Bioinformatics Teachers Guide

Welcome to the teacher's guide for Bioinformatics: An interactive intelligent textbook for Bioinformatics with a focus on graph analysis. This guide explains every feature of the textbook, how to use it in your classroom, and how to customize it for your students. No prior technical knowledge is assumed — every technical term is defined before it is used.

About This Interactive Intelligent Textbook

What is an Intelligent Textbook?

An intelligent textbook is a digital textbook that goes beyond static text and images. It includes interactive simulations, self-grading quizzes, a searchable glossary, and a structured map of how concepts relate to each other. The goal is to give students a richer, more engaging learning experience than a traditional printed textbook.

The Five Levels of Intelligent Textbooks

Not all digital textbooks are created equal. We categorize intelligent textbooks into five levels based on how interactive and adaptive they are.

Here is a MicroSim that describes the five levels:

This table also summarizes the five levels:

Level	Name	Description	Example Features
Level 1	Static Digital	A PDF or basic web version of a print textbook	Text and images only, no interactivity
Level 2	Interactive	Adds interactive elements like simulations, quizzes, and searchable glossaries	MicroSims, self-check quizzes, concept search
Level 3	Adaptive	Adjusts content based on student performance	Personalized learning paths, difficulty adjustment
Level 4	AI-Assisted	Includes an AI tutor that can answer student questions	Chatbot integration, automated feedback
Level 5	Fully Adaptive AI	Continuously learns from student interactions and optimizes the experience	Real-time content generation, predictive analytics

This textbook is a Level 2.99 Intelligent Textbook: it tries to be as interactive as possible but it does not store any information about individual students to avoid legal actions against our instructors for data privacy violations.

This textbook includes a search tool, over 54 interactive MicroSims, chapter quizzes, a 480-term glossary, a comprehensive FAQ, detailed annotated references and an interactive learning graph viewer — all freely accessible in any web browser. The structure is designed to be "Level 3" ready if you have a Learning Record Store to store student private event data.

What Makes This Textbook Different

Interactive MicroSims let students manipulate models directly in their browser — no software installation required
Graph-centric approach — every chapter connects biological data to graph-based representations, showing students how network thinking unlocks insights that tabular methods miss
Learning graph — a visual map showing how all 480 concepts connect and build on each other
Olli the Octopus — a friendly mascot character (called a "pedagogical agent") who guides students through each chapter with tips, encouragement, and key insights
Completely free and open source — licensed under Creative Commons for non-commercial use

Using the Chapters

Chapter Structure

The textbook contains 16 chapters organized in a deliberate sequence. Each chapter builds on concepts from previous chapters, so students should work through them in order:

Chapters	Topic Area
1	Foundations (molecular biology, central dogma, DNA/RNA/protein, mutations, epigenetics)
2-3	Data Infrastructure (biological databases, bioinformatics data formats)
4-5	Graph Foundations (graph theory fundamentals, graph databases, Cypher/GQL queries)
6-7	Sequence Analysis (sequence alignment, BLAST, phylogenetics, evolutionary graphs)
8-9	Structural & Interaction Biology (protein structure, AlphaFold, PPI networks)
10-11	Genomics & Transcriptomics (genome assembly, pangenome graphs, regulatory networks)
12-13	Pathways & Disease (metabolic modeling, signaling networks, drug repurposing)
14-15	Advanced Graph Applications (knowledge graphs, ontologies, multi-omics integration)
16	Python Tools and Capstone Projects

What Each Chapter Contains

Every chapter follows a consistent structure:

YAML front matter — Metadata at the top of each chapter file (title, description, reading level, version). Students don't see this; it's used by search engines and the website builder.
Summary — A brief overview of what the chapter covers and what students will learn.
Concepts covered — A numbered list of the specific concepts addressed in the chapter, drawn from the learning graph.
Prerequisites — Links to prior chapters that should be completed first.
Welcome from Olli — A mascot admonition that introduces the chapter topic in Olli the Octopus's friendly voice.
Main content — The core instructional material, written at an undergraduate reading level. Includes tables, real-world examples, and embedded MicroSims.
Mascot admonitions — Throughout the chapter, Olli appears 5-6 times to highlight key insights (thinking), offer practical tips (tip), provide encouragement on harder concepts (encourage), and warn about common mistakes (warning).
Key takeaways — A numbered summary of the most important concepts, preceded by a celebration from Olli.
Practice questions — Open-ended questions for discussion or written responses.

