This document discusses systems biology and some of its tools. It defines systems biology as the study of interactions between parts of biological systems to understand how they function. Biological networks involve interactions between pathways. Networks can be modeled as nodes and edges. Tools described for modeling and analyzing networks include Cytoscape for visualization, CellDesigner for drawing networks, and STRING for protein-protein interaction data. Databases of pathways, interactions and models are also listed.

1. SYSTEMBIOLOGY AND ITS TOOLS
BY
GAURAVDIWAKAR
44820

2. Systems Biology Definition:
• A field that seeks to the study of relationships and
interactions between various parts of a biological
system (metabolic pathways, organelles, cells and
organisms) and to integrate this information to
understand how biological systems function.
• Systems biology is a relatively new biological study
field that focuses on the systematic study of complex
interactions in biological systems.

3. What is a biological network?
• Researchers are learning that biological
pathways are far more complicated than once
thought. Most pathways do not start at point A
and end at point B. In fact, many pathways
have no real boundaries, and they often work
together to accomplish tasks. When multiple
biological pathways interact with each other, it
is called a biological network.

4. Biology Networks
A network is a set of nodes and a set of directed or undirected
edgesbetween the nodes.
Transcriptional Regulatory Network:
• Gene are the nodes and edges are directed
Signal transduction network:
• Proteins are nodes and edges are directed
Metabolite network:
• Metabolite are nodes and edges are directed

5. Parameter of Biological network
• Degree: the degree of a node in a network is
the number of connections it has to other
nodes
• Diameter: largest distance between any two
nodes in the network
• Average path length: Average distance
between any two nodesin the network

6. • Betweenness centrality: It is an indicator of a
node's centrality in a network. It is equal to
the number of shortest paths from all vertices
to all others that pass through that node.
• Clustering coefficient: A measure of the
degree to node which tend to cluster together

7. Database resources for System Biology
• Microarray gene expression database
• ArrayExpress (http://www.ebi.ac.uk/microarray-as/ae/)
• GEO (http://www.ncbi.nlm.nih.gov/geo/)
• CIBEX ( http://cibex.nig.ac.jp/index.jsp)

8. • Protein-protein interaction database
• BINDplus (Biomolecular Object Network Database)
http://www.thomsonreuters.com/products_services/scientific/BINDp
lus
• DIP(The Database of Interacting Proteins) http://dip.doe-
mbi.ucla.edu/dip/Main.cgi
• MINT(The Molecular INTeraction database)
http://mint.bio.uniroma2.it/mint/Welcome.do
• STRING(Search Tool for the Retrieval of Interacting
Genes/Proteins)
http://string.embl.de/

9. • Pathway database
• KEGG(Kyoto Encyclopedia of Genes and Genomes)
http://www.genome.jp/kegg/
• REACTOME() http://www.reactome.org/
• MetaCyc http://metacyc.org/
• EcoCyc http://ecocyc.org/

10. • KEGG: Kyoto Encyclopedia of Genes and Genomes:
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a
bioinformatics resource for linking genomes to life and
the environment.
• EcoCyc: Encyclopedia of Escherichia coli K-12 Genes
and Metabolism: EcoCyc is a scientific database for the
bacterium Escherichia coli K-12 MG1655. The EcoCyc
project performs literature-based curation of the entire
genome, and of transcriptional regulation,
transporters, and metabolic pathways.

11. • BioModels Database: BioModels Database is a
data resource that allows biologists to store,
search and retrieve published mathematical
models of biological interests.
• BiGG Database: The BiGG database is a metabolic
reconstruction of human metabolism designed
for systems biology simulation and metabolic flux
balance modeling. It is a comprehensive
literature-based genome-scale metabolic
reconstruction that accounts for the functions of
1,496 ORFs, 2,004 proteins, 2,766 metabolites,
and 3,311 metabolic and transport reactions. It
was assembled from build 35 of the human
genome. Need an username and password.

12. Network Visualization Tools
• Cytoscape ( http://www.cytoscape.org/)
• BioTapestry (http://www.biotapestry.org/)
• BioUML ( http://www.biouml.org/)
• CADLIVE ( http://www.cadlive.jp/)
• Edinburgh Pathway Editor
(http://www.bioinformatics.ed.ac.uk/epe/)

13. Modeling &Simulation tools
• CellDesigner http://www.celldesigner.org/
• Jarnac/JDesigner http://sbw.kgi.edu/
• COPASI http://www.copasi.org/
• E-Cell http://www.e-cell.org/

14. Cell Desginer
• CellDesigner is a structured diagram editor for
drawing gene-regulatory and biochemical
networks. Networks are drawn based on the
process diagram, with graphical notation
system proposed by Kitano, and are stored
using the Systems Biology Markup Language
(SBML).

19. Cytoscape
• Cytoscape is an open source bioinformatics
software platform for visualizing molecular
interaction networks and integrating these
interactions with gene expression profiles and
other state data.

23. Layouts
• 12 algorithms available through plugins
• Zooming, hide/show, alignment

24. yFiles Organic

25. yFiles Circular

27. Network Parameters

28. Graph Analysis

30. Protein-Protein Interaction Database
• STRING (Search Tool for the Retrieval of Interacting
Genes/Proteins) is a biological database and web resource
of known and predicted protein-protein interactions.
• The STRING database contains information from
numerous sources including:
Experimental data
Public text collections.
• It is freely accessible and it is regularly updated.
• The latest version 10.0 contains information on about 5.2
millions proteins from 1133 species.

31. Step 1

32. Step 2

33. Step 3

34. Step 4

35. Network parameter

36. SWISS MODEL
• SWISS-MODEL is a fully automated protein
structure homology-modelling server,
accessible via the ExPASy web server, or from
the program DeepView (Swiss Pdb-Viewer).
The purpose of this server is to make Protein
Modelling accessible to all biochemists and
molecular biologists worldwide.
• https://swissmodel.expasy.org

42. APPLICATION OF SYSTEM BIOLOGY
• System biology in Crop improvement
• System biology in drug discovery
• Network biology
• Topological analysis of Biological network

43. THANK YOU