27-30 November 2017
Max Planck Institute for Biology of Ageing
Europe/Berlin timezone

Program

We are happy to announce 3 full blown workshops with the Cytoscape team in Cologne.

Workshop 1: Protein-protein interactions workshop (introductory)

Date: 27.11.2017 - 28.11.2017
Location: Auditorium, Max Planck Institute for Biology of Ageing - http://age.mpg.de
Attendees limit: 96

Workshop 2: Cytoscape automation (advanced)

Date: 30.11.2017
Location: Auditorium, Max Planck Institute for Biology of Ageing - http://age.mpg.de
Attendees limit: 96

Workshop 3: Cytoscape Train the trainer with the Cytoscape Team

Date: 29.11.2017
Location: Seminar room 1, Max Planck Institute for Biology of Ageing - http://age.mpg.de
Attendees limit: 20

Speakers

  • Alexander Pico is the Executive Director of the National Resource for Network Biology, the Vice President of the Cytoscape Consortium, and Associate Director of Bioinformatics at Gladstone Institutes in San Francisco, CA. He has been a contributing member to Cytoscape since 2006 and has led numerous Cytoscape and Network Biology workshops and mentoring programs over the past 10 years.

  • John “Scooter” Morris is the Executive Director of the Resource for Biocomputing, Visualization, and Informatics at UCSF, the “Roving Engineer” for Cytoscape, and an Adjunct Assistant Professor of Pharmaceutical Chemistry at UCSF. He has given numerous presentations on using and extending Cytoscape and is a Cytoscape core developer as well as the developer of over a dozen Cytoscape apps, including chemViz, structureViz, clusterMaker, and cddApp.

  • Barry Demchak is the Chief Architect of Cytoscape, Secretary/Treasurer of the Cytoscape Consortium and Project Manager in the Ideker lab at UCSD. He has been a contributing member to Cytoscape development since 2012 and has led numerous Cytoscape and Network Biology workshops and mentored projects over the past 5 years.

  • Protein-protein interactions workshop (introductory)

    Date: 27.11.2017 - 28.11.2017

    Interactions between proteins, proteins and small molecules, and proteins and nucleic acids drive much of biological function. In this brief workshop-style course, we'll explore some of the tools and approaches to analyzing and visualizing these interactions at both the network (e.g. pathway) and molecular levels. We'll begin with a brief introduction to protein-protein interactions, including sources of experimental data and the current primary data repositories followed by a discussion of network approaches to visualizing and analyzing these interactions. Students will then learn how to use Cytoscape, which is an open-source tool for network analysis and visualization. Next, we'll talk about interactions at the molecular level and experimental and computational techniques for determining the molecular basis of these interactions. Students will then learn how to use UCSF Chimera, a tool for modeling and visualizing biological structures. Finally, using these tools, students will explore the function of a protein-protein interaction.

    Topics covered:
    Protein interactions and their role in biological function
    Basics of network approach to protein interactions
    Experimental sources of data
    Data repositories
    Network visualization and analysis using Cytoscape
    Basics of the structural approach to protein interactions
    Experimental sources of data
    Data repositories
    Structural visualization and modeling using UCSF Chimera
    Utilizing networks and structures to understand biological function

    Agenda:
    Day 1
    10:00 - 11:00: Introductions - Why are protein-protein interactions important?
    11:00 - 12:30: Protein-protein interaction networks - I
    - Getting the data
    12:30 - 13:30: Lunch
    13:30 - 15:00: Protein-protein interaction networks - II
    - Network approaches to visualizing and analyzing protein-protein interactions
    - Introduction to Cytoscape - I
    15:00 - 15:30: Break
    15:30 - 17:00: - Introduction to Cytoscape - II
    - Hands-on
    17:00 - 18:00: Workflows

    Day 2
    09:00 - 10:30: Protein-protein interactions at the molecular level - I
    10:30 - 11:00: Break
    11:00 - 12:30: Introduction to UCSF Chimera
    12:30 - 13:30: Lunch
    13:30 - 15:00: Comparative Modeling with UCSF Chimera
    15:00 - 15:30: Break
    15:30 - 17:00: Work on your own data

  • Cytoscape automation (advanced)

    Date: 30.11.2017

    Cytoscape is one of the most popular desktop applications for network analysis and visualization. In this workshop, we will demonstrate new capabilities to integrate Cytoscape into programmatic workflows and pipelines, for example in R and Python. We will being with an overview of network biology themes and concepts, and then we’ll translate these into Cytoscape terms. The bulk of the workshop will be a hands-on demonstration of accessing and controlling Cytoscape from R to perform a network analysis of tumor expression and variant data.

    Prerequisites:
    Prior experience with R or Python
    Some familiarity with Cytoscape (i.e., at least install it and play around before the workshop)

    Topics covered:
    When and how to use Cytoscape in your research area
    Relevant sources of interactions, networks and pathways
    Programmatic control over Cytoscape
    Integration of Cytoscape into your bioinformatics pipelines
    How to publish, share and export networks

    Agenda:
    09:30-10:00: Introductions to network biology and Cytoscape
    10:00-10:30: Finding and assessing types of networks, sources, and relevant apps
    10:30-11:00: Break
    11:00-12:00: Network visualization: data overlays & layouts
    12:00-12:30: Network analysis: topological & data-driven
    12:30-13:30: Lunch
    13:30-14:00: Overview of Cytoscape Automation and setup
    14:00-14:30: Loading disease network into Cytoscape via R
    14:30-15:00: Break
    15:00-16:30: Interacting with Cytoscape
    - CyREST, Commands and r2cytoscape package
    - Visualizing data on networks
    - Loading multiple data types into Cytoscape
    - Setting visual styles
    - Subnetwork selection
    - Data-driven and diffusion-based subnetworks
    - Saving, sharing and publishing
    16:30:17:00: Additional Topics and Q&A

  • Cytoscape Train the trainer with the Cytoscape Team

    Date: 29.11.2017

    The objective of this workshop is to prepare trainers on how to help and instruct others on cytoscape.

    (more information soon)

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