The The structure of molecular & cellular networks networks
To be able to construct and analyze a cellular network, we need to clearly define what we identify as a node and what we represent with an edge. The nodes and edges have to be at least similar to
CMPSC 497E: Graphs and networks in systems biology
Project assignment 1, due Tuesday Oct. 20
It is now time to decide your term project topics. As a reminder, your will write a term paper due on the Monday after classes end. Your term paper should be a co
PHYS 597A, CMPSC 497E: Graphs and networks in systems biology
Project assignment 2, due Tuesday Nov. 8
This assignment represents the rst component of your term project. The goal is to write a rst draft of your paper, with a clear motivation and denition
PHYS 597A, CMPSC 497E: Graphs and networks in systems 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 a
PHYS 597A, CMPSC 497E, Graphs and Networks in Systems Biology
Homework 8, due Tuesday Nov. 3
1.
Perform a topological analysis of the network below. Consider that edges terminating in edges are directed toward the endpoint of the edge (e.g. the edge from
PHYS 597A, CMPSC 497E: Graphs and networks in systems biology
Homework assignment 7, due Tuesday Oct. 27
1. Based on what we have learned in class so far, answer the following questions in your own words. You can support your answer with formulas but form
PHYS 597A, CMPSC 497E: Graphs and networks in systems biology
Homework assignment 6, due Tuesday Oct 13
Read chapter VII, Scale-free Networks, sections A-D.3 (pages 71-75) and chapter VIII, The Theory of Evolving Networks, sections A-F (pages 7683) of Sta
PHYS 597A, CMPSC 497E: Graphs and networks in systems biology
Homework assignment 5, due Tuesday Oct. 6
1. The Sept. 24 lecture surveyed a number of graph processing and visualization tools. Install one of them and use it to draw and analyze a graph. Prov
PHYS 597A, CMPSC 497E: Graphs and networks in systems biology
Homework assignment 4, due Tuesday Sept. 29
Read Systems-level insights into cellular regulation: inferring, analyzing, and modeling intracellular networks.
1. Write down four questions or idea
PHYS 597A: Graphs and networks in systems biology
Homework assignment 3, due Thursday Sept. 17
Construct a graph with 10 nodes and 15 undirected edges. Determine (a) the distance distribution (remember that not having a path corresponds to an innite dista
PHYS 597A: Graphs and networks in systems biology
Project assignment 1, due Tuesday Oct. 20
It is now time to decide your term project topics. As a reminder, you will give an in-class presentation on your projects during the last two weeks of the semester
Ecological Networks Ecological Networks
15 September 2009
Types of ecological networks Types of ecological networks
Community
nodes: species links: interactions between species p
Population
nodes: populations of one species nodes: populations of one s
Community structure in networks
Many real-world networks, especially social ones, exhibit community structure (also called modularity). Intuitively community structure can be defined as the existence of subgraphs that are densely connected but sparsely i
Community structure in networks
Many real-world networks, especially social ones, exhibit community structure (also called modularity). Intuitively community structure can be defined as the th existence of subgraphs that are densely connected but sparsel
Properties of real networks: degree distribution
10 10 10 10 10
0 -1 -2 -3 -4
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10
2
10
3
.5
1 loglog
1 0.6
semilog
Plotting power laws and exponentials Nodes with small degrees are most frequent. The fraction of highly connected nodes decreases,
Properties of real networks: degree di distribution
Nodes with small degrees are most frequent. The fraction of highly connected nodes decreases, but is not zero. Look closer: use a logarithmic plot.
10 10 10 10 10
0 -1 -2 -3 -4
10
0
10
1
10
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10
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.5
1 l
Graph concepts
Graphs are made up by vertices (nodes) and edges (links). An edge connects two vertices, or a vertex with itself loop. AC, AC - multiple edges BB loop The shape of the graph does not matter, only the way the nodes are connected to each othe
Graph concepts
Graphs are made up by vertices (nodes) and edges (links). (li An edge connects two vertices, or a vertex with itself loop. AC, AC - multiple edges BB loop The shape of the graph does not matter, only the way the nodes are connected to each
Networks, networks everywhere
Network infrastructure, social networking Network - a tool for understanding complex systems Many non-identical elements connected by diverse interactions E.g. interaction networks within cells: protein interactions, chemica
CMPSC 497E: Graphs and networks in systems biology
Homework assignment 3, due Thursday Sept. 17
Construct a graph with 8 nodes and 12 undirected edges. Determine (a) the distance distribution (remember that not having a path corresponds to an innite dista
PHYS 597A: Graphs and networks in systems biology
Homework assignment 2, due Thursday Sept. 10
1. Construct a graph or digraph with 15 nodes and 20 edges. Extra credit will be given for using the digraph framework. Determine (a) the degree distribution of
CMPSC 497E: Graphs and networks in systems biology
Homework assignment 2, due Thursday Sept. 10
1. Construct a graph or digraph with 10 nodes and 15 edges. Extra credit will be given for using the digraph framework. Determine (a) the degree distribution o
The two faces of network dynamics
Evolving network models describe the dynamics/assembly/evolution network models describe the dynamics/assembly/evolution of networks by the addition/removal of nodes and edges. It is possible to have network dynamics even
Topological perturbation of complex networks networks
Perturbations in complex systems can deactivate some of the edges or nodes. Edge loss: the edge is deleted Edge loss: the edge is deleted Node loss: the node and all its edges are deleted Effects on th
Topological perturbation of complex networks
Perturbations in complex systems can deactivate some of the edges or nodes. Edge loss: the edge is deleted Node loss: the node and all its edges are deleted Effects on the global topology:
Resilience to perturb
Network models
Properties common to many large-scale networks, independently of their origin and function: 1. The degree and betweenness distribution are decreasing scale - free functions, usually power-laws. 2. The distances scale logarithmically with th
Network models
Properties common to many large-scale networks, independently of their origin and function: 1. The degree and betweenness distribution are decreasing Th di scale - free functions, usually power-laws. 2. The distances scale logarithmically w
Network models random graphs
Properties common to many large-scale networks, independently of their origin and function: 1. The degree and betweenness distribution are decreasing functions, usually power-laws. 2. The distances scale logarithmically with t