| Lecture sessions | Exercises | Notes/Projects | |
| Week 35 28/8 |
Introduction to the course. |
5 push-ups. | |
| Week 36 4/9 |
String formatting, control structures, if/else, while,
.. Deitel: chapters 2 and 3, and sections 4.1 - 4.5. |
Codon exercise, Ex. 2.4, 2.5, 2.6, 2.7, 3.3, 3.4, 3.8, 3.6, 3.7, 3.5 |
Program names |
| Week 37 11/9 |
Functions, importing modules, lists,
tuples, .. Deitel: chapters 4 and 5 |
Codon exercise 2,
Testing exercise,
Cheating die exercise,
Ex. 4.3, 4.4 (see here), 4.5, 4.6, 4.7, 4.8, 5.3, 5.5, 5.6 |
|
| Week 38 18/9 |
No lecture and no question cafe due to conference. |
No exercises - except those you haven't already done! | |
| Week 39 25/9 |
Objects and classes, exceptions,
reading/writing files, .. Deitel: chapters 7 and 14, 12.1 - 12.4, 12.6. |
Codon exercise 3,
Ex. 7.3, 7.4, 7.5, 7.6, 7.7. |
|
| Week 40 2/10 |
Regular expressions, string functions, .. Deitel: Chapter 13. |
Codon exercise 4,
Regular expressions
exercise 1 (you may want to use the end() method from
this exercise in other exercises..) Ex. 13.5, 13.7, 13.8, 13.3, 13.6 (use this html code). |
|
| Week 41 9/10 |
Parsing. |
DNA
translation exercise, Random adjectives and spell
check exercise, GC
islands exercise - plus any unsolved previous exercises, both from and not from book (not much reading this week = lots of time for old exercises!). |
|
| Week 42 16/10 |
Holiday! |
Duh. | |
| Week 43 23/10 |
Holiday! |
Duh. | |
| Week 44 30/10 |
Introduction to XML, some introduction to the first
mandatory project. Deitel: Sections 15.1 - 15.5 and the essentials of 16.1 - 16.4. |
Project + old exercises | Project 1: translating to/from different sequence formats. |
| Week 45 6/11 |
Communication with External Programs.
Lecture Notes Deitel: Sections 18.3 - 18.4. |
Prior to the lecture: None
At the lecture: PM.1 - PM.4 After the lecture: CW.1-CW.4, CW.8-CW.10, optionally: CW.5-CW.7. For the exercises CW.8-CW.10, ignore the tree part unless you do CW.5-CW.7. |
Lecture Notes, with exercises PM.1 - PM.5
Clustal W Exercises, CW.1 - CW.10 |
| Week 46 13/11 |
Networking
Lecture Notes Deitel: Sections 20.1 - 20.2 the urllib manual and the HTMLParser manual. |
Prior to the lecture: N.1 - N.2
At the lecture: N.3 - N.8 After the lecture: NCBI.1 - NCBI.10 |
Lecture Notes, with exercises N.1 - N.11
NCBI Exercises, NCBI.1 - NCBI.10 |
| Week 47 20/11 |
CGI Scripts
Lecture Notes Deitel: Chap. 6 the cgi module manual and the W3C Forms Manual. |
Prior to the lecture: CGI.1 - CGI.6
At the lecture: CGI.7 - CGI.16 After the lecture: CGI-CW.1 - CGI-CW.3 |
Lecture Notes, with exercises CGI.1 - CGI.16
GUI for Clustal W Exercises, CGI-CW.1 - CGI-CW.6 Mandatory Project 2: Clustal W and NCBI Searches |
| Week 48 27/11 |
Databases 1
Lecture Notes Deitel: Chapter 17 |
At the lecture: DB1.1 - DB1.7
After the lecture: DB1X.1 - DB1X.5 |
Lecture Notes, with exercises DB1.1 - DB1.7
Database Access to Embl Exercises, DB1X.1 - DB1X.5 |
| Week 49 04/12 |
Databases 2
Lecture Notes Deitel: Chapter 17 |
Before the lecture: DB2.1
At the lecture: DB2.2 - DB2.8 After the lecture: DB2X.1 - DB2X.5 |
Lecture Notes, with exercises DB2.1 - DB2.8
A Database of Multiple Alignments Exercises, DB2X.1 - DB2X.5 Mandatory Project 3: A Database of Multiple Alignments |