Systems Biology

Sections in this chapter include:

• Install Cytoscape
• Create network from csv file
• Network of co-authors
• NDEx Webapp example
• List of of operations example
• ImmPort gene list example
• Gene Ontology database example

Systems Biology

Background

Systems biology, while a relatively new term in the field of molecular biology, describes mathematical and computer science approaches to studying how biological systems are put together. Systems approaches in biology can be characterized as derived from the view that “[b]ecause a system is not just an assembly of genes and proteins, its properties cannot be fully understood merely by drawing diagrams of their interconnections (p. 1662, Kitano 2002)” — in other words, drawing the connections in the network are just a first step. Systems biology “… is built on molecular biology in its special concern for information transfer, on physiology for its special concern with adaptive states of the cell and organism, on developmental biology for the importance of defining a succession of physiological states in that process, and on evolutionary biology and ecology for the appreciation that all aspects of the organism are products of selection, a selection we rarely understand on a molecular level” (p. 504, Kirschner 2005). I was introduced to systems approaches while a graduate student (working on individual variation in energetics and locomotor performance) at the University of Wisconsin-Madison; work by others focused on systems approaches, including an emphasis on lake ecosystems as an extensive research effort in the Limnology department, and Dr Warren Porter’s energetics modeling in biophysical ecology in the then Department of Zoology (now Integrative Biology).

What’s included

Materials presented here support my teaching of a Systems Biology course at Chaminade University. This portion of the manual is very much a work in progress — R scripts and Cytoscape how-tos are the primary content, with more to come in 2025 as I prepare for teaching the course for a third time in Spring 2026. Stay tuned!

References

Kirschner, M. W. (2005). The Meaning of Systems Biology. Cell, 121(4), 503–504.

Kitano, H. (2007). Towards a theory of biological robustness. Molecular Systems Biology, 3, 137.

/MD