Bacteriology
Todar's Online Textbook of Bacteriology 2023
# Archiving Todar's Online Textbook of Bacteriology
This documentation outlines the steps to archive an online textbook for offline use. We'll be using various tools and techniques to achieve this. Follow these steps carefully:
## Step 1: Download Dependencies
Before we begin, make sure you have the following dependencies installed on your system:
- **base.css** - use this css to properly format. Add to the same directory where you will be using princexml
Download from: [base.css](https://github.com/arp242/hello-css/blob/master/base.css)
- **Prince XML Converter**
Download from: [Prince XML](https://www.princexml.com/download/)
Ensure that these dependencies are installed and ready to use.
## Step 2: Download the Website
1. Open your terminal.
2. Create a directory for the archived textbook and navigate to it using the following commands:
```shell
mkdir todars
cd todars
```
3. Use `wget` to download the entire website with the necessary options:
```shell
wget --recursive --no-clobber --page-requisites --html-extension --convert-links --restrict-file-names=windows --domains textbookofbacteriology.net --no-parent http://textbookofbacteriology.net//
```
This command will recursively download all the website content while preserving its structure.
## Step 3: Convert HTML to PDF
Now that you have the website content, we will convert it to a PDF file using the Prince XML Converter.
1. Organize the HTML files in the desired order. **important: I sorted them manually using the table of contents as my reference**
2. Open your terminal and execute the following command, replacing `[paste html list here in order]` with the list of HTML files in the desired order:
```shell
prince [paste html list here in order] --page-size="US-Folio" --page-margin="20mm" --style=base.css --media="screen" -o ~/combined_all4.pdf
```
This command will use Prince XML to convert the organized HTML files into a single PDF file named `combined_all4.pdf`.
## Step 4: Generate PDF Outlines
To make navigating the PDF easier, you can generate outlines for the PDF using PDF Tocgen.
1. Download PDF Tocgen from its repository: [PDF Tocgen](https://github.com/Krasjet/pdf.tocgen).
2. Follow the installation instructions and Getting Started guide provided in the PDF Tocgen repository.
3. Once installed, use PDF Tocgen to generate outlines for your PDF:
```shell
pdf.tocgen -i ~/combined_all4.pdf -o ~/combined_all4_with_outlines.pdf
```
This command will create a new PDF file named `combined_all4_with_outlines.pdf` with outlines for easy navigation.
Table of contents :
Online Textbook of Bacteriology Table of Contents
Overview Of Bacteriology
The Impact of Microbes on the Environment and Human Activities
Structure and Function of Bacterial Cells
Nutrition and Growth of Bacteria
The Growth of Bacterial Populations
Control of Microbial Growth
Diversity of Metabolism in Procaryotes
Regulation and Control of Metabolism in Bacteria
Bacteriophage
Bacteria and Archaea and the Cycles of Elements in the Environment
Important Groups of Procaryotes
The Nature of Bacterial Host-Parasite Relationships in Humans
The Normal Bacterial Flora of Humans
Mechanisms of Bacterial Pathogenicity
Bacterial Pathogens of Humans
Immune Defense against Bacterial Pathogens: Innate Immunity
Immune Defense against Bacterial Pathogens: Adaptive or Acquired Immunity
Bacterial Structure in Relationship to Pathogenicity
Colonization and Invasion by Bacterial Pathogens
Bacterial Defense against Phagocytosis
Bacterial Defense against Specific Immune Responses
Bacterial Protein Toxins
Bacterial Endotoxin
Antimicrobial Agents in the Treatment of Infectious Disease
Bacterial Resistance to Antibiotics
MRSA Methicillin-Resistant Staphylococcus aureus
Staphylococcus aureus and Staphylococcal Disease
Streptococcus pyogenes and Streptococcal Disease
Streptococcus pneumoniae
Listeria monocytogenes
Pathogenic Neisseriae: Gonorrhea, Neonatal Ophthalmia and Meningococcal Meningitis
Haemophilus influenzae and Hib Meningitis
Pseudomonas aeruginosa
Vibrio vulnificus
Bordetella pertussis and Whooping Cough
Pathogenic E. coli
Vibrio cholerae and Asiatic Cholera
Salmonella and Salmonellosis
Shigella and Shigellosis
Pathogenic Clostridia, including Botulism and Tetanus
Bacillus cereus Food Poisoning
Bacillus anthracis and Anthrax
Diphtheria
Mycobacterium tuberculosis and Tuberculosis
Borrelia burgdorferi and Lyme Disease
Rickettsial Diseases, including Typhus and Rocky Mountain Spotted Fever
The Genus Bacillus
Lactic Acid Bacteria
Lactococcus lactis: Nominated as the Wisconsin State Microbe
