guest: systems biology

Question 1

define systems biology

Answer 1

interdisciplinary approach to studying life sciences via integration of complex biological components using mathematical and computational modelling

Question 2

how tradiitonally study biological systems

Answer 2

• complexity of biological systems constrained how we study.
• use reductionist approach

Question 3

omics technologies developed

Answer 3

study entire organism in one aspect.
- cost decreased,
- easy to obtain technology
shift from reductionist to integrative or holistic approach

Question 4

biological data to mathematical representations

Answer 4

• gene -> protein -> reaction relationship
• enzyme catalyse chemical rxn
  -reaction linked to matric
  = metabolic reconstruction in numbers

Question 5

from math to computational model

Answer 5

curate draft reconstruction by adding known GPR data from literature
- add physiological data + compute model
-train model on omics data
end product: predictive model of organism’s metabolism

Question 6

application of genome scale metabolic models

Answer 6

how to engineer bacteria to produce product of interest

• ID gaps to ID new genes
• ID metabolic pathways that are on/off
• analyze how paths are interconnected
• find in silico knowck out pathways
• ID necessary growth substrates, and interspecies interactions

Question 7

stein lab application

Answer 7

methan -> methanotrophs -> biofuel, bioplastic.

with GEM, figure out how to best metabolically engineer microbes for growth condition, product etc.

Question 8

why should u care about systms?

Answer 8

rise of big data.

• hub for lots of data
• biotech projected to boom in time