Simplify README setup instructions and update author links

- Remove detailed Part 1-5 setup instructions, refer to PDF manual instead
- Add link to Keefe Reuther's website
- Update acknowledgments section

README.md

@@ -10,12 +10,11 @@ pinned: true
 license: gpl-3.0
 short_description: AI-enhanced study app for students
 ---
-
 # Schema Study: An AI-Enhanced Study App for Biology Students
 
 Schema Study is a free, no-code, open-source web application that turns a spreadsheet of course terms into an AI-powered study coach. Designed for asynchronous student learning and inquiry, Schema Study helps biology students master core course concepts through evidence-based AI-powered conversations. The app leverages OpenAI's latest GPT models via the Responses API to provide instant formative feedback, Socratic questioning, and personalized study support.
 
-**Key Pedagogical Approach:** Schema Study uses a Socratic questioning method that (1) withholds direct solutions while providing brief, targeted feedback, (2) poses exactly one scenario-grounded follow-up question per turn, and (3) presses for mechanistic reasoning, justification, and connections between concepts. The tool provides formative practice through question-led dialogue; independent performance is evaluated in secure assessments outside the app.
+**Key Pedagogical Approach:** Schema Study uses a Socratic questioning method that (1) withholds direct solutions while providing brief, targeted feedback, (2) poses exactly one scenario-grounded follow-up question per turn, and (3) presses for mechanistic reasoning, justification, and connections between concepts. The tool provides formative practice through question-led dialogue.
 
 ## Features
 
@@ -34,16 +33,16 @@ Schema Study is a free, no-code, open-source web application that turns a spread
 
 Before creating your own copy, explore the evaluation versions:
 
-- **Version 1** (Winter 2025): [https://huggingface.co/spaces/keefereuther/Schema_Study_v1](https://huggingface.co/spaces/keefereuther/Schema_Study_v1)
+- **Version 1** (Legacy): [https://huggingface.co/spaces/keefereuther/Schema_Study_v1](https://huggingface.co/spaces/keefereuther/Schema_Study_v1)
 - **Version 2** (Current Preview): [https://huggingface.co/spaces/keefereuther/Schema_Study_Preview](https://huggingface.co/spaces/keefereuther/Schema_Study_Preview)
 
 **Note:** These are evaluation versions for testing. You'll need your OpenAI API key to interact with the chatbot on these evaluation versions. The production version can be found at [https://huggingface.co/spaces/keefereuther/Schema_Study](https://huggingface.co/spaces/keefereuther/Schema_Study).
 
 ## How to Use (Students)
+
 1. **Access the App:** Go to your Hugging Face Space URL. Enter the password provided by your instructor.
 2. **Select a Term:** Use the dropdown to pick a course term.
-3. **Start Studying:** Respond to the prompt or use a template button to begin your session.
-4. **Chat with the AI:** Ask questions, answer prompts, and explore the term in depth.
+3. **Start Studying:** Respond to the prompt or use a template button to begin your session. Ask questions, answer prompts, and explore the term in depth.
 
 ## How to Use (Instructors)
 
@@ -57,102 +56,17 @@ Before starting, you'll need:
 - Your course syllabus or a list of course learning objectives
 - About 1-2 hours to create your customized copy of Schema Study
 
