate strings

name = "ana"

greet = hi + name

greeting = hi + " " + name

do some operations on a string as defined in Python docs

silly = hi + " " + name * 3

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OUTPUT: print

used to output stuff to console
function is print

x = 1
print(x)
x_str = str(x)
print("my fav num is",	x, ".",	"x =", x)
print("my fav num is "	+ x_str	+ ". " + "x = " + x_str)

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COMPARISON OPERATORS ON �int, float, string

i and j are variable names
comparisons below evaluate to a Boolean

i > j

i >= j

j > i

i <= j

i == j ⇾ equality test, True if i is the same as j

i != j ⇾ inequality test, True if i not the same as j

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LOGIC OPERATORS ON bools

a and b are variable names (of type Boolean)

True if a is False False if a is True

not a ⇾

a and b ⇾

a or b ⇾

True if both are True

True if either or both are True

A	B	A and B	A or B
True	True	True	True
True	False	False	True
False	True	False	True
False	False	False	False

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CONTROL FLOW - BRANCHING

if <condition>:

...

if <condition>:

...

else:

...

if <condition>:

...

elif <condition>:

...

else:

...

<condition> has a value True or False
evaluate expressions in that block if <condition> is True

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BLOCKS / INDENTATION

print("x

and y are

equal"

if y != 0

print("therefore

, x / y is",

x/y

print("x

smaller"

else:

print("thanks!")

blocks are a unit of computation
Indentation matters in Python – partitions blocks
how you denote blocks of code

if x == y:

print("x and y are equal")

if y != 0:

print("therefore, x / y is", x/y) elif x < y:

print("x is smaller")

print("y is smaller")

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Assignment and Comparison: �= vs ==

if x == y:

print("x and y are equal") if y != 0:

print("therefore, x / y is", x/y) elif x < y:

print("x is smaller") else:

print("y is smaller") print("thanks!")

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Exercise: determine if a number is even or odd

Choose a number. Depending on whether the number is even or odd, print out an appropriate message to the user.

Hint: how does an even / odd number react differently when divided by 2?

Extras:

If the number is a multiple of 4, print out a different message.
Make two numbers: one number to check (call it num) and one number to divide by (check). If check divides evenly into num, tell that to the user. If not, print a different appropriate message.

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CONTROL FLOW:

while LOOPS

while <condition>:

...

<condition>

evaluates to a Boolean

if <condition> is True, do all the steps inside the while code block
check <condition> again

repeat until <condition>

is False

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CONTROL FLOW:

while and for LOOPS

iterate through numbers in a sequence

# more complicated with while loop n = 0

while n < 5:

print(n) n = n+1

# shortcut with for loop for n in range(5):

print(n)

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for LOOPS

for <variable> in range(<some_num>):

...

each time through the loop, <variable>

takes a value

first time, <variable> starts at the smallest value

gets the next value in the sequence

next time, <variable>
etc.

For is over a sequence of things

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range(start,stop,step)

default values are start = 0 and step = 1 and optional
loop until value is stop - 1

mysum = 0

for i in range(7, 10): mysum += i

print(mysum)

mysum = 0

for i in range(5, 11, 2): mysum += i

print(mysum)

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Exercise: Calculate the sum of number

Problem

Given: Two positive integers a and b (a<b<10000).

Return: The sum of all odd integers from a through b, inclusively.

Sample Dataset

100 200

Sample Output

7500

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break STATEMENT

immediately exits whatever loop it is in
skips remaining expressions in code block
exits only innermost loop!

while <condition_1>: while <condition_2>:

<expression_a>

break

<expression_b>

<expression_c>

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break STATEMENT

mysum

== 5

break

mysum += 1 print(mysum)

what happens in this program?

mysum = 0

for i in range(5, 11, 2): mysum

if mysum == 5:

break

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for VS while LOOPS

while loops

unbounded number of iterations
can end early via break
can use a counter but must initialize before loop and increment it inside loop
may not be able to rewrite a while loop using a for loop

for loops

know number of iterations
can end early via

break

uses a counter
can rewrite a for

using a while loop

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Module Questionnaire

Please take a minute or two to let us know about your experience with this module by filling out the brief zoom survey

Feel free to provide additional comments and suggestions in the slack or by email to us as well (hfennel@iu.edu)

Funding Sources: NIH U24 EB028887, NSF 2120200, 2000281, 1720625

Previous Funding : NIH R01 GM122424