Introduction to Complex Systems
Semester II, 2006
comp4006 and comp7011

Course Profile
comp4006, comp7011

Assessment
deliverables

CxSys
Software

Further
Readings

Newsgroup
uq.itee.comp4006

Project suggestions

Archive: Complex systems in 2005 comp4001 

LECTURES are open to all UQ staff and students. Labs are for enrolled students only.
Lectures: Monday 2-4pm in 78-420, starting from week 1.
Labs: Tuesday 11am-1pm in 78-110, starting from week 1.

Wk

Date

Proposed Schedule (subject to change)

1

24 Jul

2pm Janet Wiles Introduction to Complex Systems
3pm Invited lecture: Prof Michael Ward – Complex Systems Challenges in Healthcare, (slides, data)

2

31 Aug

2pm Janet Wiles Network Analysis
3pm Invited lecture: Prof Jennifer Stow, IMB
 CPM (references to slides)

3

7 Aug

2pm Janet Wiles Agent Based Modelling
3pm Invited lecture: Kathryn Kerr, Auscert

4

14 Aug

Jim Hanan L-Systems Modelling http://algorithmicbotany.org/virtual_laboratory/

5

21 Aug

Janet Wiles
Part 1. Challenges in Biocomplexity, Part 2 Navigation

6

28 Aug

Mikael Boden
Evolutionary Computation (slides 2pp or 6pp) (Evolving critters applet) (Mitchell and Forrest, 1993) (Downs, Evolutionary Computation)

7

4 Sep

Mikael Boden
Evolutionary Computation (slides 2pp or 6pp)
Biological systems and data (slides 2pp or 6pp)

8

11 Sep

Mikael Boden
Finding Patterns in biological data (slides 2pp or 6pp) (Bertone and Gerstein, 2001)

9

18 Sep

Andre Leier (slides pdf)
Systems Biology I – Introduction (feedback on questions)

Break

10

2 Oct

Andre Leier (slides pdf) – slides will be available the day before the lecture
Systems Biology II – Modelling of GRNs (feedback on questions)

11

11 Oct

Andre Leier (slides pdf) – slides will be available the day before the lecture
Systems Biology III – The Role of Noise: From ODEs to Stochastic Simulations (feedback on questions)

12

16 Oct

Andre Leier (slides pdf) – slides will be available the day before the lecture
Systems Biology IV – Delays: From DDEs to DSSA (feedback on questions)

13

23 Oct

Review (L1-3,5-ppt) (L6-8)

15-16

6-17 Nov

Exam period
Sample exam format
Sample questions from lectures 1-5
Sample questions from lectures 6-8
Sample questions from lectures 9-12

Requirement
& Marks

Deliverable Components
All assignments are available from wk 1
Assessment criteria are provided with the assignment sheet

Time estimate
(total 130 hours)

Advice / Handouts/Feedback

Participation (10%)

Wks 1-13

Marks will be given for participation in class.

Lectures: 26 hrs
Labs: 6 hrs  (includes 6 hrs prep)

Participation means taking part in class discussions, asking and answering questions. Students who prefer not to speak during the class may hand in written questions for the lecturer at the end of the class.

Asgt 1 (10%)

Wk 4

Asgt 1a. Summary of a software tool (5%)

6 hours

Online submission is at
http://submit.itee.uq.edu.au/select.php?coursecode=COMP4006
ITEE asgt cover sheet (required for all asgts) (.pdf)

Wk 5

Asgt 1b. Presentation & Demo (5%)

6 hours

Asgt 2. Project (50%)

Wk 8

Asgt 2a. Proposal and lit review (10%)

20 hours

Wk 13

Asgt 2b. Project report (40%)

60 hours

Exam (30%)

Study in your own time

Week

Date

DRAFT (will be finalised in week 1)
Tutorials

1

Introduction to software packages for complex systems modelling

2

Network analysis using Pajek
Lab sheet: Tutorial 2
Network file: Yeast data
Background Readings:
Strogatz, S.H. (2001). Exploring Complex Networks, Nature 410, p. 268-276 (local copy).
Watts, D.J, and Strogatz, S.H. (1998). Collective Dynamics of Small World Networks, Nature 393, p. 440-442 (local copy).

3

Cellular Automata using NetLogo (pdf)
Readings:- Original 1970 Scientific American article on Conway?s Game of Life.
Wolfram’s 1983 Science paper on Cellular Automata

4

Student simulation package reviews

5

Project work

6

Project work

7

Project work

8

Project work

9

Project work

10

Project work

11

Project work

12

Project work

13

Project work

15-16

Exam period (no classes)