-### Part 1: Setting Up Accounts
-
-#### 1. Create a Hugging Face Account
-
-Your chatbot will run inside a Hugging Face Space. Sign-up is browser-based and takes approximately 2 minutes.
-
-1. Go to [huggingface.co](https://huggingface.co) → Sign Up
-2. Verify your email before continuing
-
-#### 2. Open an OpenAI Platform Account
-
-**NOTE: This is different from a ChatGPT account.** An API (Application Programming Interface) is a way for your application to talk to OpenAI's systems. An API Key is like a special password that gives you permission to use OpenAI's services and keeps track of how much you're using.
-
-**Pricing Information:**
-- **GPT-4.1:** ~$2 per million input tokens, ~$8 per million output tokens
-- **GPT-5.1:** ~$1.25 per million input tokens, ~$10 per million output tokens
-- **GPT-5.2:** ~$1.75 per million input tokens, ~$14 per million output tokens
-
-*Note: One million tokens ≈ 750,000 words. Prices may vary by deployment tier.*
-
-1. Visit [platform.openai.com](https://platform.openai.com)
-2. Follow the [walkthrough video](https://www.youtube.com/watch?v=QiJ6cWm9Dx4) to generate an API key
-3. Preload $5-10 in API credits
-4. **Important:** Copy and save your API key in a secure place. You will need it later.
-
-### Part 2: Creating Your Terms CSV File
-
-1. **Download the template:** Use the `terms.csv` file as a starting point
-2. **Refine your TERM entries:**
-   - Do not alter column headers (TERM and CONTEXT)
-   - Edit the TERM column to contain terms and phrases relevant to your course learning objectives
-   - Terms can include concepts, case studies, people, course policies, mathematical/computing functions, or anything else you want students to learn deeply
-   - Add as many rows as you like
-3. **Tip:** Feed your syllabus to a generative AI chatbot (ChatGPT, Gemini, Claude) to generate a first draft of terms, then curate manually
-
-**CSV Format:**
-- First column: TERM (the term or concept name)
-- Second column: CONTEXT (definition, explanation, or course-specific context)
-
-### Part 3: Setting Up Your Hugging Face Space
+### Setup Instructions
 
-1. **Fork or Duplicate the Space:**
-   - Go to [https://huggingface.co/spaces/keefereuther/Schema_Study](https://huggingface.co/spaces/keefereuther/Schema_Study)
-   - Click "Duplicate this Space" to create your own copy
-   - Or clone via git:
-     ```bash
-     git clone https://huggingface.co/spaces/<your-username>/<your-space-name>
-     cd <your-space-name>
-     ```
+For comprehensive setup instructions, including account creation, terms CSV file creation, Hugging Face Space configuration, customization options, and sharing/embedding, please see the **[Schema Study User Manual](S2_user_manual_v3.pdf)** included in this repository.
 
-2. **Edit Configuration:**
-   - Update `config.py` for your course (title, instructions, prompt templates, etc.)
-   - Configure AI model settings:
-     - `ai_model`: Choose "gpt-5.2" (default), "gpt-5.1", or "gpt-4.1"
-     - `reasoning_effort`: For GPT-5.2 and GPT-5.1, set to "none" (fastest), "minimal", "low", or "medium"
-     - `enable_web_search`: Set to `True` or `False` (default: True)
-   - Place your terms CSV (e.g., `terms.csv`) in the root directory
-
-3. **Set Secrets:**
-   - In your Hugging Face Space, go to **Settings > Repository secrets**
-   - Add the following secrets:
-     - `username`: Your desired username for app access
-     - `password`: Your desired password for app access
-     - `OPENAI_API_KEY`: Your OpenAI API key
-
-4. **Push Changes:**
-   ```bash
-   git add .
-   git commit -m "Update configuration and terms"
-   git push
-   ```
-
-### Part 4: Customizing Schema Study
-
-All customization is done through `config.py`. Key sections include:
-
-- **A. Basic App Settings:** App title, terms CSV file, warning messages
-- **B. AI Model Settings:** Model selection, reasoning effort, temperature, web search
-- **C. Student Instructions:** Instructions displayed in the expander
-- **D. Prompt Template Buttons:** Five customizable conversation starters
-- **E. Attribution & License:** Sidebar footer information
-- **F. Resources List:** Sidebar links and downloadable files
-- **G. AI System Prompt:** Advanced customization of the tutor's behavior
-
-See the user manual (S2_user_manual_v3.pdf) for detailed configuration instructions.
-
-### Part 5: Sharing and Embedding
-
-1. **Share via Direct Link:** Copy your Space URL and share with students along with the username & password
-2. **Embed in LMS:** In the Space header, select "Embed this Space" and copy the `<iframe>` snippet. Post or embed inside your LMS (e.g., Canvas) along with the username & password. Students can authenticate seamlessly within your course platform.
-
-### Model Selection Guide
-
-- **GPT-5.2** (default): Latest reasoning model, fastest with reasoning="none", supports web search
-- **GPT-5.1**: Reasoning model with reasoning="none" default for faster responses, supports web search
-- **GPT-4.1**: Use if you need temperature control or prefer non-reasoning model, excellent web search support
+The user manual provides step-by-step guidance for:
+- Setting up Hugging Face and OpenAI accounts
+- Creating and customizing your terms CSV file
+- Configuring your Hugging Face Space
+- Customizing all app settings through `config.py`
+- Sharing and embedding Schema Study in your LMS
+- Model selection and pricing information
 
