BiS437 Bio-Data Engineering

Spring 2012

Doheon LeeDept. of Bio and Brain Engineering, KAIST

dhlee@kaist.ac.kr

Who I am

• Doheon Lee, Professor, Dept. of Bio and Brain Engineering, KAIST• Ph.D. in Computer Science (KAIST, 1995), KIT CS86• Stanford(2010), Indiana Univ.(2009), NIH(2002), Univ. of Texas(1999) etc.. • Certified information system auditor• Over 200 academic papers for bioinformatics and data mining• Director – Bio-Information System National Research Lab • Director – IBM-KAIST Bio-Computing Research Center• Director – WCU Neuro-Systems Research Group• Ways to reach

1. mailto: dhlee@kaist.ac.kr2. call: 042-350-43163. visit: CMS Building (E16), #1111 (Ace-Poker) 4. encounter: KAIST campus, outside sometimes

3S for Saying Hello

1. Sense them(see, feel, guess) 2. Have them See you(gesture and sound)3. Show your Smile

Try !!!

Course Outline

• Three goals of this course1. Communicational knowledge of computer science and technology2. Actionable experience of information system implementation3. Primer appreciation of the essential power of bioinformatics

• Grading (Higher between two plans)

• Textbooks– J. Brookshear, Computer Science, Ed. 11(or Ed. 10), Addison-Wesley, 2011– D. Lee, Biomedical Information System for Personalized Medicine, BISL, 2012

• Course Website: Moodle• E-mail: dhlee@kaist.ac.kr• TA: 황우창, 김준호, 류하선, 김광민 (bis437ta@biosoft.kaist.ac.kr)

Plan A Plan B

Class Participation and Quiz 10% 10%

Project 40% (10+15+15) 40% (10+10+20)

Mid-Term Exam. 20% 10%

Final Exam. 30% 40%

Why you should take this course

Society Bio-Medical Science

Ancient Hunting, Collection, FarmingExperience,Observation

~20th Century IndustrializationControlled

Experiments

21st Century Information Bioinformatics

Future Dream, Emotion You create!

The Origin of Computing Machines

• Abacus: the ancient Greek and Roman, merely a data storage system• Technology of gears (19C)

– Pascal (France): Adder hard-wired in gears– Leibniz (German): Several selectable operations hard-wired in gears– Charles Babbage (England)

• Difference Engine• Analytical Engine: Read instructions in the form of holes in paper cards

– The first programmer: Ada Byron– cf. Jacquard’s loom

• Electromechanical machines: MARK I, Harvard, 1944• Vacuum tube machines

– 1941, Atanasoff-Berry machine at Iowa State Univ.– Colossus, to decode German messages in England during World War II– 1946, ENIAC (Electro Numerical Integrator And Calculator), Univ. of Penn.

• Semiconductor substrate-based bipolar digital logics– 1958: Jack Kilby’s IC (Nobel prize)– 1962: TTL (Transistor-transistor logic)– 1974: ECL (Emitter-coupled logic)

• CMOS (Complementary Metal Oxide Silicon)-based machines• Biochemical computing machines ?

Jacquard’s Loom (1801) – The first programmed machine

• The steps to performed during the weaving process were determined by patterns of holes in paper cards

Mark-I (1944) – The first electro-mechanical computer

ENIAC (1946)- The first electronic-digital computer

Stored-Program Concept

Single built-in ring

Selectable built-in rings

Downloadable rings(= color ring)

Single built-in program

(Calculator)

Selectable built-in programs

(Organizer)

Loadable programs(von Neumann Computer)

cf. Data vs. program

How to Assemble Your PC - Components

• CPU: The processing part of a brain – e.g. Intel Pentium 4 2.0A GHz (Cache 512KB)

• RAM: The memory part of a brain– e.g. Samsung Elec. 256MB DDR SDRAM(PC2100)

• Main board: A scaffold– e.g. Unitec TANK ULTRA DDR (P4X266A)

• HDD: A notebook– e.g. Seagate Barracuda 4 60GB (7200RPM)

• FDD: A letter– e.g. Samsung 3.5 inch Floppy Disk Drive (becoming non-necessary)

• ODD: A long letter or a log– e.g. Samsung Elec. 52x CD-ROM Drive

• Power Supply: A digestive organ for energy supply– e.g. DAO for Pentium 4 250W

• Case: The outer skin– e.g. DAO C710(ATX)

• Monitor, Keyboard, Mouse, Speaker, Camera, LAN Card, Modem, Printer, etc

Tools

nipper

screwdriver

Pliers (long nose)

Components in Wrappers

Main Board

CPU and CPU Socket on the Main Board

CPU with Cooler Installation

RAM Installation

Main Board in the Cabinet

Sound Card Installation

Main Board Slots for CDD, FDD, and HDD

CDD, FDD, HDD Installation

CDD FDD

HDD Assembly

Inside of a Completed PC

PC and Supercomputer

How expensive your computer is

• You (or your parents) bought a PC: 2,000,000 KRW• Usually, you will use it for three years• Three years = 1,095 days• 2,000,000 KRW / 1,095 days = 1,826 KRW / day• 2,000,000 KRW / (1,095 days * 24 hours) = 76 KRW / hour

• Your PC is consuming ~2,000 KRW each day from your (or your parents’) pocket no matter how frequently you use

How to keep the value of your (or your parents’) money =>

Use it as frequently as possible