September 17th, 2019


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


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, “new” students need to attend at least 70% of the classes

“Old” students do not need to attend, but they must sign when they attend

You need to use your student card to control attendance

Do not forget it


Attendance means that you pay attention to the class

If you

  • browse the internet
  • use the cell phone
  • read a book
  • sit in the last rows

then you are not attending


  • You can sit in the last row if the first rows are full
  • You can use the cellphone for one specific class, that we will announce
  • If you are waiting for an urgent call, please wait for it outside the classroom
  • If you arrive late, enter quietly, respecting the rest of the group
  • If you get bored, ask questions about the class


We have two classes every Tuesday

We control attendance at the beginning of the first and at the end of the second

The attendance book is updated every week and published online


We will have several quizzes and homework during the semester

They are mandatory and personal

You can (and must) talk with your friends about the homework, but answers are individual


All answers must be sent to

Send your answers always, especially if you do not solve the question

I use your answers to adapt the classes


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
  • Big Data, Machine Learning


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

🎶🎵A Ö æ ñ j r

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

One byte = One character

For technical reasons modern computers handle memory in bytes

  • memory big enough to hold a single character
    • like W or @
  • Or a small integer number (0 to 255)
Byte = Integer between 0 and 255 = One letter

Floating point

Numbers with decimals can be represented using scientific notation \[1.8466 \cdot 10^{19}\]

In the computer we write 1.8466E19

Notice the meaning of E inside a number

Can also represent special values

  • Inf: Positive Infinity, 1/0
  • -Inf: Negative Infinity, -1/0
  • NaN: Not a number, 0/0
  • NA: Not Available, missing data

This has some limitations

We have a fixed number of digits

Not all numbers are represented exactly

For example \[\frac{1}{3}=0.33333333\cdots\] cannot not be represented exactly with 10 digits

We can also represent more complex things things

Example: Sound

  • Sound is transformed into electricity by a microphone.
  • The voltage is measured 44100 times each second
  • Each sample is stored as a number in a CD

Two steps: sampling (in time) and discretization (in voltage)

Example: Greyscale Image

Example: Greyscale Image

  • Each “point” has a value between 0 (black) and 255 (white)
  • correct name is pixel picture element
  • they are stored line by line

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

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

This was Von Neumann idea

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