Class 12: Drawing biological graphs

Systems Biology

Andrés Aravena, PhD

November 23, 2021

What is Science

The role of science is to create (or discover) new knowledge about nature

This knowledge is given as explanations of phenomena we observe

The scientific method

Graphs in Science

Explanations can be given in text or in drawings

A picture is worth a thousand words… or more

Drawings can have a lot of details

Or can have only the essential This work is licensed under a Creative Commons Attribution-NonCommercial 2.5 License.

WNT pathway

Naito et al. Wnt signaling and aging-related heart disorders. doi:10.1161/CIRCRESAHA.110.223776

Another explanation of WNT pathway

Sawa H., Korswagen H. C. “Wnt signaling in C. elegans” (December 9, 2013), WormBook, doi:10.1895/wormbook.1.7.2, http://www​ Copyright: © 2013 Hitoshi Sawa and Hendrik C. Korswagen.

Which one is better?

Less, but better

Scott McCloud (1993) “Understanding Comics: The Invisible Art”

Abstraction means generalization

Making your own drawing

PowerPoint: you already have it


  • You can draw the way you want


  • You must decide how to draw each part
  • You must do it manually, every time

Only good for simple things

Graphviz is open source graph visualization software

Describe your graph, the computer draws it for you

Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks

Official site:

Online editors:


digraph dogma {
DNA -> Transcription -> RNA -> Translation -> Proteins
Transcription [shape=box]
Translation [shape=box]

Science example

digraph {
node [shape=box];
edge [arrowhead=open; arrowtail=open];
test  -> prediction -> explanation [dir=back];
nature -> observation -> pattern -> question -> explanation;
observation -> knowledge -> "peer-review" -> test [dir=back];
{rank=same nature "peer-review" test}
{rank=same observation knowledge prediction}
{rank=same pattern question explanation }


Another picture from WNT pathway

Naito et al. Wnt signaling and aging-related heart disorders. doi:10.1161/CIRCRESAHA.110.223776

and this

and this also

The need for standardization

The Systems Biology Graphical Notation is a project by the most important researchers in this area, including:

  • Nicolas Le Novère
  • Ugur Dogrusoz
  • Kurt Kohn
  • Hiroaki Kitano

Example: Phosphorylation of ERK

We can immediately understand the meaning

Three levels of description

Same without colors



Draw your work:

  • What is your hypothesis?
  • What is the model you are trying to test?

The End Dilbert by Scott Adams © 2021, Andrews McMeel Syndication