 ## Configuration
 
@@ -169,6 +83,7 @@ See the user manual (S2_user_manual_v3.pdf) for detailed configuration instructi
 Schema Study enforces structured pacing to prevent cognitive overload. The system prompt enforces **one focused question plus one short, realistic application example per turn** to reduce confusion from multiple simultaneous follow-ups.
 
 **Universal Design for Learning (UDL) Adjustments:**
+
 - **For additional scaffolding:** Modify `term_prompt` to allow brief clarifying questions
 - **For advanced students:** Add instructions to keep responses focused and move efficiently toward connections
 
@@ -183,6 +98,7 @@ The five prompt templates provide structured entry points for students who need
 ## Technical Details
 
 ### API & Models
+
 - **API Framework:** OpenAI Responses API (streaming-enabled)
 - **Supported Models:** GPT-5.2 (default), GPT-5.1, GPT-4.1
 - **Streaming:** Real-time token-by-token response streaming
@@ -200,6 +116,7 @@ The five prompt templates provide structured entry points for students who need
 - `S2_user_manual_v3.pdf` — Comprehensive user manual with detailed setup and configuration instructions
 
 ## License
+
 This project is licensed under the GNU GPL-3 License. See the [LICENSE](LICENSE) file for details.
 
 ## Best Practices for Integration
@@ -214,7 +131,7 @@ Based on classroom testing and iterative refinement, here are recommended best p
 
 ## Research & Citation
 
-This app, its corresponding manuscript, and all documentation was authored, edited, and tested by Keefe Reuther, [Liam O Mueller](https://biology.ucsd.edu/research/faculty/lomueller), Grace Constantian, Albert Nguyen, and the members of the Reuther Lab.
+This app, its corresponding manuscript, and all documentation was authored, edited, and tested by [Keefe Reuther](https://keefereuther.com), [Liam O Mueller](https://biology.ucsd.edu/research/faculty/lomueller), Grace Constantian, and Albert Nguyen.
 
 Schema Study was developed to address critical challenges in undergraduate biology education: providing immediate, personalized formative feedback to increasingly large, diverse classes. The app uses evidence-based teaching practices and Socratic questioning to deepen understanding, correct misconceptions, and encourage students to find connections among course concepts.
 
@@ -228,10 +145,8 @@ The production version of this app can be found at [https://huggingface.co/space
 
 ## Acknowledgments
 
-Developed by Keefe Reuther, Assistant Teaching Professor in the UC San Diego School of Biological Sciences. Special thanks to Dr. Liam O Mueller, Grace Constantian, Albert Nguyen, and the members of the Reuther Lab for their support and contributions.
-
 This work was supported by University of California, San Diego intramural grants TG114333 and RG113974.
 
 ## Support
 
-For questions about creating your own version of this application for use in your classroom, please email kdreuther@ucsd.edu.
+For questions about creating your own version of this application for use in your classroom, please email kdreuther@ucsd.edu.