Module 3 Practical Session

(additional instruction)
PyCharm working environment

Folder/Project tab Script/File view

Python Console
Terminal
Variables
Packages
Documentation
Problems (for
correcting error)
Rosalind Practice
• Create your account
• Finish Python Village Exercise first
• Then Bioinformatics Stronghold Exercises
Example: Counting DNA Nucleotides

“Click to expand” to know about

biology background of the problem

Problem description, requirements…

Example input and output

How to solve problem (step by step)
• Step 1: Study the question to understand the background and
requirements
• Step 2: Draft the algorithms to solve the problem
How to solve problem (step by step)
• Step 3: Write your code and save it in script

Define input sequence

Define counting variables

For loop and condition to count number of

nucleotides

Print the result

Run the script from Terminal

python script.py
How to solve problem (step by step)
• Step 4: Download dataset from Rosalind
• Step 5: Modify the input in your script corresponding to the dataset
• In this step, if you know how to handle file with Python, you can take directly
the downloaded dataset file as input (no need to modify the code)
• Step 6: Submit the output in time on Rosalind to validate your
solution
List of exercises to discuss
• In Rosalind:
• List view: Based on
computational skill
• Tree view: Based on
biology knowledge
• We will discuss some of these
problems for the next class

Try your best to learn as much as

possible !!!