We will learn about

- computing
- data science
- descriptive statistics
- documenting results

and maybe (if we have time)

- how computers work
- how internet works

We will learn about

- computing
- data science
- descriptive statistics
- documenting results

and maybe (if we have time)

- how computers work
- how internet works

Even if my passport says

**Andrés Octavio Aravena Duarte**

I have a short and a long version of my name

Türkçe bilmiyorum

- 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”

- Big and small computers
- Telecommunication Networks
- Between 2003 and 2014 I was the chief research engineer
- on the main bioinformatic group in my country
- in the top research center (CMM)
- in the top university (University of Chile)
- of my country

Small country of ~17 million people

Universities ranks similar to Turkish ones

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

The most successful soap opera last year was Bin Bir Gece

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

- Corn is from North and South America
- spanish name is
*maiz*

- spanish name is
- Tomato is Mexican:
*tomates* - Potato is from Chile and Peru:
*patatas*

Diversity increases opportunities

USA is not America

America is the continent, from Patagonia to Alaska

USA is one country in part of the North of America

The same way as Australia is not Oceania

If you don’t understand me, just ask

The only silly question is the one not asked

If you don’t understand, probably you are not the only one

Ask for help, from me or your classmates

The purpose of this course is to learn to think with data

Not to study

Not to teach

But to **learn**

To learn is to change our behavior rules

We think different, we act different

We think with two strategies:

- analytical
- automatic

So learning has to be in two stages

We learn what we do, not what we study

Like riding a bike

Can you learn to dance only reading Wikipedia?

Some theory, a lot of practice

Failure is expected. We learn from failure. Try judo

Not always. Kids learn easily.

We have difficult learning new things because we have to **unlearn** old habits.

So we will need to make an extra effort

According to cognitive research, there are three main ways of remembering

- A few people remembers what they see
- Some people remembers what they listen
- Most people remembers what they do
- Kinesthetic sense: body position

Moreover **logic** is tightly connected with **language**

Google: *Cornell Method*

It’s easy to get distracted,

specially when we don’t like the task

We learn by getting out of or “comfort zone”

Learning is uncomfortable, even annoying

We have to push ourselves to focus

- set a timer for 25 minutes
- force yourself to focus on that period
- no email, no Facebook, no toilet, no coffee/cigarettes
- in case of interruption, restart from zero
- when the bell rings
*STOP*working for 5 minutes - every 3 Pomodoros, take a 20 min break

We will use this technique in this course

We have roughly three stages of memory

- very short term memory (seconds)
- medium term memory (hours)
- long term memory (years)

Transition between medium and long term memory happens when we sleep (and dream)

Ideally we need 2 sessions per week

All the ideas we will discuss are available for free on line

I *understand* you will learn from the web

I *encourage* you to do so

and then come and teach

mesomething new

Attend to classes regularly (always!)

Bring a notebook and a pen

Handwrite what we speak, and your own questions

Summarize at the end of the class (*Cornell Method*)

Speak with your classmates

Sleep well (but not during the class)

**I will give a subject every week.**

You have to research and present it in 25 min

**IU Computers for Molecular Biology**

https://groups.google.com/d/forum/iu-cmb

Group email address

`iu-cmb@googlegroups.com`

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

1 Empiric

- observation of isolated facts
- description of related facts
- e.g. Botany

2 Theoretical

- Abstract models and theories
- Usually expressed in mathematical formulas
- Correct predictions validate the models
- e.g. Mendel laws of inheritance

3 Simulation Based

- Models that cannot be expressed in formulas
- Formulas that cannot be solved
- e.g. Protein structure prediction

4 Data Based

- Discovering patterns hidden in data
- Huge volumes of data
- Complex interactions
- e.g. Bioinformatics

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

Then they say *H2LL4* (they are just kids)

**Using the same idea** we can represent any text

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

There are three things in the Universe

- Matter
- Energy
- Information

Information can be put in digital (numeric) form

- 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 and handles data

**Bilgisayar:** (Turkish) Information/Data counter

Do you have a computer at home?

What do you use it for?

- 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

First usage of electronic computers was to solve ballistic equations

Same approach enabled landing on the moon

Let’s find the value \(x\) that satisfies \[24x^3-70x^2+19x+15=0\]

Let us put a name to the formula. Let’s call it \(f(x)\). \[f(x) = 24x^3-70x^2+19x+15\]

We want to find \(x\) that makes \(f(x)=0.\) We can write \[f(x) = (24x^2-70x+19)x+15\] or even \[f(x) = ((24x-70)x+19)x+15\]

- Take a piece of paper and
**write**\(x\) in the first line **Write**24**Multiply**the last two numbers**Add**-70**Write**\(x\) (from the first line)**Multiply**the last two numbers**Add**19**Write**\(x\) (from the first line)**Multiply**the last two numbers**Add**15**Compare**to 0

I will assign roles to each one

I will write \(x\) in a sheet and give it to the first person

Each one does a *single* task and delivers to the next person

I will collect all results and tabulate them

- Take a piece of paper and
**write**\(x\) in the first line **Write**24**Multiply**the last two numbers**Add**-70**Write**\(x\) (from the first line)**Multiply**the last two numbers**Add**19**Write**\(x\) (from the first line)**Multiply**the last two numbers**Add**15**Compare**to 0

We solved a complex mathematical question using a simple set of rules

- write
- multiply
- add
- compare

This decomposition in simple steps is called **a program**

In this exercise we used

- memory (paper)
- arithmetic/logic units (you: adding, multiplying, deciding)
- input/output (me)

Many different questions can be solved with the same rules

It is just a matter of changing the *program*

First electromecanic computers were like us:

A sequence of devices, each one feeding the next

Changing the program required physical change of pieces

John Von Neuman 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)

Since old times physical tools are called *hardware*

That includes al the physical parts of the computer

(what you can kick)

Programs determine the function of the computer, but they are not “physical”.

That is *software* (what you can only insult)

All cell components are hardware

The sequence of the DNA is the software

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

- How information is coded in numbers
- How these numbers are stored and organized
- How we interact with computers
- Start using an specific tool:
**RStudio**

- Prepare a presentation about
*NCBI* - Install
*R*and*RStudio* - Register in the Google Group