Suggested Classroom Use

Before class: Assign the chapter as reading homework. The MicroSims keep students engaged during independent reading.
During class: Use the MicroSims on a projector for whole-class demonstrations. Ask students to predict what will happen when you change a slider, then test their predictions.
After class: Assign the practice questions. Use the quiz (separate page) for a quick formative assessment.
Pacing: Each chapter is designed for approximately one week of instruction (2-3 class periods of 75-90 minutes each). Some chapters with more MicroSims may take longer.

Using the MicroSims

What is a MicroSim?

A MicroSim (short for "micro-simulation") is a small, interactive simulation that runs directly in a web browser. Students don't need to install any software — MicroSims work on any device with a modern web browser (Chrome, Firefox, Safari, Edge).

Each MicroSim lets students manipulate one or more variables (using sliders, buttons, or drag-and-drop) and immediately see how the model responds. This "learn by doing" approach helps students build intuition for abstract concepts.

How MicroSims Are Embedded

MicroSims appear within chapter text as rectangular interactive areas. They are embedded using iframes — a web technology that displays one web page inside another. You don't need to understand how iframes work; just know that the MicroSims load automatically when students view the chapter page.

Types of MicroSims

The textbook includes over 53 MicroSims built with different visualization technologies:

Technology	What It's Good For	Example MicroSims
p5.js	Interactive animations with sliders and buttons	BFS vs DFS Traversal, Dynamic Programming Alignment Matrix, Volcano Plot
vis-network	Network diagrams showing connections	Biological Database Ecosystem, PPI Knowledge Graph Schema, Signaling Cascade

Tips for Using MicroSims in Class

Project them on a screen — MicroSims are designed to be visible on a projector. Have students call out predictions before you move a slider.
Let students explore independently — After a demonstration, give students 5-10 minutes to experiment on their own devices.
Use the "Reset" button — Every MicroSim has a reset button. Encourage students to reset and try different scenarios.
Connect to the text — Each MicroSim is placed near the concept it illustrates. After exploring the sim, have students re-read the surrounding text.
Offline access — MicroSims require an internet connection unless you have built the site locally (see "Customizing Your Own Textbook" below).

Olli's Tip: Embed MicroSims Anywhere!

You can add any MicroSim to any web page — a Google Site, a WordPress blog, an LMS like Canvas or Schoology, or even a plain HTML file. Just paste a single line of HTML:

<iframe src="https://dmccreary.github.io/bioinformatics/sims/YOUR-MICROSIM-NAME/main.html"
    width="100%" height="450px"
    scrolling="no">
</iframe>

Replace YOUR-MICROSIM-NAME with the name of any MicroSim from the MicroSims list. That's it — one line of code and your students have an interactive simulation on any page you control.

Using the Glossary

What is the Glossary?

The glossary is an alphabetical list of all 480 key terms used in the textbook, each with a precise, concise definition. It serves as a quick-reference dictionary for students encountering unfamiliar vocabulary.

How to Access the Glossary

Click "Glossary" in the left navigation sidebar from any page
Use the browser's built-in search (Ctrl+F on Windows/Linux, Cmd+F on Mac) to find a specific term on the glossary page
Use the site-wide search bar at the top of any page to search for a term across the entire textbook

Tips for Using the Glossary in Class

Vocabulary preview — Before starting a new chapter, have students look up the key terms in the glossary to build familiarity.
Definition matching — Create a warm-up activity where students match glossary definitions to terms from the current chapter.
Student-generated definitions — After reading a chapter, have students write their own definitions, then compare with the glossary.
Glossary quizzes — Use glossary terms for quick formative assessments (flash cards, quiz games, etc.).

Using the FAQ

What is the FAQ?

The FAQ (Frequently Asked Questions) is a curated list of common questions students ask about bioinformatics, organized by topic. Each question includes a clear, concise answer written at the same reading level as the chapters.

How the FAQ is Organized

The FAQ covers questions across all 16 chapters. Questions are grouped into six categories: Getting Started, Core Concepts, Technical Details, Common Challenges, Best Practices, and Advanced Topics.

