17.05.19

Lecture 2 - Bioprogramming

* What is programming?
   ► Communication with computer.
   ► By learning programming, we can solve the problem step by step.

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+ Functions in Perl
   - use : call function.
   - strct : check error (it is library, that is set of books).
   - warning : warn to me when error is occurred (it is also library).
   - my : restrict boundary of storing section among all sections of computer memory.

 + Variables in Perl
   - @ : array (sets in cage)
   - % : hash (key and value)
   - $ : scaler (one unit)

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* Two aspect of bioprogramming
   1) Bioprogramming as the natural process of information propagation in the universe. (ex. bacteria also do bioprogramming)
   2) Bioprogramming as programming technique in bioinformatics.
       ► Different with IT programming
       ► Bioinformatics always use biological data for finding natural rule. So, experiment is needed to get biological data.

 

* Semiconductor of life
  ► Nano scale chemicals and molecules.
  ► Protein is key molecule for information processing.
  ► Information processing is occur or isn't occur based on pressure, temperature, or pH.
  ► Protein is modules for bioprogramming (it is basic building block of programming) : we have to know structure of protein.

 

* Bioinformatics is that hacking circuit about protein or other biological data and analze it.
  ► Controlling circuit to knowing specific function : active or suppress some factors.

 

* Important things of bioinformatics
  ► Guru level coding ability.
  ► Understanding computer hardware.
  ► Parsing ability (text manipulation).
  ► Database : flat file, relational (MySQL - special program dealing text).

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* What is a compiler?
  ► Compiler is computer program that transforms source code (ex. perl code or genome) written in a programming language into another computer language (binary form). The most common reason for converting a source code is to create an executable program (ex. protein).

+ machine code (0,1) -> assembly code -> C code -> basic easy program -> ... -> perl

 

* What is a grammar?
  ► To translate source code, we need to know rules of compiler function.
  ► compiler = rule = grammar
  ► What is the best rule? -> Chomsky's rule : there are similar backbone among different languages.
  ► To understand life, we have to understand grammar of life.

 

1._Lecture