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Saint Louis University

Computer Science 1020
Introduction to Computer Science: Bioinformatics

Michael Goldwasser

Spring 2018

Computer Science Department


Please note that the schedule for future classes is tentative.

Also note: For each lecture, we denote both a topic as well as the associated reading in the textbook. The live link on the 'topic' leads to a page of my personal notes for that lecture. Those personal notes are not nearly as complete or polished as the associated readings from the text. In truth, they exist mostly to provide a brief outline of the day's lecture. Students are expected to read the associated sections of the text. In cases where my notes include material which is not explicitly in the text, I will add the word "notes" to the explicit reading list.

Week Day Topic Reading Due
Jan 17-Jan 19 Wed Introduction, Course Administration syllabus
Fri DNA profiling notes
Jan 22-Jan 26 Mon Introduction to Python
Use of Strings in Python
Ch. 0.0-0.10
Summary of str methods
my notes
Wed Lab: Python Warmup lab01
Fri Genomics and the Central Dogma slides
my notes
Jan 29-Feb 2 Mon Overview of Python's Control Structures
functions, for loops, conditionals
my notes
(skim Ch. 1 of text)
Wed Lab: Control Structures lab02
Fri Continued work on lab02 lab02
Feb 5-Feb 9 Mon Review of lab02 solutions
Introduction to lists, range, index-based loops
my notes
(skim Ch. 2 of text)
Wed More with lists, range, index-based loops
Alternative approach to lab02 solutions
Fri Open Reading Frames (ORFs) and Genes Ch. 3,4
my notes
Feb 12-Feb 16 Mon Lab: Open Reading Frames and Genes lab03
Wed Finding ORFs in Python
Techniques: dictionaries, lists, tuples, modularity
Fri Introduction to the Longest Common Subsequence (LCS) problem. Ch. 6.3 of text
Feb 19-Feb 23 Mon Algorithms for LCS
recursive thinking for problem reduction
Ch. 6.3 and 7.6 of text
Wed Dynamic Programming solution for LCS
Reconstructing the actual LCS
sample table
Fri First Exam - info
Feb 26-Mar 2 Mon Generalizing Sequence Alignment Scores Ch. 8 hw03
Wed Lab: Global Sequence Alignments
Fri Introduction to hw04
memoAlignScore function
Ch. 8 lab04*
actually due
Saturday 11:59pm
Mar 5-Mar 9 Mon Continuation of hw04
allScores function
Wed Continuation of hw04
closestMatch function
Fri Continuation of hw04
printBRH function
Mar 12-Mar 16 Mon No Class: Spring Break
Mar 19-Mar 23 Mon Introduction to trees my notes,
Ch. 9.1
Wed Tree algorithms my notes,
Ch. 9.2
Fri Introduction to lab05: Phylogenetic Tree Visualizations
Mar 26-Mar 30 Mon Continued work on lab05: Phylogenetic Tree Visualizations hw05
Wed No Class: "Pre-Easter" Break lab05
Fri No Class: Easter Break
Apr 2-Apr 6 Mon
Wed UPGMA clustering algorithm Ch. 11,
Fri UPGMA continued resulting tree for our data set
Apr 9-Apr 13 Mon Introduction to Sequence Assembly:
hands-on activity
Wed Review for exam
Fri Second Exam - info
Apr 16-Apr 20 Mon Sequencing Technologies (Dr. Ted Ahn)
Wed Sorting by Reversals (Dr. David Letscher)
Fri Sorting by Reversals (Dr. David Letscher)
Apr 23-Apr 27 Mon Assembly Algorithms:
Overlap/Layout/Consensus (OLC)
De Bruijn graph assembly (DBG)
OLC notes
DBG notes
Wed lab06: Sorting by Reversals
Fri lab06: Sorting by Reversals lab06
Apr 30-May 4 Mon Lab06 post-analysis (including extra credit)
Wed Bioinformatics Research (Dr. Maureen Donlin)
Fri RNA secondary structure prediction Ch. 12 hw06
May 7 Mon

May 9 Wed Final Exam (2:00-3:50) - info

Michael Goldwasser
CSCI 1020, Spring 2018
Last modified: Sunday, 06 May 2018
Course Home | Assignments | Computing Resources | Data Sets | Lab Hours/Tutoring | Python | Schedule | Submit