05.20 class

Two aspects of BioProgramming
1) Bioprogramming as the natural process of information propagation in the universe - what the cell does right now
2) Bioprogramming as programming technique in bioinformatics - what people do

Trying to understand 1) via 2)

hacking - invading or understanding of code
cracking - illegally breaking into

IFE: Infinitely Fractal Encapsulation
Semiconductor of life is protein
How to program life = to understand life?
1. Experiments! - to make a proper "data"
( data collecting is the first step of science ) we collect data to understand the biological circuits 
immunoprecipitation , Y2H is to find the interactions between proteins (protein to protein)
Network biology - means any set of biological desciplines which tries to
Biology is an Onion - different layers of networks form a supernetwork of networks, each layer's processing unit can be distinct and encapsulated
Protein Internet - the same principles can be applied to protein interactions and human interactions in Internet, generality of topology, generality of self-similarity
Reciprocal network : safety increases, but resource efficiency decreases
Scalefree network : need to balance well between safery and resource efficiency

Everything is networked and network is everything - any meaning or information is derived from networks in biology, network is the ultimate representation of biological data, network shows emergence of functions

why do we study biology? To understand the "architecture" of bionetworks
(Understanding the "architecture" leads to understanding of interactions)

biological bodies (biobody)
-textome (not organized chunk of text elements loosely interacting)
-archiome (well organized chunk of text element tightly interacting)
-metabolome (well organixed elements of bioentities in a directed

why do we use the computer? To simulate the model
for example, ppt slide is simulating paper o0o
Homework : define 20 words the most important in your life and write on your wiki

coding - a tool for programming Even robots and computers can code
programmnig - designing the architecture and simulating it
Guru is MASTER! (indian word) You need to be a Guru (You need to understand the principle!)

programming for bioinformatics - automation is the key, use fast prototyping, solve problems, reuse scripts, use public resources, use openfree resources(GitHub)