Tips for Using the FAQ in Class

Discussion starters — Pick 2-3 FAQ questions at the start of class and have students discuss before revealing the answer.
Homework support — Point students to the FAQ when they have questions outside of class hours.
Extension reading — The FAQ often covers angles not addressed in the main chapter text, making it good supplementary material.
Test review — Students can use the FAQ as a study guide before assessments.

Using the Quizzes

What Are the Quizzes?

Each chapter has an accompanying quiz page with 10 multiple-choice questions designed for self-assessment. Quizzes test understanding of the concepts covered in that chapter and are aligned to specific items from the learning graph.

How Quizzes Work

Quizzes are accessed by clicking the "Quiz" link under each chapter in the left navigation
Each quiz contains multiple-choice questions at varying Bloom's Taxonomy levels
Questions are presented as expandable sections — students can click to reveal the answer and explanation after attempting the question
Quizzes are not graded automatically — they are designed as formative self-check tools, not summative assessments

Tips for Using Quizzes in Class

Exit tickets — Have students complete the quiz at the end of a class period as a quick check for understanding.
Pre-reading check — Assign the quiz before the chapter to see what students already know (diagnostic assessment).
Post-reading review — Use the quiz after reading to identify concepts that need re-teaching.
Collaborative quiz — Have students work in pairs to discuss each question before revealing the answer.
Custom assessments — Use the quiz questions as a bank to create your own tests. The questions are openly licensed (see "Understanding the License" below).

Bloom's Taxonomy Levels

Each quiz question is tagged with a Bloom's Taxonomy level. Bloom's Taxonomy is a framework that classifies thinking skills from simple to complex:

Level	Name	What It Means	Example Verb
L1	Remember	Recall facts and definitions	Define, list, name
L2	Understand	Explain concepts in your own words	Explain, describe, compare
L3	Apply	Use concepts to solve problems	Calculate, demonstrate, solve
L4	Analyze	Break down and examine relationships	Differentiate, organize, compare
L5	Evaluate	Make judgments based on criteria	Assess, argue, justify
L6	Create	Produce original work or solutions	Design, construct, propose

A well-balanced assessment includes questions across multiple levels. The quizzes in this textbook primarily target levels L1-L4, with practice questions in the chapters targeting L5-L6.

Using the References

What Are the References?

Each chapter has an accompanying references page with a curated list of 10 high-quality sources that students can use for further reading. References prioritize Wikipedia articles for accessibility and reliability, supplemented by authoritative textbooks and online resources.

How References Are Organized

Each reference includes:

Title — The name of the source
URL — A clickable link to the source (where applicable)
Relevance — A brief description of why this source is useful and how it connects to the chapter content

A Note About Link Rot

Link rot is when a web link (URL) stops working because the page has been moved, renamed, or deleted. This is a common problem with any resource that links to external websites. While we prioritize Wikipedia (which has very stable URLs), some links may become outdated over time.

If you or your students encounter a broken link:

Try searching for the article title on the source website
Use the Wayback Machine to find archived versions of the page
Report the broken link using GitHub Issues (see "Feedback" below)

Feedback

Reporting Issues and Suggestions

This textbook is an open-source project hosted on GitHub, a website where software and content projects are developed collaboratively. You don't need to understand programming to report a problem or suggest an improvement.

What is a GitHub Issue?

A GitHub Issue is like a support ticket — it's a way to report a bug, suggest an improvement, or ask a question. Each issue gets a unique number and can be discussed by the project team and community.

How to Submit Feedback

Go to the textbook's GitHub repository: dmccreary/bioinformatics
Click the "Issues" tab at the top of the page
Click the green "New issue" button
Give your issue a clear title (e.g., "Broken link in Chapter 5 references" or "Suggestion: Add MicroSim for topic X")
In the description, provide as much detail as possible:
- Which page or chapter has the problem
- What you expected to see vs. what you actually see
- Your browser and device (if relevant)
Click "Submit new issue"

You will need a free GitHub account to submit issues. If you prefer not to create an account, you can email feedback to the author using the contact page.

Types of Feedback Welcome

Typos and errors — factual mistakes, spelling errors, broken formatting
Broken links — URLs that no longer work
MicroSim bugs — simulations that don't load or behave unexpectedly
Content suggestions — topics that should be covered, examples that could be improved
Accessibility issues — content that is difficult to read or navigate for students with disabilities

Understanding the License

What is a Creative Commons License?

