Introduction to Ontologies, Pathways, and Networks (2019)

Matt Rogon   2019-05-27   Comments Off on Introduction to Ontologies, Pathways, and Networks (2019)

Date(s) - 2019-05-27 - 2019-05-29
09:30 CEST - 16:30 CEST

Introduction to Ontologies, Pathways, and Networks

Dates: 27 – 29 May 2019
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 bioinformatics tasks in analysis and
visualisation of biological data using online tools, databases, and Cytoscape.

You will learn how to:

  • Use public resources (databases such as String, pathway tools e.g. Reactome, and text mining) to explore data
  • Use Cytoscape as the main platform for bio-data analytics,
  • Construct biological networks, import and integrate experimental data
  • Apply basic concepts in visualisation to analyse, and interpret biological information.
  • Perform enrichment tests against ontologies (gene, disease, drug) and pathway databases.

Schedule details:

Day 1

    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

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

2. Automating the retrieval of data from public resources

  • protein-protein interaction data (overview and usage of interaction databases)
  • integrative databases – introduction to STRING, IntAct
  • pathway databases – Reactome and KEGG
  • protein complexes – Complex Portal, Corum
  • how to do text mining
  • downloading entire interactomes
  • ——————————————————————————
    Day 3

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

    Registration closes May 19th at 4pm.

    Once the course is full you are welcome to send an empty email with the title “waiting list: IOPN2019” to
    You will be placed on a waiting list.


    Bookings are closed for this event.