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 www.spoken-tutorial.org
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 following 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 www.python.org
Open terminal by pressing Ctrl+Alt+T at the same time.	First of all, let's check if IPython3 is installed on our system. To do so, open the termiI have changed the text here.nal by pressing Ctrl+Alt+T simultaneously. Now, at the prompt, type ipython3 and press Enter.
Cursor on the terminal Point to “>>>” symbol.	You will see few lines of information on Python like, the version number etc. You will also see the IPython promptI added this. Pls verify In[1] on the terminal.
Cursor on the terminal.	In case you don't, then manually install the latest version of IPython, by typing sudo apt-get install ipython3 and press Enter.
Cursor on the terminal.	Wait for a few minutes for the installation to complete. Python3 does not overwrite the default Python.on the system.Here we are installing manually. But what happens to the already installed Python? Does it get overwritten?
Open the terminal Type ipython3 and press Enter.	To check whether ipython3 is installed successfully on your system, Type ipython3 at the prompt and press Enter.
Point to IPython prompt point to In[1]	In[1] indicates that IPython3 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.
Type in the terminal, my_DNA = "ATGCGCAT" Highlight my_DNA Press Enter	Type, my_DNA equal to ATGCGCAT within double quotes Press Enter.
Cursor on the panel.	We call this as assigning a variable.
Cursor on the panel	For writing a code, we can use the variable name instead of the string itself.
Type, my_DNA and press Enter	To print this sequence, type my_DNA and press Enter.
Highlight the output, ATGCGCAT	This will print the DNA sequence, ATGCGCAT within single quotes as it is a string.
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 and DNA after ATGCGCAT within double quotes. Press Enter.
Type, print(my_DNA) and press Enter	Type, print(my_DNA) and press Enter.
Highlight the output ATGCGCAT DNA	The output prints the sequence on two separate lines as, ATGCGCAT DNA <<PAUSE>>
Slide 9 Assignment	As an assignment, Using example of a short protein sequence: CNLTFTWPEADFYPI Protein Print the above sequence on a single line, and also on two separate lines. <<PAUSE>>
Cursor on the terminal	Let's go back to the terminal and learn a few more functions and methods.
	Another useful built-in tool in Python is the len function. It is used to calculate the length of a string.
Press up arrow key my_DNA = "ATGCGCAT"	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 10 Assignment	Another assignment for you Calculate the length of the given DNA sequence `ATGGCATGCGC' Store the output in a variable.
	Lets go back to the terminal
	Many times in biochemistry, sequences are represented either in  lowercase or uppercase  alphabets.
Type protein =” ” Press Enter Type my_DNA.lower() Press Enter.	To convert the uppercase alphabets in a string to  lowercase: We make use of lower() method. Type, my_DNA=”ATGCGCAT”.  Press Enter Then type, my_DNA.lower(). 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 11 Assignment	As an assignment, Using example of a short protein sequence:  cnltftwpeadfypi Convert the sequence to uppercase. Hint: Use upper() method.
	Back to terminal again
Type my_protein = "alspadkanl"	Lets take an example of an amino acid sequence. Store it in a variable called protein my_protein = "alspadkanl"
Cursor on the terminal	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	For example to know the number of times amino acid Alanine occurs in the string Type my_protein.count ('a') Press enter
Cursor on the terminal	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') Press enter
Cursor on the terminal	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 ocurrences of basepairs .
Slide 12 Summary	Let us summarize, In this tutorial we have 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 13 Summary	* Find the length of the string Change case of the string Count the number of times a character appears in a string
Slide 13 Assignment	Here is an assignment, Calculate GC content in the given DNA sequence. 'ATGGCATGCGC'
Slide 14 About Spoken Tutorial Project	The video available at the following link summarizes the Spoken Tutorial project. Pls watch it.
Slide 15 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 16 Acknowledgement	Spoken Tutorial ProjecThese 3 slides remain as before, on LaTeX. Only the narration will now be as given here.t is supported by the 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