Biological networks and Systems Biology
What is Systems Biology?
Probably the most abused term in biology today.
Let's try an unconventional definition: The first Systems Biology was Ira Herskowitz, who wrote the book on lamdba and several chapters on Saccharomyces cerevisiae. He never ran a gel or did a microarray experiment, let he was continuously looking at the big picture, the system that made an organism do what it does: He placed findings in context.
A loose definition: Systems Biology has to do with with networks (regulatory, metabolic...) and different -omes.
Model organisms
Escherichia coli, Saccharomyces cerevisiae, Xenopus laevis,
Drosophila melanogaster, Caenorhabditis elegans, Zebrafish, Mus musculus and baboon,
Arabidopsis thaliana
All of the models exist to better understand ourselves: Homo sapiens (aka human)
Yeast: the ultimate model?
First eukaryotic genome to be sequenced (1996: Life with 6000 genes)
16 chromosomes, 1 mitochondrial chromosome. About 17 million bps (Chr III 300 K bps: first sequenced and most well-studied). About 6000 genes.
Let's talk about pathways
Important: pathways don't exist in nature: they are solely concepts to wrap our minds around partial information.
Not all pathways are created equal. we can extend the central dogma of molecular biology to a central dogma of systems biology:
DNA -> RNA -> protein -> protein complex -> metabolite
Pathways in S. cerevisiae
Pathways in A. thaliana
An alternate take on plant metabolic pathways
Now look at a more complete view of Glycolysis or TCA cycle
Pathways in other organisms
The 3 Is of Systems Biology: Integration, integration, integration
Genomics, proteomics, metabolomics, ...
Different pathway databases
Cytoscape
Start cytoscape from the command prompt with Cytoscape &.
Let go through some tutorials.
Cytoscape plugins
Cytoscape is not only an application, but also a platform (like R, or MatLab, or Linux...)
So, exit Cytoscape and let's have look at some of the extensions that are available.
Download the following plugins: Subgraph creator and OmicsViz. Copy both files to your Cytoscape plugins folder (use location plugin | grep "ytoscape" to find the folder). Do not download the dot plugin: it's incompatible with the current version of Cytoscape. Dot and GraphViz are really cool tools though when doing network visualization!
Now let's learn how to use these:
