Class 03: Programming Bioinformatics

Held: Thursday, 1 September 2011

Summary: We continue our exploration of the basics of bioinformatics by doing a bit of programming.

Related Pages:

• EBoard.
• Due: Write up of Web exploration 1.

Notes:

• About the papers.
• We have posted answers to your questions on the introductory survey.
• We will soon post answers to your more administrative questions.
• A note on Piazza.
• For the next class, read Chapter 2 of Exploring Bioinformatics and bring questions. (You don't need to do the chapter 2 Web exploration yet, and you certainly don't need to understand all of the code.)
• As you may have noted, we will use a different language in class than they use in the book. We will explore the differences in the lab and reflection.
• EC: CS Extra today at 4:30 - HCI for Peace.
• EC: Bio Grad School seminar Friday at noon.
• Chase will hold a mentor session ___ and will have office hours ___.

Overview:

• Reflections on the web exploration.
• About algorithm design.
• A sample algorithm.
• More Python basics.
• Lab: Project 1.4.
• Reflection.

Reflection on the Web Exploration

• What did you learn from the Web exploration?
• Some things you might have noted:
  • There's a lot of information on each page. Often, you have to spend some effort to find the key info you want.
  • There's a lot of information in the databases, you just need to know how to find it.
  • Talking things out is a good idea.
  • You may need to rely on colleagues for help.
  • Conversely, when you notice something particularly interesting, you should share it.

Algorithms and Programming

• So, what did St. Clair and Visick teach you about algorithms and programming?

A Sample Algorithm: Sorting Students

• Suppose we have a small group of students and want to put them in order by the distance of their home from Grinnell.
• Write instructions that a relatively clueless faculty member could follow.
  • Biology students should write the instructions.
  • CS students should ask questions to help the Biology students write better instructions.
• And yes, I'll try to follow them.

More Python Basics

What you've learned so far

• The model we're using
  • Long-standing code goes at the top.
  • Interactive experimentation in the bottom.
• Assignment
  • We have named storage locations and can store and change the values in them.
• Functions
• Lists/Sequences
  • Used to provide an indexed collection of values.
• Strings
  • Surrounded by quotation marks.
• Getting help
  • help(thing)
• Organization
  • Indentation is significant Some new topics
• Conditionals

  if test:
    consequent
  else:
    alternate
  

• Adding elements to lists/sequences

  sequence.append(value)
  

• Loops

  for var in sequence:
    instructions
  for var in range(lb,ub+1):
    instructions
  

Lab Exercise

• Labs based on the book are in the Exploring Bioinformatics with Python section of the Web site, which you can reach by clicking on ExBioPy at the top of any page.
• I'll try to set up our labs link to link to them (directly or indirectly).
• For today's lab, you'll look at two things in ExBioPy.
  • Start by reading a translation of Algorithm 1.3 into Python.
  • Continue with followup exercises.
• You may have to continue the lab on your own.
• You do not need to turn anything in, but you should finish it.

Followup

• What went well in the lab?
• What went poorly?
• What do you see as the strengths and weaknesses of the Rebelsky/Python appoach vs. the St.Clair+Visick/Perl approach?