arashabadi · h-asadkhanipour · Dec 8, 2025
diff --git a/.gitignore b/.gitignore
@@ -1,2 +1,3 @@
 /.quarto/
-/docs/
+/docs/
+**/*.quarto_ipynb
diff --git a/_quarto.yml b/_quarto.yml
@@ -7,12 +7,17 @@ book:
   author: "<a href='https://arashabadi.github.io/'>Arash B. Abadi</a>"
   date: last-modified
   cover-image: images/patoq_cover_t.png
+  repo-url: https://github.com/arashabadi/patoq
+  repo-actions: [edit, issue]
+
   chapters:
     - index.qmd
-    - part: "Prerequisites"
-      chapters:
-        - prerequisites.qmd
-    - part: "Main Sections"
+    - part: prerequisites.qmd
+      chapters: 
+        - biology_fundamentals.qmd
+        - mathematics_fundamentals.qmd
+        - computer_science_fundamentals.qmd
+    - part: "Special topics"
       chapters:
         - omics-data.qmd
         - modeling-simulation.qmd

diff --git a/biology_fundamentals.qmd b/biology_fundamentals.qmd
@@ -0,0 +1,19 @@
+# Biology fundamentals and resources
+
+## Key Concepts In Biology
+- Molecular Biology: DNA, RNA, proteins, gene expression
+- Cell Biology: Cell structure, organelles, and functions
+- Genetics: Inheritance, genetic variation, genomics
+- Biochemistry: Metabolic pathways, enzyme kinetics
+- Biophysics: Physical principles in biological systems  
+
+## Recommended Resources
+- **Books**:
+  - *Molecular Biology of the Cell* by Bruce Alberts
+  - *Lewin's Genes* by Jocelyn E. Krebs et al.
+  - *Lehninger Principles of Biochemistry* by Nelson and Cox
+  - *Physical Biology of the Cell* by Rob Phillips
+
+- **Online Courses**:
+  - [Introduction to Biology: The Secret of Life](https://www.edx.org/course/introduction-to-biology-the-secret-of-life) on edX
+  - [MIT OpenCourseWare: Introduction to Biology](https://ocw.mit.edu/courses/7-01sc-fundamentals-of-biology-fall-2011/)
diff --git a/computer_science_fundamentals.qmd b/computer_science_fundamentals.qmd
@@ -0,0 +1,191 @@
+# Computer science fundamentals and resources
+
+  - *Bioinformatics Data Skills* by Vince Buffalo
+
+
+
+# Operating system Linux
+## Linux basic resources
+### Books
+### Online courses
+
+## Linux advanced resources
+### Books
+### Online courses
+
+## Linux persian reources
+
+## Linux fast tutorial
+
+
+# Git and Github
+
+## Git basic resources
+
+### Books
+- [head first git](https://i-love-git.com/)
+
+### Online courses
+- [git - the simple guide - no deep shit!](https://rogerdudler.github.io/git-guide/)
+- [Git Tutorial - Medium by Jaaeehoonkim](https://medium.com/@jaaeehoonkim/git-tutorial-1-31d0b1db1940)
+
+## Git advanced resources
+### Books
+- The best and most reliable: [Free book of Pro Git](https://git-scm.com/book/en/v2)  
+- [Happy Git and GitHub for the useR](https://happygitwithr.com/)
+
+### Online courses
+- [Introduction to Git and GitHub](https://www.coursera.org/learn/introduction-git-github) on Coursera
+
+## Git persian reources
+- [ دوره رایگان، جذاب و خیلییی کوتاه گیت جادی تو فرادرس](https://faradars.org/courses/fvgit9609-git-github-gitlab)  
+- [Milad Bahrami youtube playlist](https://www.youtube.com/playlist?list=PLhpS3tgUDZcpamFNTdjXyRKzFGaBAkcLq)  
+- [Ashkan Rahmani youtube playlist](https://www.youtube.com/playlist?list=PLG-hncsy5aQ4keIG-pNoGj-zzU7TpFNPR)  
+- [Git mag youtube playlist](https://www.youtube.com/playlist?list=PL1xdRbCBrpofX93iVIkyujskR4cCy261S)  
+- [Salar Hagh youtube playlist](https://www.youtube.com/playlist?list=PLprvbQiR3cN9M3g22ui3MiEFkqLpVubAU)  
+- [neolearn youtube video](https://www.youtube.com/watch?v=TEx_mRpIDkA)  
+- [Sarvin Style Coding youtube video](https://www.youtube.com/watch?v=xDdal3QSypE)  
+
+
+## Git fast tutorial
+<div style="text-align: center">
+![Source: Google Images](./images/git/git_finalfinal.jpg){.image width="700px"}
+</div>
+
+### What is Version Control?
+
+Imagine you're writing a research paper. You make changes, save different versions, and sometimes want to go back to previous versions. Version control is like having a time machine for your files - it helps you track changes, collaborate with others, and maintain a history of your work.
+
+Git was made by Linus Torvalds, the same person who made Linux! It is like a super-powered save system. Instead of saving files with names like `paper_FINAL_final_UPDATED_NEW.docx` or `proj_NEW_LASTEST.R`, Git keeps track of all changes automatically.
+
+### Basic Git Concepts & Commands
+
+- **Repository (Repo)**: Think of it as a project folder that Git watches. Like a photo album that keeps track of all your project's versions. **Local repo** is a copy of the remote repo on your computer. **Remote repo** can be the version stored on GitHub or GitLab.
+
+- **Commit**: Like taking a snapshot of your work. Each commit is a saved point you can return to. Like saving a checkpoint in a video game or giving your file a name/version.
+
+<div style="text-align: center">
