This is the home page for the Collaboratory Workshop, Introduction to Protein Protein Interactions and Cytoscape.
Slide Handouts and Schedule [Legacy Handouts]
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Day 1 [Handout]:
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Experimental Methods
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Experiment uncertainties
- Ambiguous interaction types
- Ambiguous protein identification
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Database Record Contents
- Binary expansion
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Database Record Formats
- PSI-MI MIF/MITAB
- BioGRID
- Cytoscape (.sif)
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Protein Interaction Resources
- Primary Databases
- Integrators
- Web Services
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Day 2 [Handout]:
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Interaction Data Processing
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PSI-MI MIF Format
- Record structure
- Compact vs expanded form
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PSI-MI Controlled Vocabulary
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Parsing XML Files
- Python lxml toolkit
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SIF (Cytoscape) Format
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MIF to SIF conversion
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Day 3 [Handout]:
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Introduction to Cytoscape
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Interaction Networks
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Cytoscape Overview
- Installation
- Basic features
- Apps/Plugins overview
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Loading Interaction Data
- Local files
- Public resources
- Network Annotation
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Basic Network Visualization
- Node/Edge Attribute Mapping
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