Introduction to Ontologies, Pathways, and Networks

Introduction to Ontologies, Pathways, and Networks

Dates: 04 – 06 October 2016
Location: Seminar Room 202, Heidelberg
Requirements: laptops and enthusiasm
This course is free and open to all, including outstations.
During the workshop you will learn how to perform a range of basic computational tasks in analysis and
visualisation of biological data using online tools and Cytoscape.

You will learn how to:

• Use public resources (databases such as String, pathway tools e.g. Reactome, and text mining) to explore their data
• Construct biological networks, import and integrate experimental data
• Apply basic concepts in visualisation to analyse, and interpret biological information.
• Perform enrichment and depletion tests against ontologies and pathway databases

Schedule details:

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Day 1
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1. Introduction to network biology
• Introduction to Cytoscape
• Loading and manipulating networks
• Integrating experimental data



2. Visualizing data on networks

• Visual Styles – how to make pretty graphics
• Automatic layouts can improve visualisations
• Using data to enhance network graphics – displaying pie-charts, heatmaps,
  line charts etc. on networks

3. Filtering complex networks using experimental measurements and metadata
4. Protein/gene/transcript identifier systems such as Entrez, Ensembl, UniProt explained

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Day 2
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1. Using web services: String, IntAct, Complex Portal, Reactome, Kegg


2. Automating the retrieval of data from public resources

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Day 3
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1. Enrichment analysis using ontologies (GO, KEGG, Reactome, Complexes, Drugs, Diseases)
2. BYOD – bring your own data

Bookings