+![Git in a nutshell - [Source](https://medium.com/@jaaeehoonkim/git-tutorial-1-31d0b1db1940)](./images/git/git-medium.png){.image width="600px"}
+</div>
+
+- **Branch**: Like creating a parallel universe for your work. You can experiment without affecting the main project. Like writing a draft of your paper without changing the original. Also can be used to collaborate with others, simultaneously working on the same project! You can **Merge** your changes back to the main branch after you are done. Master/Main branch is the main branch of the repo.
+
+<div style="text-align: center">
+![Git Branches - [Source](https://www.nobledesktop.com/learn/git/git-branches)](./images/git/git-branches-merge.png){.image width="500px"}
+</div>
+
+```bash
+# Start a new project (create a new repository)
+git init
+
+# Check the status of your files
+git status
+
+# Add files to be saved (staging)
+git add filename.txt    # Add specific file
+git add .              # Add all files
+
+# Save your changes (commit)
+git commit -m "Description of changes"
+
+# See your project history
+git log
+
+# Reset your branch to the latest commit
+git reset --hard
+```
+
+### GitHub: Your Project's Home on the Internet
+
+![GitHub vs Bitbucket vs GitLab](./images/git/github.jpg)
+
+GitHub is like a social network for your code. It's where you can store your projects online, collaborate with others and share your work with the world. GitHub has **Repository Hosting** - a cloud storage specifically for code, **Issue Tracking** - a to-do list for your project and bug reporting, **Pull Requests** - suggesting changes to someone else's work or requesting changes to your own work, **Code Review** - peer review process for your code, and **CI/CD** features. 
+Common workflows in GitHub: **Fork a Repository**: Like making a copy of someone else's project. You can modify it without affecting the original. **Push Changes**: Like uploading your changes to GitHub. **Clone a Repository**: Like downloading a project to your computer.
+
+```bash
+# Clone a repository
+git clone https://github.com/username/repository.git
+
+# Get updates from remote repository
+git pull
+
+# Send your changes to remote repository
+git push
+
+```
+
+### Common Scenarios and Best Practices
+
+When working with Git, follow these key practices: write short & clear commit messages to document changes, create feature branches for new work, keep your local copy updated regularly, and review changes before committing. For beginners, **start with basic commands and simple projects**, you can utilize visual tools like GitHub Desktop or VS Code's Git integration but I prefer to use the command line (more straightforward), learn from mistakes. Git maintains history so you can always revert!!
+
+What usually happens daily:
+
+1. **Starting a New Project**
+   ```bash
+   git init
+   git add .
+   git commit -m "Initial commit"
+   ```
+* **Note**: I prefer to initialize a new repository in GitHub with a README file and LICENSE, and then clone it to my local machine.
+
+2. **Updating Your Work**
+   ```bash
+   git pull
+   # Make changes
+   git add .
+   git commit -m "Description of changes"
+   git push
+   ```
+
+3. **Working with Branches**
+   ```bash
+   git checkout -b new-branch-name
+   # Make changes
+   git add .
+   git commit -m "Description of changes"
+   git push
+   git checkout main
+   git merge new-branch-name
+   ```
+
+<div style="text-align: center">
+![Git and B Cell Analogy!](./images/git/git-bcell-r.png){.image width="500px"}
+</div>
+
+
+# R
+## Link to fast tutorial
+
+## R basic resources
+
+### Books
+
+### Online courses
+
+## R advanced resources
+
+### Books
+
+### Online courses
+
+## R persian reources  
+  - *R for Data Science* by Hadley Wickham
+  - [R Programming](https://www.coursera.org/learn/r-programming) on Coursera  
+
+## R fast tutorial
+
+# Python
+
+## Python basic resources
+### Books
+  - *Python for Biologists* by Martin Jones
+### Online courses
+
+## Python advanced resources
+### Books
+### Online courses
+  - [Python for Data Science and AI](https://www.coursera.org/learn/python-for-applied-data-science-ai) on Coursera
+
+## Python persian reources
+
+## Python fast tutorial
diff --git a/images/bioinformatics_ven_diagram.jpg b/images/bioinformatics_ven_diagram.jpg
diff --git a/index.qmd b/index.qmd
@@ -1,67 +1,11 @@
-## Welcome
+# Welcome {.unnumbered}
 
-PATOQ (پاتوق) is a curated collection of resources & quick tutorials around Bioinformatics, Data Science, ML, etc. The term "Patoq" is a Persian (Farsi) word that means "gathering place" or "social hangout". PATOQ is a gathering place where individuals interested in bioinformatics, computational biology, data science, machine learning, and related fields can find valuable information and stay current with the latest advancements.
+PATOQ (پاتوق) is a curated collection of resources & quick tutorials around Bioinformatics, Data Science, ML, etc.  
 
