• 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

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)

• Its contents disappear if the power is turned off
• and all this currently active information is lost

That’s why it’s prudent to save your work often

Electric problems can be a real disaster

You can think of the RAM as

• a large collection of identical little boxes
• numbered from 1 up to 1000000000
• each box can hold a small amount of information.

Capacity is measured in bytes

What is the capacity of your computer?

When they don’t have energy, they forget all

All data must be stored in secondary memory

Today secondary memory is

• hard disk
• USB stick
• Cloud storage

Besides the data itself, files have metadata

That is, data about the data. For example

• Files have a name
• Files have a modification date, maybe other dates too
• Files have a size
• Files have permissions

The names of the files are “words”: a series of letters, numbers and some symbols

Technically, a filenames is a String or list of characters

Maximum length of a filename is 250 characters

Avoid /, :, +, |, <, *, >, " and '

Use letters (A-Z, a-z), numbers (0-9), ., -,   and _

In some systems small caps and BIG CAPS are not equivalent. Be systematic and coherent

If the filename includes ., the text after it is called extension

In Microsoft Windows (c) extensions are usually 3 letters

• EXE, JPG, DOC, XLS, TXT, CSV
• These are hints on how to interpret the file

At low level there is only one type of file

For us, it is useful to separate in two:

Text Files:

each byte is a character, we can read it

Binary Files:

bytes are grouped in binary numbers, representing images, sounds, etc.

Among binary files we have EXE files, which are programs for Windows

• are universal
• are easy to read and write from a program
• do not have any style like bold or italic
• are like books without figures

Microsoft Word files (doc or docx) are NOT text files

• Binary files are hard to read
  • unless you have the correct program
• Text files can be read by humans
  • Each byte is a letter
• Text files can be read by computers
  • Data must be recyclable
  • The output of one program is the input of another program

Many people feel like “computers are not helping”

Instead they feel like computers make things harder

The same happened when electric engines were invented

You will get a new window with an example text

It is a text file. One character takes one byte

Colors are only a guide for you. They are not part of the text

Today we will learn how to write text files for our course

An alternative to ordinary Word Processors is to use text files with a few rules to mark the role of each element.

Text files can be read with any computer, and will be accessible for ever.

Today the Structured Text format most often used is Markdown

Paragraphs

Consecutive lines of text are one paragraph. They are separated by an empty line

Chapters, Sections, subsections

# Header 1, ## Header 2, ### Header 3

No space before #, one space after

Unordered Lists

Use + or - in the first column, and one space after

Sublists are marked with 4 spaces on the left

Ordered Lists

Like unordered lists but with numbers

Use 1. on the left and separate with one space

Important paragraph|Quotation

To show something important

Use > on the left side, and one spae after

Images

You have to indicate the web address of the image
![optional text](http://example.com/logo.png)

or the name of a file in the same directory
![optional text](images/logo.png)

Computer code

use ``` before and after the block

exactly 3 ticks

This will be very important in the rest of the course

Metadata

Data about the data: date, purpose, bibliography, etc.

This part uses a format called YAML

use --- (three hyphens) before and after

Header

Metadata at the beginning of the file

Uses YAML format

Declare title, author, and date

---
title: "Midterm Exam"
subtitle: "Computing in Molecular Biology 1"
author: "Put your name here"
number: STUDENT_NUMBER
date: "September 24, 2019"
output: html_document
---

ALWAYS write your name and student number

Put all the references somewhere in the document, with --- before and after.

• [@WatsonCrick1953] produces (Watson and Crick 1953)
• [@WatsonCrick1953, pp. 33-35, 38-39] becomes (Watson and Crick 1953, 33–35, 38–39).
• [@WatsonCrick1953; @Collado-Vides2009a] becomes (Watson and Crick 1953; Collado-Vides et al. 2009).
• @WatsonCrick1953 [p. 33] says blah becomes Watson and Crick (1953, 33) says blah

If you have a long list of all papers, and you use it on several documents, then you should put the references in a separate file

Then you write

bibliography: references.yml

in the document metadata

It is good that RMarkdown uses all these formats

There are many tools to manage your paper collection

It is not enough to download PDF and store them in a folder. They need to be organized and have a structure

Two good and free programs are Mendeley and Zotero

Bibliographies will be placed at the end of the document. Normally, you will want to end your document like this:

last paragraph...

# References

The bibliography will be inserted after this header. More info at

http://rmarkdown.rstudio.com/ authoring_bibliographies_and_citations.html

Links

clickable text.

Inline code

We can speak about x and data

Footnotes

find how to write them

• Help -> Markdown Quick Reference
• https://www.rstudio.org/links/r_markdown_cheat_sheet
• https://www.rstudio.org/links/r_markdown_reference_guide
• http://rmarkdown.rstudio.com/
• Google “Markdown”