Instructor: Prof. Ted Perkins
Prerequisites: None. This course is intended for students in life science departments with little or no computer science background. It is not open to Computer Science majors or joint majors, nor to students who have or are taking COMP 208 or COMP 250. It is a 300-level course in the Faculty of Science, and thus counts towards the overall 300-level-or-above credit totals required by some programs.
Sample solutions to Homework 1
Sample solutions to Homework 2 (Note that the TA's answer to 5A may be different from yours; it's different from what I found. He will grade this one accordingly.)
New: Sample Questions for Quiz 1
Sample solutions to Homework 3
Hand-in sheet: HandinSheet.txt. For homeworks, O = on-time, L = late, X = not handed in. For quizzes, Y = taken, N = not taken.
| Lecture | Date | Topics & Materials |
| 1 | Jan 4 | Topics: Welcome, syllabus, activating accounts. Handout: Syllabus |
| 2 | Jan 7 |
Topics: Computer terminology, linux file system, terminal & terminal commands. Lecture Notes: comp364_lec2_notes.doc Optional Reading: A tutorial on linux at about the level we're covering it. |
| 3 | Jan 9 |
Topics: More terminal commands. Lecture Notes: comp364_lec3_notes.doc Optional Reading: A tutorial on linux at about the level we're covering it. |
| 4 | Jan 11 |
Topics: File permissions and changing them. Scripts. Lecture Notes: comp364_lec4_notes.doc Terminal Log: comp364_lec4_terminal.txt (Descriptive comments surrounded by #s) Optional Reading: A tutorial on linux at about the level we're covering it. Handout: Homework 1 |
| 5 | Jan 14 |
Topics: Terminology on computer architecture and programming languages. Beginning Perl programming: print, scalar variables. Lecture Notes: comp364_lec5_notes.pdf Terminal Log: comp364_lec5_terminal.txt Perl Programs: Hello.pl Vars.pl Reading: Moorhouse and Barry Chapter 3 Optional Reading: Jamison Chapter 2 |
| 6 | Jan 16 | Topics: More on strings in Perl. Taking input from the keyboard. More on numbers and operators in Perl. Lecture Notes: comp364_lec6_notes.doc Terminal Log: comp364_lec6_terminal.txt (May be slightly different from in class. I deleted that by accident and had to recreate it.) Perl Programs: Case.pl Term.pl Input1.pl Madlib1.pl Madlib2.pl Madlib3.pl Madlib4.pl Reading: Moorhouse and Barry Chapter 3 Optional Reading: Jamison Chapter 2 |
| 7 | Jan 18 | Note: Homework 1 due by end of class. Topics: More on number operations. Control flow, including if, if-else, while and conditions (or tests) on numbers. Lecture Notes: comp364_lec7_notes.rtf Terminal Log: comp364_lec7_terminal.txt Perl Programs: Numbers.pl Compare.pl Compare2.pl Hypotenuse.pl Countdown.pl Reading: Moorhouse and Barry Chapter 3 Optional Reading: Jamison Chapter 4 |
| 8 | Jan 21 |
Note: Last chance for late turn in Homework 1. Topics: More on conditions, comparisons (especially character and string comparison), logical operators !, && and ||. Lecture Notes: comp364_lec8_notes.doc Handout: Summary of conditions and comparisons in Perl Reading: Moorhouse and Barry Chapter 3 Optional Reading: Jamison Chapter 4 |
| 9 | Jan 23 | Practice exercises: PracticeLecture9.html |
| 10 | Jan 25 |
Topics: Going over solutions to the practice exercises from wednesday. Lecture Notes: comp364_lec10_notes.doc |
| 11 | Jan 28 |
Handout: Homework 2 Topics: Boolean logic, including the operators !, && and !!, truth tables, and various "laws" of Boolean logic. Lecture Notes: comp364_lec11_notes.pdf Optional Reading: Wikipedia's entry on Boolean logic (But beware they show truth tables in a different -- worse! -- way than I presented them.) |
| 12 | Jan 30 |
Topics: Arrays (mostly) and hashes (a brief intro only) Lecture Notes: comp364_lec12_notes.doc Reading: Moorhouse and Barry Chapter 4 Optional Reading: Jamison Chapter 3 |
| 13 | Feb 1 | Topics: Sorting arrays ASCII-betically or numerically, looping through arrays Lecture Notes: comp364_lec13_notes.doc or comp364_lec13_notes.txt Terminal Log: comp364_lec13_terminal.txt Perl Programs: Sort.pl Sort2.pl Big.pl IsIn.pl |
| 14 | Feb 4 |
Topics: Array indexing Lecture Notes: comp364_lec14_notes.doc or comp364_lec14_notes.pdf |
| 15 | Feb 6 |
Note: Homework 2 due by end of class. Topics: Hashes Lecture Notes: comp364_lec15_notes.doc Terminal Log: comp364_lec15_terminal.txt Perl Program: Squares.pl |
| 16 | Feb 8 |
Note: Last chance for late turn in Homework 2. Topics: Hashes Lecture Notes: comp34_lec16_notes.doc Terminal Log: comp364_lec16_terminal.txt Perl Programs: PrintHash.pl PrintHash2.pl PrintHash3.pl CountWords.pl |
