September 26, 2019

I am Andres Aravena

  • Assistant Professor at Molecular Biology and Genomics Department
  • Mathematical Engineer, U. of Chile
  • PhD Informatics, U Rennes 1, France
  • PhD Mathematical Modeling, U. of Chile
  • not a Biologist
  • but an Applied Mathematician who can speak “biologist language”

I come from Chile


Why computers?

for Science and beyond

Computers are rule changers

Modern computers were created to solve math equations

Then they were used to handle big databases

They became cheap and found everywhere

They became communication tools

They transformed society and science

How many computers do you use?

  • Cellphone
  • TV
  • Cable decoder
  • Microwave oven
  • Washing machine
  • Car motor
  • Metro
  • Elevator
  • Notebook

Computers transformed

  • The banking industry
  • The air travel industry
  • The manufacturing
  • The cars
  • The movies
  • Science

Four Paradigms of Science

according to Microsoft

1 Empiric

  • observation of isolated facts
  • description of related facts
  • e.g. Botany, naming stars, Arab astronomers, Galileo, Tycho Brahe, Carl Linneaus

2 Theoretical

  • Abstract models and theories
  • Usually expressed in mathematical formulas
  • Correct predictions validate the models
  • e.g. Mendel laws of inheritance, Darwin natural selection theory, Kepler law of planet’s motion, Newton’s law of Gravity

3 Simulation Based

  • Models that cannot be expressed in formulas
  • Formulas that cannot be solved
  • e.g. Protein structure prediction, three body problem, galaxy modeling
  • Computational Astronomy, Computational Biology

John Von Neumann

4 Data Based

  • Discovering patterns hidden in data
  • Huge volumes of data
  • Complex interactions
  • e.g. Bioinformatics, Astroinformatics, Data mining


Short history

First electronic computers. Used in the 2nd World War. Solving models for Manhattan project
Big computers sold to Governments for census, taxes
Programs written manually by experts
Big computers in Banks and Airlines. Room size
Mini-computers in research institutes. Wardrobe size
First high level programming languages

More history

UNIX system made all mini-computers compatible
first micro-computers at home. Desktop
Internet at the US military
IBM made the first Personal Computer
Microsoft created D.O.S. for personal computers
Apple Macintosh, first home computer with windows and mouse
Internet on Universities
Internet at home
UNIX on personal computers

What does Computer means?

A computer is a counter

Normally was a person that did calculations

Sometimes with the help of mechanical devices

So, computers are devices handling numbers

A Computer

“but I don’t use numbers …”

Don’t worry. Using numbers we can represent other things

  • Images
  • Audio
  • Movies

although not yet

  • smell
  • taste
  • tact

What can a computer do?

Computers handle numbers

Numbers represent information

Computers can transform and transfer information

So, What is a Computer

(English) counter, calculator
(French) sorter, gives order to data, handles data
(Turkish) Information/Data counter

What is a computer?

Is a general purpose device that can

  • read, process and write numbers
    • (and things that can be represented by numbers)
    • to and from the memory
  • following a program stored also in the memory
    • many simple steps

Changing the program changes the purpose of the machine

What is inside a computer?

  • logical organization
    • what are the pieces
    • what they do
    • how they are connected
  • physical structure
    • what the pieces look like
    • how they are built
  • what acronyms and numbers mean

Logical organization

Same Logic: motor, fuel, seats, wheels

Physically different: faster, safer, more reliable

The same is true of computers.

  • Logically, today’s computers are similar to those of the 1950s
  • physical differences
    • much smaller,
    • cheaper,
    • faster and
    • more reliable
    • literally a million times better in some properties

This is why computers are so pervasive

Parts of a computer

Processor(CPU) Interface(I/O) Memory(RAM) Secondary storage (Hard disk) Network

This was Von Neumann idea


The processor or central processing unit (“CPU”) is the brains of the computer

  • does arithmetic,
  • moves data around,
  • controls the operation of the other parts
  • can decide what to do next based on the previous results

CPU can do only a few things, and it does them very fast

RAM: random access memory

The primary memory or random access memory

  • stores information that is in active use
    • the data that the CPU is currently working on,
    • the instructions that tell the CPU what to do
  • its contents can be changed by the CPU

This is a important point

By loading different instructions into memory, we can make the CPU do a different computation.

