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

The pipettepen http://www.thepipettepen.com/a-picture-is-worth-a-thousand-words-or-more/

Drawings can have a lot of details

https://www.tintin.com/en/albums/king-ottokar-s-sceptre © Hergé - Moulinsart 2021

Or can have only the essential

https://xkcd.com/1954/ 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

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

Advantages:

You can draw the way you want

Disadvantages:

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: https://graphviz.org/

Online editors:

Example

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

Science example

digraph {
rankdir=LR;
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 }
}

Standardization

Another picture from WNT pathway