Python for Biologists/C2/Introduction-to-Python-for-Biologists/English

Title of script: Introduction to Python for Biologists

Author: Trupti Rajesh Kini & Snehalatha

Keywords: video tutorial, Python, DNA seqences, Protein sequences, Biologists

Visual Cue	Narration
Slide 1	Welcome to the spoken-tutorial on Introduction to Python for Biologists.
Slide 2 Learning Objectives	In this tutorial we will learn, Installation of Python/IPython interpreter. Simple Python programs using examples of DNA and Protein sequences.
Slide 3 System Requirements	To record this tutorial, I am using Ubuntu OS version 12.04 Python 3.2.3 IPython 0.12.1
Slide 4 Prerequisites	To practice this tutorial you should be familiar with, Basic biochemistry You can also refer to Spoken Tutorials on Python for better understanding of this tutorial. These are available at the given link.
Slide 5 Why Python for biologists?	Some of the features of Python useful for biologists are as follows: Python has many tools to write small programs that are useful in biology. It has a consistent syntax. It has built-in-libraries for common tasks. We can manipulate DNA and protein sequences easily .
Slide 6 Why Pyhton for biologists?	It has a large user base as it is commonly used in bioinformatics. Listed here are examples of few bioinformatic tools in Python: Biopython, Modeller, chemopy, BLASTorage, Pymol For more information, refer the given website: http://pythonforbiologists.com
Slide 7 Installation	Python comes installed, by default on Ubuntu. IPython is an interactive terminal for Python To install Python on Windows, Mac OS and Android devices, visit the given link
Open terminal by pressing Ctrl+Alt+T at the same time.	Open the terminal by pressing Ctrl+Alt+T simultaneously. Python comes installed, by default on Ubuntu.
Type sudo apt-get install ipython3 and press Enter.	In case you don't, then manually install the latest version of IPython, by typing sudo apt-get install ipython3 and press Enter. Give root password if asked.
Cursor on the terminal.	Wait for a few minutes for the installation to complete. Note : Python3 does not overwrite the default Python on the system.
Open the terminal Type ipython3 and press Enter.	To check whether ipython3 is installed successfully on your system, type ipython3 and press Enter.
Cursor on the terminal Highlight the prompt	You will see few lines of information on Python like, the version number. You will also see the Ipython prompt on the terminal. Prompt indicates that Ipython is installed successfully.
Cursor on terminal	Let's type a few simple Python commands with an example of a DNA sequence.
Cursor on terminal	To begin with, we will store data, i.e DNA sequence, in a variable called my_DNA.
Slide 8 What is a string?	In Python language, data such as protein and DNA sequences are called as strings. A string is a data in the form of a text. Let us go back to the terminal. Let us first clear the terimal by typing clear and press Enter.
Type in the terminal, my_DNA = "ATGCGCAT" Highlight my_DNA Press Enter	Type, my_DNA is equal to within double quotes ATGCGCAT. Press Enter.
Highlight my_DNA	We call this as assigning a variable.
Highlight my_DNA	For writing a code, we can use the variable name instead of the string itself.
Type, print(my_DNA) and press Enter	To print the DNA sequence, we will use print function. For that type, print inside brackets my underscore DNA and press Enter.
Highlight the output, ATGCGCAT	We get the sequence as output.
Cursor on the terminal.	Now let us print the sequence on two separate lines.
Press up arrow Add \n and DNA after ATGCGCAT. my_DNA = "ATGCGCAT\nDNA" Press Enter	Press up arrow on the key board till we get this command on the terminal. my_DNA = "ATGCGCAT” Lets edit this line. Type \n DNA after the sequence within double quotes. Press Enter.
Type, print(my_DNA) and press Enter	Type, print inside brackets my underscore DNA and press Enter.
Highlight the output ATGCGCAT DNA	The output prints the sequence on two separate lines.
Slide 9 Assignment	As an assignment, Using example of a short proteinsequence given Print the sequence on a single line, And print the sequence on two separate lines.
Cursor on the terminal	Let us now learn a few more functions and methods.
Slide 10	Another useful built-in tool in Python is the len function. It is used to calculate the length of a string.
Let us go back to the terminal. Press up arrow key my_DNA = "ATGCGCAT" Press Enter	Let us go back to the terminal. Press up arrow on the key board till we get this command on the terminal. my_DNA = "ATGCGCAT” Press Enter
Type: len(my_DNA)	To find the length of the DNA sequence in a variable, type, len within brackets my_DNA Press Enter.
Cursor on the terminal	The output on the screen shows the number 8. This is the length of the DNA sequence stored in the variable my_DNA.
Slide 11 Assignment	Another assignment for you Calculate the length of the given DNA sequence 'ATGGCATGCGC' And Store the output in a variable.
Slide 12	Many times in biochemistry, sequences are represented either in lowercase or uppercase alphabets.
Type, my_DNA=”ATGCGCAT” Press Enter Type my_DNA.lower() Press Enter.	To convert the uppercase alphabets in a string to lowercase, we make use of lower() method. Let us go back to the terminal. Type, my_DNA=”ATGCGCAT” and press Enter Then type, my_DNA dot lower open and close brackets . In a method, we write, The name of the variable first, followed by a period(.), then the name of the method, then we open and close parentheses. Press Enter.
Highlight  'atgcgcat'	The output shows the string in lowercase.
Slide 13 Assignment	As an assignment, Using example of a short protein sequence given Convert the sequence to uppercase Hint: Use upper() method.
	Let us go back to terminal again.
Type my_protein = "alspadkanl"	Lets take an example of an amino acid sequence. Store it in a variable called my_protein. So type my_protein = "alspadkanl" and press Enter.
Slide 14	To find out the number of times an amino acid or a sequence of amino acids occurs in a string, we make use of count function.
Type my_protein.count ('a') Press Enter	Let us go back to the terminal. For example, to know the number of times amino acid Alanine occurs in the string, type my_protein.count ('a') my underscore protein dot count open and close brackets within single quotes a Press Enter
Highlight 3	Output shows number 3. There are 3 Alanines in the string.
Type my_protein.count('l') Press Enter	Similarly to find number of Leucines in the string, type my_protein.count('l') my underscore protein dot count open and close brackets within single quotes l Press Enter
Highlight 2	We get an output as 2. There are 2 Leucines in the string.
Cursor on the terminal	Similarly, we can use DNA or an RNA sequence as string to count the ocurrances of basepairs.
Slide 15 Summary	Let us summarize. In this tutorial we learnt: Installation of IPython Interpreter Storing data in variables using examples of DNA and Protein sequences. Printing a sequence in single and on two separate lines
Slide 16 Summary	Find the length of the string Change case of the string Count the number of times a character appears in a string
Slide 17 Assignment	As an assignment, Calculate GC content in the given DNA sequence. 'ATGGCATGCGC'
Slide 18 About Spoken Tutorial Project	The video available at the following link summarizes the Spoken Tutorial project. Pls watch it.
Slide 19 About Spoken Tutorial workshops	The Spoken Tutorial Project Team conducts workshops and gives certificates to those who pass an online test. For more details, please write to us.
Slide 20 Acknowledgement	Spoken Tutorial Project is supported by NMEICT, MHRD, Government of India. More information on this Mission is available at this link.
	This script is contributed by Snehalatha and Trupti Kini. And this is Trupti Kini from IIT Bombay signing off. Thanks for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak, Trupti