CBNA 2023: Dynamic Networks Visualization

Santhust Santhust   2023-06-01   Comments Off on CBNA 2023: Dynamic Networks Visualization

Date(s) - 2023-06-01 - 2023-06-02
10:00 CEST - 16:00 CEST

Dynamic Networks Visualization

Date: 1-2, June 2023 (2 days)
Time: 10:00 – 12:00 and 14:00 – 16:00
Location: Seminar Room-13-518 + ONLINE!
Places: 12 on-site, 13 online (Total 25)

Have you come across thinking that a movie of network could be a better way of conveying the biological story you want to tell, than the static images of network? They say that a picture is a thousand words! Perhaps then, a movie is a million!

If so, then you might want to not miss this opportunity of getting to know the state of art for movie-fying your time changing biological networks.

Course goals

During this 2-days course participants will :

  • come to know which module/library can be used in Python and R to create dynamic network visualizations
  • get familiar with the module/library itself and learn basics
  • practice hands-on along with the demonstrator
  • discuss your personal use case

Yes you got it right: both Python and R. I wished to offer something to both audience. Intention is to offer one day to working in each language.

After the course you would:

  • know what resources are available
  • know what it takes to make a movie of evolving (or time-changing) network
  • be in a position to think from a new perspective to tell your story
  • not be a Pro but well begun

Course organization & philosophy

Each day follows a simple step-wise philosophy: Know, Learn, Apply (KLA).

  • Know: the features of the package
  • Learn: the basics
  • Apply: to a practical real research question

The course would make use of Reveal.js slides for step-by-step development and delivery of the course material. The commands from the slides could be copy-pasted into "Notebooks" (Python/R) and run.

Yes, you would have to make that effort at least. Yes, I could have given you .ipynb or .rmd files and you could have push one button to run all: we are not doing that!

The idea for having the presentation at our disposal is:

  • to keep a lively organized flow of the theme
  • to not loose time in typing [when needed]
    • (we will ofcourse try/test/run/fiddle with small chunks of code for better understanding.)
  • to focus on "what is available out there"
  • hands-on for those who wish to try
    (Aside: I wish you try along me. I strongly recommend. I believe, that’s when one learns the most.)


  • Most important: Laptop and enthusiasm!
  • Mild programming experience: if you have done some introductory Python/R course, that would be more than sufficient. You will not be required to write programs on own. The code will be available through slides. You can copy paste and run! And I will explain the code, ofcourse!
  • Installation: You would be required to install the packages graph-tool (Python) and ndtv (R).
    • Help available: Installation help is available for the uninitiated or when faced with problems. Please contact no less than three days before the course begins ( or
    • Recommendations: It is recommended that you install the above packages under virtual environments. For Python: Anaconda or venv. For R: renv.
  • Network science: A rough idea about networks will be useful, but not necessary in case you just want to see and increase your awareness about resources and possibilities associated with the theme. Depending on the interest/requests, a quick initiation into Network Biology can be provided.


If you would like to register to receive these announcements early, please send an empty message with the title ‘Subscribe’ to
If you have further questions please don’t hesitate to contact.


  • This course is for EMBL-all-sites only.
  • A longer version of the course can be planned/repeated depending upon the interest.


  • If you have already attended my previous course introductory course on Cytoscape, then you already have enough knowledge about biological networks.
  • There are plans to repeat the above indicated introductory course on Cytoscape followed by an intermediate course on Cytoscape.

Best wishes,


Bookings are closed for this event.