A license is a legal document that explains what others are allowed to do with a piece of work. A Creative Commons (CC) license is a standardized, easy-to-understand license used for educational and creative content. It tells you exactly what permissions you have without needing a lawyer.

This Textbook's License

This textbook uses the CC BY-NC-SA 4.0 license. Here's what each part means:

Code	Full Name	What It Means
CC	Creative Commons	A standard open license
BY	Attribution	You must give credit to the original author
NC	Non-Commercial	You cannot use the material to make money
SA	Share-Alike	If you modify the material, you must share it under the same license
4.0	Version 4.0	The version of the license (the current standard)

What You CAN Do

Copy the entire textbook or individual chapters for your students
Share the textbook link with other teachers, students, or parents
Print chapters for classroom use
Modify the content — add your own examples, remove sections, change the order
Translate the content into other languages
Create derivative works — build your own version of the textbook based on this one

What You CANNOT Do

Sell the textbook or charge students for access
Remove attribution — you must credit the original author (Dan McCreary)
Use a different license — if you modify and share, it must remain CC BY-NC-SA 4.0
Claim it as your own work — the attribution requirement means you must acknowledge the original source

For the full legal text, see the Creative Commons License page.

Customizing Your Own Textbook

One of the most powerful features of this textbook is that you can create your own customized version. This section explains how, step by step.

Key Technical Terms

Before we begin, here are some terms you'll need to understand:

Repository (repo) — A folder on GitHub that contains all the files for a project. Think of it as the project's home directory.
Git — A version control tool that tracks changes to files. It lets you see what changed, when, and by whom.
Clone — Making a complete copy of a repository on your own computer.
Fork — Making a complete copy of a repository on your own GitHub account (stays on GitHub, not your computer).
MkDocs — The software that converts the textbook's markdown files into a website. You don't need to learn MkDocs deeply — just enough to make basic changes.
Markdown — A simple text formatting language. If you can write an email, you can write Markdown. **bold** makes bold, # Heading makes a heading, and - makes a bullet point.
mkdocs.yml — The main configuration file for the textbook website. It controls the site title, navigation structure, colors, and which features are enabled.

Step 1: Create a GitHub Account

If you don't already have one, go to github.com and create a free account.

Step 2: Fork or Clone the Repository

Option A: Fork (easier, stays on GitHub)

Go to dmccreary/bioinformatics
Click the "Fork" button in the upper-right corner
This creates a copy in your own GitHub account that you can edit

Option B: Clone (more control, works on your computer)

Install Git on your computer (git-scm.com)
Open a terminal (Command Prompt on Windows, Terminal on Mac)
Run this command:

1	`git clone https://github.com/dmccreary/bioinformatics.git`

This downloads the entire textbook to your computer.

Step 3: Make Changes

All content files are in the docs/ folder. They are written in Markdown (.md files) — plain text files with simple formatting. You can edit them with any text editor.

Changing the Title and Description

Open mkdocs.yml and edit these lines:

site_name: "Your Custom Textbook Title"
site_description: "Your description here"
site_author: "Your Name"

Changing the Colors

In mkdocs.yml, find the palette section:

theme:
  palette:
    primary: teal      # Change to: blue, red, purple, green, etc.
    accent: white      # Change the accent color

MkDocs Material supports these primary colors: red, pink, purple, deep purple, indigo, blue, light blue, cyan, teal, green, light green, lime, yellow, amber, orange, deep orange, brown, grey, blue grey.

Changing the Logo

Replace the file docs/img/logo.png with your own logo image (PNG format, approximately 128x128 pixels).

Step 4: Preview Your Changes Locally

Install Python (version 3.8 or newer) from python.org
Install MkDocs and the Material theme:

pip install mkdocs mkdocs-material

Navigate to the project folder and start the preview server:

cd bioinformatics
mkdocs serve

Open your browser to http://127.0.0.1:8000/bioinformatics/ to see your customized version

The preview server watches for file changes. When you edit and save a Markdown file, the page automatically refreshes in your browser.

Step 5: Publish Your Version

To publish your customized textbook as a free website using GitHub Pages:

1	`mkdocs gh-deploy`

This command builds the website and publishes it to https://YOUR-USERNAME.github.io/bioinformatics/. The process takes about 1-2 minutes.

Customizing Your Analytics

What is Web Analytics?

