COMP 14 - Computational Concepts in Biological and Cognitive Sciences

Fall 2009

• Instructor: Anselm Blumer, 214 Halligan Hall, x73651, ablumer at cs dot tufts dot edu
  Office hours: Tuesday, 10:30-11:30 and Wednesday, 4:30-5:30 in 118 Halligan
  Thursday, 2-3 in 214 Halligan
  
• TA: Okuary Osechas, Room 137 Halligan Hall, okuary at gmail dot com
  Office hours: Monday 11:45-1:15 and 4:15-6, Tuesday 12:30-2:30, and Thursday noon-1:30 in 137 Halligan
  
• Texts: Learning Perl, by Schwartz, Phoenix, and foy (O'Reilley, 2005)
  Discrete Mathematics and Its Applications, Sixth Edition, by Kenneth H. Rosen (McGraw Hill, 2007)
• Description:
  A second course in Computer Science for interdisciplinary students in the biological and cognitive sciences. Programming skills relevant to problems in biology and cognitive science, including data structures, algorithms, algorithm analysis techniques, discrete mathematics, and probability. Students will complete programming projects in languages appropriate to these disciplines.
  
  Prerequisite: COMP 11 or equivalent.
• Lab: There will be weekly lab assignments posted here. I will be in the lab in 218 Halligan on Tuesdays at 10:30 and Wednesdays at 4:30 for help with the labs.
  • Lab 1: The Perl debugger
  • Lab 2: Random numbers, timing, and linear search
  • Lab 3: Timing user input
  • Solution to Lab 3
  • Lab 4: Recursion and files
  • Solution to Lab 4
  • Lab 5: Recursion and references
  • Lab 6: Sets and hashes
  • Lab 7: Binary and ternary search trees
  • Lab 8: Random graphs
• Links
• Exams: There will be three 45-minute in-class exams. Exams will be held on October 14, November 4, and December 2. The final will be on Thursday, 17 December from noon to 2:00. Exams will be open book and open notes, but no electronic devices are allowed. Exams count 50% toward the final grade.
  
• Homework (counts 50% toward the final grade):
  • Homework 1, due Wednesday, 16 September
  • Homework 2, due Wednesday, 23 September
  • Homework 3, due Wednesday, 30 September
  • Homework 4, due Wednesday, 7 October
  • Homework 5, due Wednesday, 14 October
  • Homework 6, due Wednesday, 21 October
  • Homework 7, due Wednesday, 28 October
  • Homework 8, due Wednesday, 11 November
  • Homework 9, due Wednesday, 18 November
  • Homework 10, due Wednesday, 2 December
• Class notes:
  • Simple Perl programs
  • Print a truth table
  • Boolean values in Perl programs
  • Insertion sort
  • Set operations using unordered lists
  • Set operations using ordered lists
  • The power of recursion
  • Merge sort
  • References
  • Subroutine parameters
  • Basic probability concepts
  • Bayesian inference
  • Binary search trees
• Policy on collaboration: On homework exercises collaboration is allowed at the level of discussing ideas, but credit must be given to the other parties whether you gave or received help. A simple statement on the homework sheet, such as "I helped Don Knuth on problem 1." or "Alan Turing helped me with part c of problem 2." or "Grace Murray Hopper and I discussed the design of COBOL." will suffice. Copying or working out the details of assignments collaboratively is not allowed. Failure to follow these guidelines may result in severe disciplinary action for all parties involved. See the booklet "Academic Integrity" available from the Dean of Students' Office.
• Late policy: Assignments are to be handed in as specified on the assignment page. 20% per weekday late will be deducted unless some other arrangement is agreed to before the due date.