September 17th, 2019

Who

What

Why

How

- 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”

Visit `anaraven.bitbucket.io/blog/2019/cmb1`

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

`andres.aravena+cmb@istanbul.edu.tr`

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

I use your answers to adapt the classes

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**

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

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

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

- 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

- 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

- Discovering patterns hidden in data
- Huge volumes of data
- Complex interactions
- e.g. Bioinformatics, Astroinformatics, Data mining
- Big Data, Machine Learning

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**

*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

… that we have represented *sounds* by *signs* for centuries

🎶🎵A Ö æ ñ j r

The key word here is **represent**

There are three things in the Universe

- Matter
- Energy
- Information

Information can be put in digital (numeric) form

For technical reasons modern computers handle memory in bytes

- memory big enough to hold a single character
- like
`W`

or`@`

- like
- Or a small integer number (0 to 255)

Byte = Integer between 0 and 255 = One letter

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**

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

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

- 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)

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

- Images
- Audio
- Movies

not yet

- smell
- taste
- tact

Computers handle numbers

Numbers represent information

Computers can **transform** and **transfer** information

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

- 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

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