Class 1: Why “Computing in Molecular Biology”?

Computing for Molecular Biology and Genetics 1

Andrés Aravena, PhD

19 October 2020

Welcome

to “Computing in Molecular Biology 1”

Today’s questions

Who
How
Why
What

Who?

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”

How?

This is a new course

If you are doing this course for second time, you must pay attention

This course is different

The way we handle vectors will be different

The way we plot graphics will be different

Homework

We will give homework during the semester

They are mandatory and personal for everybody

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

Homework

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

That email is only for answers

If you have any question, send it to

iu-cmb@googlegroups.com

This is the email of the Course’s Forum

You must register into the forum before

Registering in the Course’s Forum

In the course homepage you will find a link to the course’s online forum

You must follow that link and ask to be registered

Please do this after this presentation

Course Homepage

Visit http://dry-lab.org/blog/2020/cmb1/

Classes will be published there (slides and videos)

I will upload the lessons before the class day

You must watch the lesson before the class

Online survey

You must fill the online survey in the homepage later today

Everybody must fill it. Even if you filled it before

There are no wrong answers. Just be honest

Attendance

We have two classes every Monday

We control attendance

  • at the beginning of the first class
  • and at the end of the second class

The attendance book is updated every week and published on the course homepage

Why?

Why are you here?

Answer now with your voice

Why do we use computers?

in Molecular Biology and Genetics

Computers are rule changers

Computers were created to solve math problems

Then they were used to handle big databases

They became cheap and found everywhere

They became communication tools

They transformed society and science

For example

today banks do not handle money

Banks handle data about money

All movies are now made with computers

Factories are computer-controlled

Manual jobs are now done by computers

Will a robot replace you?

World biggest companies (May 2020)

Rank Company name Market value
1 Saudi Arabian Oil Company 1,684.8
2 Microsoft 1,359.0
3 Apple 1,285.5
4 Amazon 1,233.4
5 Alphabet (Google) 919.3
6 Facebook 583.7
7 Alibaba 545.4
8 Tencent Holdings 509.7
9 Berkshire Hathaway 455.4
10 Johnson & Johnson 395.3
11 Visa 383.9
12 Walmart 344.4

Computers are everywhere

How many computers do you use?

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

Do you have a computer at home?

What do you do with your computer?

Are you loosing your time playing computer games?

Watching other people’s lives in Facebook or Instagram?

Watching videos?

Is your computer controlling you?

Wouldn’t it be nice if you controlled you computer instead?

We want to use Computers to do Science

What?

What will we do in this course?

Look at this article

What do you see here?

What do they have in common?

All are based in numbers presented as graphics

We want to handle tables like this one

COVID-19 cases in Turkey

Date_reported New_cases Cumulative_cases New_deaths Cumulative_deaths
2020-03-11 1 1 0 0
2020-03-12 0 1 0 0
2020-03-13 0 1 0 0
2020-03-14 4 5 0 0
2020-03-15 1 6 0 0
2020-03-16 12 18 0 0

We want to make graphics like these

This is what we want to do

What we do not do here

  • Teach how to use Microsoft Windows®
  • Programming
  • Bioinformatics
  • Social Media
  • Use Word®, Excel®, or PowerPoint®
    • Ok, maybe just a little

How to use computers in the right way

Are computers making things easier?

Some people say “computers are not helping”

They feel that computers make things harder

The same happened over 100 years ago
when electric engines were invented

First factories had only one big steam engine

Energy was transported everywhere using belts

One motor moving all machines

Later, electric motors replaced the steam engines

But the factories did not improve

The real change happened when each machine got its own motor

Today we have electric motors everywhere

Doing the same thing gives the same results

Just changing the technology does not change the world

The real change happens when we do things in a different way

What about this?

Computers are not Typewriters

If we only replace typewriters by word processors, nothing changes

Microsoft Word is a technology for 19th century

We need a new way to use computers

What is the plan

  • We use computers to do Science
  • We create new knowledge from experiments
  • Experiments produce a lot of data
    • Especially in Molecular Biology
  • Producing the data is the easy part
  • Understanding the data is hard
  • To understand the data, we use structures

Structures

Organizing to understand

The first step to extract knowledge from data is to organize it

There are essentially three kinds of structures that we will use

  • Tables
  • Hierarchies
  • Networks

Plan of this course

  • Structured documents
    • Markdown
  • Structured data
    • R and RStudio
    • Tidyverse
  • Grammar of Graphics

Questions?

Now you must register on the Course’s Forum

Visit dry-lab.org/blog/2020/cmb1 and follow the link