September 17th, 2018


to “Computing for Molecular Biology 1”




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




17 million people

Spanish colony 500 years ago (so language is Spanish)

Independent Republic 200 years ago

First Latin American country to recognize Turkish republic

Everyday life very similar to Turkey

Chileans like Turkish soap operas


Latin America in Turkey

Foreigners enrich the hosting countries. Just look at the food:

  • Corn is from North and South America: maiz
  • Tomato is Mexican: tomates
  • Potato is from Chile and Peru: patatas

tomato potato corn

Diversity increases opportunities


Course Homepage


Classes will be published there

You must fill the online survey in that page

That will give you access to the course forum


By regulation from the Rectory, students need to attend at least 70% of the classes

The attendance book is updated every week and published online

We will have several quizzes and homework during the semester


Why do I ask “why?”?

This idea is from author Simon Sinek

Search him on Google. It is interesting

Tell me what you think about his ideas

Why are you here?

Why computers?

for Molecular Biology and Genetics

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


What does Computer means?

A computer is a counter

Normally was a person that did calculations

Sometimes with the help of mechanical devices

During the 2nd World War people invented electronic computers

So, computers are devices handling numbers

A Computer

“but I don’t use numbers …”

Don’t worry

Using numbers we can represent other things

In my country kids play this game:

They change vowels A, E, I, O, U by the numbers 1, 2, 3, 4, 5

Then they write H2LL4

Using the same idea we can represent any text

Notice …

… that we have represented sounds by signs for centuries

The key word here is represent

Numbers can represent other things

There are three things in the Universe

  • Matter
  • Energy
  • Information

Information can be put in digital (numeric) form

Numbers can represent a lot of things

  • Images
  • Audio
  • Movies

not yet

  • smell
  • taste
  • tact

What can a modern 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


Who invented computers?

What do you do with a computer?

Do you have a computer at home?

What do you use it for?

What can you do with these?

What can a computer do?

  • calculate formulas
  • solve (some) equations
  • store and retrieve huge quantities of data
  • find patterns in data
  • find data matching a pattern
  • transform data in useful ways
  • compress data
  • move data at low cost without distortion

Parts of a computer

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


Many different questions can be solved with the same rules

It is just a matter of changing the program

First electromechanical computers were like us: A sequence of devices, each one feeding the next

Changing the program required physical change of pieces

Stored program

The key step

John Von Neumann realized that the set of steps can be also stored in memory (coded as numbers, obviously)

We only need to include

  • a pointer to the current instruction
  • a system to decide which arithmetic/logic rule apply

This is called Central Process Unit (CPU)

In summary

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

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