 
Summary: PHYS 597A, CMPSC 497E: Graphs and networks in sys
tems biology
Homework assignment 9, due Tuesday Nov 17
1. Read the article "Boolean network simulations for life scientists" by I.
Albert, J. Thakar, S. Li, R Zhang and R. Albert, in Source Code for Biology
and Medicine 3, 16 (2008). You can download the article from the journal's
webpage
http://www.scfbm.org/content/3/1/16
Write down three questions or ideas that you had while reading it. Follow
up on your questions and let me know what you find.
2. Construct a network of four nodes, such that each node's indegree is
one or two. Associate a Boolean rule to each node. Assume that each node's
state changes at the same time (synchronous update).
a) Determine analytically (by taking away time from the Boolean rules,
and solving the resulting system of equations) the fixed points of the system.
b) Map the state transitions in the system. Start with an initial state, and
update the state of the nodes for a sufficient number of steps for determining
the attractor. Then start from a state that was not encountered yet, and
repeat until all states were considered. Draw a state transition network in
which the nodes are the states of the system and the directed edges mean
