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 | 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