You'll work in groups on some assignments. The list of groups provides information about each group.
Lesk refers to Introduction to Bionformatics, by Arthur Lesk, and Horstmann refers to Java Essentials, by Cay Horstmann
| Monday | Wednesday | Friday |
|---|---|---|
| 8/23 First Day of Class Introduction, why computer science, why genome science
notes for viewing | 8/25 Vocabulary objects and classes, loops and collections
iTunes: how to program (to
understand this you'll want
to consult the
Java Essentials
book,especially
Chapter 2 at first)
| 8/27 Terminology: compiler, loop, method, array, variable, class, ... |
| 8/30 Vocabulary: nucleotides, dna, rna, amino acids, proteins, genes From strings to sequences, understanding loops and iterators
group work on compsci/genetics | 9/1 English and Genetic palindromes
Compsci != Programming | 9/3 Finish group work on bioinformatics and iTunes programming.
|
| 9/6 GC content, ORFs Read Lesk, pp1-39
notes for viewing
| 9/8 Algorithmic and Program Design Read Chapter 3Java Essentials
notes for viewing
| 9/10 Protein Practice
|
| 9/13 Proteins and Programs
| 9/15 Aesthetics of Programs student solutions to Part I of dna-to-protein | 9/17 Arrays and ArrayLists
notes for viewing
|
| 9/20 Arrays continued, Eclipse | 9/22 Refactoring
notes for viewing
| 9/24
|
| 9/27 Review for test
test practice
| 9/29 Exam I | 10/1 Exam I Redux (to be discussed on Monday) |
| 10/4 Getting data Factories, Readers, java.io.* lists, maps, java.util.*; Fasta, Genbank, EMBL, SwissProt, ... Parsing, URLS, Files, Web | 10/6
| 10/8 What's an object? An iterator?
notes for viewing class arrays again Midterm Grades Due |
| 10/11 Fall Break | 10/13 Arrays, ArrayLists, shotgun sequencing, Iterators, code | 10/15 Iterators and shotgun continued |
| 10/18 Interfaces
| 10/20 MergeTest.java testing code from class
| 10/22 Alignment, Matching, Algorithms From arrays to algorithms
|
| 10/25 interfaces towards efficiency. | 10/27 | 10/29 |
| 11/1 notes for viewing notes for printing
| 11/3 Read Lesk/Bioinformatics: Chapter 4, 160-178, 187-196 Markov Models, text generation/prediction Efficiency, O-notation | 11/5 notes for viewing notes for printing Visualizing and understanding information GUIs Gene-boy |
| 11/8 Overview of Everything, shared with ISIS notes for viewing notes for printing
| 11/10 Overview of Everything, shared with ISIS | 11/12 Review/Shotgun |
| 11/15 Exam II | 11/17 Object-oriented Design patterns notes for viewing notes for printing Shotgun interfaces and factories
| 11/19 Sorting/Searching |
| 11/22 Understanding hierarchies and recursion. | 11/24 Under the hood of biojava What's in a library? Thanksgiving | 11/26 Thanksgiving |
| 11/29 Understanding hierarchies and recursion. notes for viewing notes for printing
| 12/1 Last Day of Class What is Computer Science? | 12/3 |
| 12/6 code to look at for final, test answers, shotgun code, ... | 12/8 Final Exam, 7:00 PM | 12/10 |