Thermodynamics ,types of system,formulae ,gibbs free energy .pptx
Quick Introduction to Cytoscape for Undergraduates
1. Biological Network Visualization with Cytoscape
Keiichiro Ono
Cytoscape Core Developer Team
UC, San Diego Trey Ideker Lab / National Resource for Network Biology
!
5/12/2014 Workshop for Undergraduate Bioinformatics Club at UCSD
8. Outline
• Part 1: Introduction to Cytoscape
• What is Cytoscape?
• Basic Features
• Part 2: Hands-On Tutorial
• Visualize gene expression
values and network
• Import data from public
databases (optional)
10. An Open Source Platform for Biological Network Data
Integration, Analysis and Visualization
Cytoscape
11.
12. Cytoscape
- Open Source (LGPL)
- Free for both commercial and academic use
- Developed and maintained by universities,
companies, and research institutions
- De-facto standard software in biological network
research community
- Expandable by Apps
- This is why Cytoscape is a Platform, not a
simple desktop application
37. Cytoscape Apps
- Extension programs to
add new features to
Cytoscape (were called
Plugins)
- Large App developer/
user community
- This is why Cytoscape
is so successful in life
science community!
39. Quick Overview of Apps
A travel guide to Cytoscape plugins
!
Rintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski, Peng-
Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey Ideker (2012)
Nature Methods 9 (11) p. 1069-1076
46. Tools
• In some cases, you can finish exact same tasks using different tools
• Example: Data preparation (cleansing)
• But if you choose right tools, you can do it 100x faster than
others.
• ex: Re-formatting complex data sets
• Excel vs Python Script
• Some recommendations:
• R/Bioconductor, Python/Pandas, Git/GitHub/Gist
50. - Goal: Help others to
understand your data
- Emphasize what you
want to tell
- Use color, shape,
size of objects
effectively!
- Excellent resource for
data visualization
- Tamara Munzner’s Web Site:
http://www.cs.ubc.ca/~tmm/
Data Visualization
54. Design is complicated,
because humans are complicated.
Design is a process to avoid bad designs.
Mike Bostock (New York Times Visualization Team. Creator of D3.js)
55. It is hard to generalize the design process, but we
can avoid pitfalls by following some basic rules.
58. Avoid Data Overload
• Mapping too many attributes makes your visualization
awful!
• It is hard to see the overall trend of your data sets if too
many channels are used in a image
68. Navigation
- Pan: Middle-Click + Drag or
Command + Left-Click + Drag on Mac
- Zoom
- IN: Mouse Wheel UP
- OUT: Mouse Wheel DOWN
- Selection: Left-Click and Drag
- Fit to Window
- Selected region
- Entire network
74. NCBI Gene ID 672
On Chromosome 17
GO Terms
DNA Repair
Cell Cycle
DNA Binding
Ensemble ID
ENSG00000012048
BRCA1
75. Data Tables for Cytoscape
- Example:
- Numeric
- Gene expression profiles
- Network statistics calculated in other
applications, such as R
- Confidence scores for edges
- Text (or categorical)
- GO annotation for genes
- List of genes related to disease X
- Targets for FDA approved drugs
- Genes on KEGG Pathway Y
- Clusters / group / community calculated
in external programs
- …
76. Your Data Sets
- Anything saved as a table can be
loaded into Cytoscape
- Excel
- Tab Delimited Document
- CSV
- As long as proper mapping key is
available, Cytoscape can map them to
your networks.
89. Visual Styles
- Defaults + Mappings
- Expression values to node color
- Gene function to node shape
- Interaction detection method to edge line
type
- Confidence score to edge width
91. Data Controls The View
• Photoshop / Illustrator
• You control the pixels and objects on the display
• Data Visualization Tools (including Cytoscape)
• Data points are mapped to visual properties
• Color
• Size
106. What is cytoscape.js?
A Javascript Library for network visualization,
not a web application!
Need to write some code to use it on the web browsers…
107. Complete desktop
application for network
analysis and visualization
!
Written in Java
!
Expandable by Apps
!
For Users
A Javascript Library for
network visualization,
not a web application!
!
Written in JavaScript
!
Expandable by Extensions
!
For Developers
JS
115. Further Readings
• My presentation slides
• http://www.slideshare.net/keiono
• (This deck of slides will be uploaded tonight)
116. Further Readings 1
- Introduction to Network Biology
- Deciphering Protein–Protein Interactions. Part I. Experimental
Techniques and Databases
Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein
Interactions. Part I. Experimental Techniques and Databases. PLoS
Comput Biol 3(3): e42.doi:10.1371/journal.pcbi.0030042
- Deciphering Protein–Protein Interactions. Part II. Computational
Methods to Predict Protein and Domain Interaction Partners
Shoemaker BA, Panchenko AR (2007) Deciphering Protein–Protein
Interactions. Part II. Computational Methods to Predict Protein and
Domain Interaction Partners. PLoS Comput Biol 3(4): e43. doi:10.1371/
journal.pcbi.0030043
117. Further Readings 2
- Overview of Cytoscape Apps (Plugins)
- A travel guide to Cytoscape plugins
Rintaro Saito, Michael E Smoot, Keiichiro Ono, Johannes Ruscheinski,
Peng-Liang Wang, Samad Lotia, Alexander R Pico, Gary D Bader, Trey
Ideker (2012) Nature Methods 9 (11) p. 1069-1076
- Sample Protocol (based on 2.x)
− Integration of biological networks and gene expression data using
Cytoscape
Cline, et al. Nature Protocols, 2, 2366-2382 (2007).
118. Further Readings 3
- Cytoscape Tutorial Booklet:
Analysis and Visualization of Biological Networks with Cytoscape
- http://www.rbvi.ucsf.edu/Outreach/Workshops/ISMBTutorial.pdf
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