This makes the stored-program computer a general-purpose device: the same computer can

  • run a word processor and a spreadsheet,
  • surf the web,
  • send and receive email,
  • show a movie

RAM is volatile

  • Its contents disappear if the power is turned off
  • and all this currently active information is lost

That’s why it’s prudent to save your work often

Electric problems can be a real disaster

Your computer has a finite amount of RAM

You can think of the RAM as

  • a large collection of identical little boxes
  • numbered from 1 up to 1000000000
  • each box can hold a small amount of information.

Capacity is measured in bytes

  • memory big enough to hold a single character
    • like W or @

What is the capacity of your computer?

Disks and secondary storage

  • The RAM is expensive, so we it is not too big
    • its contents disappear when the power is turned off
  • Secondary storage holds data even when the power is turned off
  • The most common kind are magnetic disks
    • also called the hard disk or hard drive
  • The disk stores much more information than RAM
  • data on the disk stays there indefinitely
    • even if power fails

Old disks were not “hard disks”

Floppy disks (70’s)

Micro-Floppy disk (90’s)

Secondary storage is slow

Data, instructions, and everything else is stored on the disk for the long term

And brought into RAM only for a short time

Disk space is about 100 times cheaper than RAM

But accessing information is much slower.

Physical Construction

All these parts are connected to a Motherboard

Computers are built from basic elements

The most important of these is the logic gate

  • computes a single output value based on one or two input values
  • it uses input voltage to control an output voltage or current

Logic gates used to be built from vacuum tubes or individual transistors

Vacuum tubes and transistors

Today logic gates are on integrated circuits

ICs, often called chips or microchips

  • all the components and wiring of an electronic circuit
  • on a single flat surface (a thin sheet of silicon)

Smaller and more reliable than discrete-component circuitry

The picture below shows an integrated circuit in its package; the actual circuit part is at the center, and is about 1 cm square.

Silicon Valley

The fact that integrated circuits are based on silicon led to the nickname Silicon Valley for the region in California south of San Francisco where the integrated circuit business first took off

Integrated circuits are central to digital electronics, but other technologies are used as well: magnetic storage for disks, lasers for CDs and DVDs, and lasers and optical fiber for networking

Moore’s Law

In 1965, Gordon Moore, co-founder and CEO of Intel, published an article entitled “Cramming more components onto integrated circuits.”

  • as technology improved, the density of transistors was doubling approximately every year,
    • he later revised to every two years
    • others have set at 18 months

Transistors and Computing Power

Since the number of transistors is a correlated to computing power, this meant that computing power was doubling every two years if not faster

In 20 years there would be ten doublings and the number of devices would have increased by a factor of 210, that is, about one thousand

In forty years, the factor is a million or more.

Moore’s Law today

This will change

Arthur C Clarke’ın öngürülerinin ne kadar gerçek oldu?

1974 interview to Arthur C. Clark


also known as Interface

Speaking to the human

Computers would be useless if we cannot interact with them

Human interfaces include:

  • Screen/monitor/display
  • keyboard/buttons
  • printer
  • microphone
  • speakers/earphones
  • mouse
  • touch screen

Early interface

One of the first ways to enter text was invented in 1928

They were first used in 1890

The 1890 US census was done using punched cards

That was the origin of International Business Machines (IBM)

This is how you write them

This is a paragraph of text

This is how they were stored

Each card had 80 columns

Cards were replaced by screens

Mini-computers had screens

IBM PC had also a screen

And this is what you see on the screen

Everything is text!