| 17 | Feb 11 |
Topics: Discussion of some of the sample quiz questions, array and hash problems Lecture Notes: comp364_lec17_notes.doc or comp364_lec17_notes.txt |
| 18 | Feb 13 |
Quiz 1! The quiz itself: Quiz1.html Sample solutions: Quiz1Soln.html |
| 19 | Feb 15 |
Topics: Array and hash problems Lecture Notes: comp364_lec19_notes.rtf Terminal Log: comp364_lec19_terminal.txt Perl Programs: RemDup2.pl RemDup3.pl RemDup4.pl |
| 20 | Feb 18 | Handout: Homework 3 |
| 21 | Feb 20 |
Topics: The join and split functions. Beginning pattern matching. Readings: Jamison 3.3.4 for join. For split, look on-line. Pattern matching is Ch. 7 in Moorhouse, and Ch. 6 in Jamison. Lecture Notes: comp364_lec21_notes.doc Terminal Log: comp364_lec21_terminal.txt Perl Program and Data: EachOnALine.pl EachOnALine2.pl Ishmael.pl MobyDick.txt |
| 22 | Feb 22 |
Topics: Pattern matching: Alternation and character classes. Readings: Ch. 7 in Moorhouse, and Ch. 6 in Jamison. Lecture Notes: comp364_lec22_notes.doc Terminal Log: comp364_lec22_terminal.txt Perl Program and Data: FirstOccur.pl FirstOccur2.pl Gal4.txt |
| 23 | Mar 3 |
Topics: Pattern matching: Brief review and repetition. Readings: Ch. 7 in Moorhouse, and Ch. 6 in Jamison. Lecture Notes: comp364_lec23_notes.rtf or comp364_lec23_notes.doc Terminal Log: comp364_lec23_terminal.txt Perl Program and Data: Pat1.pl Pat2.pl Pat3.pl Pat4.pl Pat5.pl Pat6.pl |
| 24 | Mar 5 |
Topics: Pattern matching Readings: Ch. 7 in Moorhouse, and Ch. 6 in Jamison. Lecture Notes: comp364_lec24_notes.pdf [Note, however, that the last few examples, which were done on the board, are wrong. As explained in lecture 27 / March 12, parentheses in a pattern affect what is returned by the global search. The last few examples here would be correct if the "(" in the pattern were replaced by "(?:".] Terminal Log: comp364_lec24_terminal.txt Perl Program and Data: Hb.txt AASearch.pl |
| 25 | Mar 7 |
Topics: Pattern matching: More example problems. Readings: Ch. 7 in Moorhouse, and Ch. 6 in Jamison. Lecture Notes: comp364_lec25_notes.doc Terminal Log: comp364_lec25_terminal.txt Perl Program and Data: Hb.txt Intron1.pl Intron2.pl Intron3.pl Tent1.pl Tent2.pl |
| 26 | Mar 10 |
Topics: Pattern matching: More example problems. Readings: Ch. 7 in Moorhouse, and Ch. 6 in Jamison. Lecture Notes: comp364_lec26_notes.doc Terminal Log: comp364_lec26_terminal.txt Perl Program and Data: Exon0.txt Exon1.txt Exon2.txt FindAspartic.pl FindAspartic2.pl CountAspartic.pl DNAtoAAS.pl |
| 27 | Mar 12 |
Topics: Some tips and hints, for HW3 and in general. Lecture Notes: comp364_lec27_notes.doc |
| 28 | Mar 14 |
Topics: Images: Pixel-based vs. object-based. Colors. File formats. Lecture Notes: comp364_lec28_notes.doc Programs and data: Expr_BcdLate.jpg Expr_BcdLate.pbm MyImage.pbm MyPic2.pl MyPic2.pbm |
| 29 | Mar 17 |
Topics: Images: More on colors, greyscale and color images. Computing the total intensity of an image. Lecture Notes: comp364_lec29_notes.rtf Terminal Log: comp364_lec29_terminal.txt Programs and data: e_coli-dk.jpg e_coli-dk.pgm e_coli-dk.ppm TotalIntensity.pl Test.pgm |
| 30 | Mar 19 | Quiz 2! |
| 31 | Mar 20 | Handout: HW4.html |
| 32 | Mar 26 |
Topics: Image file sizes and compression Lecture Notes: comp364_lec32_notes.doc Example images: logo.jpg logo.ppm logo-raw.ppm |
| 33 | Mar 28 |
Topics: Relational databases. SQL: Table creation, adding data, selection. Lecture Notes: comp364_lec33_notes.doc Terminal Log: comp364_lec33_terminal.txt Reading: Ch. 12 in Moorhouse Supplementary Material: SQL tutorial |
| 34 | Mar 31 |
Topics: More SQL: Selection, 3-valued logic, backing up a table, deleting rows Lecture Notes: comp364_lec34_notes.doc Terminal Log: comp364_lec34_terminal.txt Supplementary Material: SQL tutorial |
| 35 | Apr 2 |
Topics: SQL: Deleting rows, updating info, group function in SELECT Lecture Notes: comp364_lec35_notes.doc Terminal Log: comp364_lec35_terminal.txt Supplementary Material: SQL tutorial |
| 36 | Apr 4 |
Handout: Homework 5 Topics: SQL: GROUP BY, SELECTing from multiple tables Lecture Notes: comp364_lec36_notes.doc Terminal Log: comp364_lec36_terminal.txt Supplementary Material: SQL tutorial |
| 37 | Apr 7 |
Topics: Multi-table SELECT queries
Lecture Notes: comp364_lec37_notes.rtf Terminal Log: comp364_lec37_terminal.txt Supplementary Material: SQL tutorial |
| 38 | Apr 9 |
Topics: More on multi-table queries, variables, views Lecture Notes: comp364_lec38_notes.rtf Terminal Log: comp364_lec38_terminal.txt Supplementary Material: SQL tutorial |
| 39 | Apr 11 |
