Saint Louis University |
Computer Science 1020
|
Computer Science Department |
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 |
hw01 | |
| 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 |
hw02 | |
| Feb 12-Feb 16 | Mon | Lab: Open Reading Frames and Genes | lab03 | |
| Wed |
Finding ORFs in Python
Techniques: dictionaries, lists, tuples, modularity |
software | ||
| Fri | Introduction to the Longest Common Subsequence (LCS) problem. |
Ch. 6.3 of text
examples |
||
| Feb 19-Feb 23 | Mon |
Algorithms for LCS
recursive thinking for problem reduction |
Ch. 6.3 and 7.6 of text
software |
|
| Wed |
Dynamic Programming solution for LCS
Reconstructing the actual LCS |
sample table
software |
||
| 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 |
hw04 | ||
| Mar 12-Mar 16 | Mon | No Class: Spring Break | ||
| Wed | ||||
| Fri | ||||
| 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,
examples |
||
| 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 | ||