cytoscape is open source network analyses tools, in this slides we define the basic features of this tool, and a brief tutorial of how can you use this tool in innovative way.

1. Social Network Analyzing
Amer Al-Hosary - Luay Al-Assadi - Molham Al-Maleh
Presented by:

2. It is an open source bioinformatics software platform
for visualizing molecular interaction networks and integrating
with gene expression profiles and other state data.
was originally created at the Institute of Systems Biology in Seattle
in 2002.

3. visualize and analyze network graphs of any kind involving nodes and
edges (e.g., social networks).
Cytoscape has a JavaScript-centric sister project named Cytoscape.js
that can be used to analyze and visualize graphs in JavaScript
environments, like a browser.
Additional features are available as Apps (formerly called Plugins).

4.  Simple interaction file (SIF or .sif format)
 Nested network format (NNF or .nnf format)
 Graph Markup Language (GML or .gml
format)
 XGMML (extensible graph markup and
modelling language).
 SBML BioPAX
 PSI-MI Level 1
 2.5 GraphML
 Delimited text
 Excel Workbook (.xls, .xlsx)
 Cytoscape.js JSON
network/pathway files written in the
following formats:
External Database.
Ontologies
…… etc.

5. SOURCE
DESTINATIO
N
Edge
attribute
Source node
attribute
target node
attribute

6. Grid Layout
The simplest layout that
Cytoscape provides is the
Grid Layout, which simply
places all of the nodes in a
grid arrangement.
Circular Layout
Hierarchical Layout
Grid is very fast, but often not very helpful.

7. Grid Layout
Circular Layout
places all of the nodes in
a circular arrangement,
Partitions the network
into disconnected parts
and independently lays
out those parts.
Hierarchical Layout
Very quick, Usually not very informative.

8. Grid Layout
Circular Layout
Hierarchical Layout
Hierarchical Layout forces
the nodes into a tree
structure
Works best when the network is naturally tree-structured
Also works reasonably well when the network is mostly
hierarchical.

9. Degree Sorted Circle
Orders the node around a
circle based on node degree
(number of edges)
Attribute Circle Layout
Group Attributes
Layout

10. Degree Sorted Circle
Attribute Circle Layout
Orders the node around
a circle based on the
value of some attribute
Group Attributes Layout

11. Degree Sorted Circle
Attribute Circle Layout
Group Attributes
Layout
Groups the nodes based
on the value of some
attribute

12. Node Style
Edge Style
Network Style

13. Node Style
Edge Style
Network Style

14. Node Style
Edge Style
Network Style

15.  Select nodes and edges
based on a node or edge
columns.
 Dynamic filtering for
numerical values.
 Build complex filters
using AND, OR, NOT
relations.
 Define topological filters
(considers properties of
near-by nodes)

16.  select attribute(s) of each source
network to identify the nodes in the
network.
 merge the attribute of source networks
into attributes in the resulting network.
 let the user decide some rule based on
priorities of networks, priorities of ID
types, etc.. Or let the user assign which
attribute value should be used for each
node
N1
N2

17. For every node in a network, NetworkAnalyzer compute:
 degree (in- and out-degrees for directed networks)
 the number of self-loops
 edge betweenness for each edge in the network
 Closeness centrality
 Betweenness centrality
 Clustering Coefficient
 Neighborhood Connectivity

18. Betweenness
centrality
Closeness centrality
How important a node is to the shortest paths through
the network
• Undirected Networks

19. Betweenness
centrality
Closeness centrality
• Directed Networks

20. Betweenness
centrality
Closeness centrality
How close a node is to all other
nodes in the network

21.  AverageShortestPathLength
Average length of a shortest path between n and any other node
 Neighborhood connectivity
 The connectivity of a node is the number of its neighbors. The
neighborhood connectivity of a node n is defined as the average
connectivity of all neighbors of n
 Stress
This attribute counts the number of shortest paths passing
through a node.

22. Sessions save pretty much everything: Networks,
Properties, Visual styles, Screen sizes
Export networks in different formats: SIF, GML,
XGMML, BioPAX, PSI-MI 1 & 2.5
Publication quality graphics in several formats: PDF,
EPS, SVG, PNG, JPEG, and BMP