Web analytics is the process of measuring how visitors use a website — which pages they visit, how long they stay, and where they come from. For an educational textbook, analytics can help you understand which chapters students read most, which MicroSims they interact with, and where they might be struggling.

Google Analytics

This textbook can be configured with Google Analytics — a free service from Google that tracks website visits. If you create your own fork, you can set up your own analytics.

Setting Up Your Own Google Analytics

Go to analytics.google.com and sign in with a Google account
Create a new property (Google's term for a tracked website)
Google will give you a Measurement ID — a code that looks like G-XXXXXXXXXX
In your mkdocs.yml, update this section:

extra:
  analytics:
    provider: google
    property: G-YOUR-MEASUREMENT-ID

Rebuild and deploy your site. Analytics data will start appearing within 24-48 hours.

What You Can Learn from Analytics

Which chapters are most/least visited — helps you identify where students might be skipping content
Average time on page — longer times may indicate engagement or confusion
Device breakdown — what percentage of students use phones vs. computers
Geographic distribution — where your students are accessing from
Search terms — what students search for on your site

xAPI Monitoring (Advanced)

xAPI (Experience API, also called "Tin Can API") is an advanced standard for tracking detailed learning activities — not just page views, but specific interactions like "student moved a slider to position X" or "student answered quiz question 3 correctly."

What is an LRS?

An LRS (Learning Record Store) is a database that stores xAPI learning records. Think of it as a specialized analytics system designed specifically for education. If you use an LRS, you can track granular student learning data.

Important: Regulatory Considerations

Before collecting student-specific learning data, be aware of these regulations:

FERPA (Family Educational Rights and Privacy Act) — U.S. federal law that protects student education records. If you collect data that can identify individual students, you must comply with FERPA.
COPPA (Children's Online Privacy Protection Act) — U.S. federal law that applies to children under 13. If any of your students are under 13, additional restrictions apply.
State laws — Many U.S. states have additional student privacy laws.
GDPR (General Data Protection Regulation) — European Union law that applies if any of your students are in the EU.

Recommendation: The Google Analytics setup described above is anonymous by default — it tracks aggregate page views, not individual students. This is the safest approach. If you want individual student tracking via xAPI, consult your school district's data privacy officer before proceeding.

The Learning Graph

What is a Learning Graph?

A learning graph is a visual map showing how concepts in the textbook depend on each other. It is structured as a DAG (Directed Acyclic Graph) — a diagram where arrows show which concepts must be understood before others.

For example, understanding "Flux Balance Analysis" requires first mastering "Metabolic Network," "Stoichiometric Matrix," and "Constraint-Based Modeling." The learning graph makes these dependency chains visible.

How Teachers Can Use the Learning Graph

Prerequisite checking — Before teaching a concept, verify that students have covered its prerequisites
Remediation — If a student struggles with a concept, trace back to its prerequisites to find the gap
Curriculum mapping — Compare the learning graph to your existing syllabus to identify coverage gaps
Enrichment — Advanced students can explore concepts ahead of the current chapter by following the graph forward

The interactive Learning Graph Viewer is available in the "Learning Graph" section of the left navigation.

Olli the Octopus: Your Pedagogical Agent

What is a Pedagogical Agent?

A pedagogical agent is a character that appears throughout a textbook to guide students. Research shows that pedagogical agents improve student engagement and perception of learning — a phenomenon called the persona effect.

How Olli Appears

Olli the Octopus appears as colored callout boxes (called admonitions) throughout each chapter. There are seven types:

Type	Color	Purpose	Frequency
Welcome	Green	Introduces the chapter	Every chapter opening
Thinking	Orange	Highlights key insights	1-2 per chapter
Tip	Green	Shares practical advice	As needed
Warning	Red	Alerts to common mistakes	As needed
Encourage	Blue	Supports on harder concepts	Where students may struggle
Celebration	Purple	Celebrates progress	Every chapter ending
Neutral	Gray	General notes	As needed

Olli appears no more than 5-6 times per chapter to avoid overuse. Mascot admonitions are never placed back-to-back.

Tips for Teachers

Read Olli's tips aloud — They're written in a conversational tone that works well when spoken
Use as discussion prompts — Olli's "thinking" admonitions highlight the most important insights in each chapter
Encourage struggling students — Point students to Olli's "encourage" admonitions when they're frustrated with a concept
"Let's connect the dots!" — Olli's catchphrase is a natural prompt for asking students to relate concepts to each other