-## Table of Contents
+The term "Patoq" is a Persian (Farsi) word that means "gathering place" or "social hangout".  
 
-- Prerequisites
-  - Biology Fundamentals
-  - Programming Fundamentals
-  - Mathematics Fundamentals
-  - Statistics and Probability Fundamentals
-  - Project Management and Communication Skills
-  - Case Studies and Practical Applications
+PATOQ is a gathering place where individuals interested in bioinformatics, computational biology, data science, machine learning, and related fields can find valuable information and stay current with the latest advancements.
 
-- Main Sections
-  - Omics Data Analysis and Interpretation
-    - Genomics
-    - Transcriptomics
-    - Proteomics
-    - Metabolomics
-    - Epigenomics
-    - Metagenomics
-    - Network and Pathway Analysis
-  - Modeling and Simulation
-    - Molecular Modeling and Dynamics
-    - Systems Biology
-    - Computational Ecology, Evolution and Phylogenetics
-    - Computational Pharmacology and Drug Design
-    - Mathematical Modeling of Biological Systems
-  - Integrated Platforms, Tools, and Technologies
-    - Version Control: Git & GitHub
-    - SaaS Platforms
-    - Cloud Computing and Data Management
-    - High-Performance Computing (HPC)
-    - Collaborative Research Tools
-    - Data Visualization Techniques
-    - Big Data Analysis
-  - Specialized Topics
-    - Artificial Intelligence
-    - Clinical Bioinformatics
-    - Agricultural Bioinformatics
-    - Synthetic Biology
-    - Personalized Medicine
-    - Environmental Bioinformatics & Epidemiology
-    - Biomolecular Engineering
-    - Genetic Engineering
-
-- Additional Resources
-  - YouTube Channels
-  - Persian Resources (بنمایگان پارسی)
-  - Open-Source Projects and Repositories
-  - Courses
-  - Books
-  - Scientific Journals & Publications
-  - Vignettes & Websites
-  - R packages
-  - Miscellaneous
-  - Topic Based
-  - Conferences, Workshops, and Webinars
-  - Career Guidance and Job Opportunities
-  - Networking and Collaboration
-  - Regular Updates
-
-<!-- End of Table of Contents -->
 
 This book is a Quarto-based online HTML book for the PATOQ project. See [CONTRIBUTING.md](https://github.com/arashabadi/patoq/blob/main/CONTRIBUTING.md) for more information.
 

diff --git a/mathematics_fundamentals.qmd b/mathematics_fundamentals.qmd
@@ -0,0 +1,37 @@
+# Mathematics fundamentals and resources
+
+## Key Concepts
+- Linear Algebra: Vectors, matrices, and their applications
+- Calculus: Differential and integral calculus
+- Discrete Mathematics: Combinatorics, graph theory
+- Algorithms and Data Structures
+- Numerical Methods
+
+## Recommended Resources
+- **Books**:
+  - *Introduction to Linear Algebra* by Gilbert Strang
+  - *Discrete Mathematics and Its Applications* by Kenneth H. Rosen
+  - *Numerical Recipes* by William H. Press et al.
+
+- **Online Courses**:
+  - [Linear Algebra](https://www.edx.org/course/linear-algebra-foundations-to-frontiers) on edX
+  - [Calculus 1A: Differentiation](https://www.edx.org/course/calculus-1a-differentiation) on edX
+
+# Statistics fundamentals and resources
+
+## Key Concepts
+- Probability Theory: Distributions, random variables
+- Statistical Inference: Hypothesis testing, confidence intervals
+- Regression Analysis: Linear and non-linear models
+- Multivariate Statistics
+- Machine Learning Basics
+
+## Recommended Resources
+- **Books**:
+  - *The Elements of Statistical Learning* by Trevor Hastie et al.
+  - *Applied Multivariate Statistical Analysis* by Richard A. Johnson
+  - *Statistical Inference* by George Casella and Roger L. Berger
+
+- **Online Courses**:
+  - [Statistics and Data Science](https://www.edx.org/professional-certificate/mitx-statistics-and-data-science) on edX
+  - [Probability and Statistics](https://www.coursera.org/learn/probability-intro) on Coursera