add files

.devcontainer/devcontainer.json

@@ -0,0 +1,33 @@
+{
+  "name": "Python 3",
+  // Or use a Dockerfile or Docker Compose file. More info: https://containers.dev/guide/dockerfile
+  "image": "mcr.microsoft.com/devcontainers/python:1-3.11-bullseye",
+  "customizations": {
+    "codespaces": {
+      "openFiles": [
+        "README.md",
+        "app.py"
+      ]
+    },
+    "vscode": {
+      "settings": {},
+      "extensions": [
+        "ms-python.python",
+        "ms-python.vscode-pylance"
+      ]
+    }
+  },
+  "updateContentCommand": "[ -f packages.txt ] && sudo apt update && sudo apt upgrade -y && sudo xargs apt install -y <packages.txt; [ -f requirements.txt ] && pip3 install --user -r requirements.txt; pip3 install --user streamlit; echo '✅ Packages installed and Requirements met'",
+  "postAttachCommand": {
+    "server": "streamlit run app.py --server.enableCORS false --server.enableXsrfProtection false"
+  },
+  "portsAttributes": {
+    "8501": {
+      "label": "Application",
+      "onAutoForward": "openPreview"
+    }
+  },
+  "forwardPorts": [
+    8501
+  ]
+}

.gitignore

@@ -0,0 +1,165 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+*copy.py
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Streamlit stuff:
+.streamlit/
+secrets.toml
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+.pybuilder/
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/#use-with-ide
+.pdm.toml
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/

LICENSE

@@ -0,0 +1,674 @@
+                    GNU GENERAL PUBLIC LICENSE
+                       Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc. <https://fsf.org/>
+ Everyone is permitted to copy and distribute verbatim copies
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+
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+(such as an express permission to practice a patent or covenant not to
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+
+  If you convey a covered work, knowingly relying on a patent license,
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+available, or (2) arrange to deprive yourself of the benefit of the
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+consistent with the requirements of this License, to extend the patent
+license to downstream recipients.  "Knowingly relying" means you have
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+
+  If, pursuant to or in connection with a single transaction or
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+
+  A patent license is "discriminatory" if it does not include within
+the scope of its coverage, prohibits the exercise of, or is
+conditioned on the non-exercise of one or more of the rights that are
+specifically granted under this License.  You may not convey a covered
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+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+  Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+  12. No Surrender of Others' Freedom.
+
+  If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License.  If you cannot convey a
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+not convey it at all.  For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+  13. Use with the GNU Affero General Public License.
+
+  Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU Affero General Public License into a single
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+section 13, concerning interaction through a network will apply to the
+combination as such.
+
+  14. Revised Versions of this License.
+
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+be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+  Each version is given a distinguishing version number.  If the
+Program specifies that a certain numbered version of the GNU General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation.  If the Program does not specify a version number of the
+GNU General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+  If the Program specifies that a proxy can decide which future
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+
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+  15. Disclaimer of Warranty.
+
+  THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
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+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

@@ -12,3 +12,90 @@ short_description: Study app chatbot based on OpenAI API
 ---
 
 Check out the configuration reference at https://huggingface.co/docs/hub/spaces-config-reference
+
+# Schema Study: An AI-Enhanced Study App for Biology Students
+
+Schema Study is a DIY AI-Enhanced Study App designed to assist biology students in mastering core course concepts through interactive study sessions. This application leverages AI technology to provide instant feedback and guidance, making it a valuable tool for both students and educators.
+
+## Pedagogical Value
+
+Schema Study enhances the learning experience by:
+
+- **Promoting Active Learning:** Students engage with course material interactively, which helps reinforce their understanding.
+- **Providing Instant Feedback:** The AI-powered chatbot offers immediate responses, allowing students to correct misconceptions in real-time.
+- **Encouraging Critical Thinking:** By using the Socratic method, the app guides students to explore concepts deeply and make connections between different terms.
+- **Customizable Content:** Educators can tailor the app to their curriculum by uploading specific terms and schemas, ensuring relevance to their course.
+
+## Features
+
+- **Password Protection:** Ensures secure access to the app.
+- **Customizable Terms:** Educators can upload a CSV file with their own terms and schemas.
+- **AI-Enhanced Feedback:** Utilizes OpenAI's GPT-4o model to provide detailed explanations and formative feedback.
+- **Interactive Chat:** Engages students in a dialogue with the AI chatbot to deepen their understanding.
+
+## How the App Works
+
+### For Students
+
+1. **Access the App:** Open your web browser and navigate to `http://localhost:8501`. Enter the password when prompted.
+2. **Upload Terms:** Use the sidebar file uploader to upload a CSV file containing terms and schemas. The file should have two columns: `TERM` and `SCHEMA`.
+3. **Start Studying:** Click the button to select a random term and begin your interactive study session with the AI chatbot.
+4. **Engage with the AI:** Use the chat interface to ask questions and receive feedback on your understanding of the term.
+
+### For Instructors
+
+1. **Clone the Repository:**
+
+   ```bash
+   git clone https://github.com/keefereuther/schema_study.git
+   cd schema_study
+   ```
+
+2. **Install the Required Packages:**
+
+   ```bash
+   pip install -r requirements.txt
+   ```
+
+3. **Set Up Your Configuration:**
+
+   Update the `config.py` file with your desired settings.
+
+4. **Create a '.streamlit/secrets.toml' file and directory.**
+
+   Add your OpenAI API key and the app password:
+
+   ```toml
+   [general]
+   OPENAI_API_KEY = "your-openai-api-key"
+   password = "your-app-password"
+   ```
+
+5. **Run the App:**
+
+   ```bash
+   streamlit run app.py
+   ```
+
+## Configuration
+
+The `config.py` file contains customizable settings for the app. Key settings include:
+
+- `app_title`: The title of the app.
+- `app_author`: Author information.
+- `instructions`: Instructions for using the app.
+- `sidebar_title`: Title for the sidebar section.
+- `default_terms_csv`: Default CSV file for terms.
+- AI model settings like `ai_model`, `temperature`, `max_tokens`, `frequency_penalty`, and `presence_penalty`.
+
+## Contributing
+
+Contributions are welcome! Please fork the repository and submit pull requests for any improvements or bug fixes.
+
+## License
+
+This project is licensed under the GNU GPL-3 License - see the [LICENSE](LICENSE) file for details.
+
+## Acknowledgments
+
+Developed by Keefe Reuther and Liam O Mueller, Assistant Teaching Professors in the UC San Diego School of Biological Sciences. Special thanks to the members of the Reuther Lab for their support and contributions.

app.py

@@ -0,0 +1,305 @@
+############################################################################################################
+# Importing Libraries
+
+import streamlit as st
+import hmac
+import pandas as pd
+import random
+import os
+import time
+import base64
+import logging
+import io
+import config
+from openai import OpenAI
+
+############################################################################################################
+# Password protection
+
+def check_password():
+    """Returns `True` if the user had the correct password."""
+
+    def password_entered():
+        """Checks whether a password entered by the user is correct."""
+        if hmac.compare_digest(st.session_state["password"], st.secrets["password"]):
+            st.session_state["password_correct"] = True
+            del st.session_state["password"]  # Don't store the password.
+        else:
+            st.session_state["password_correct"] = False
+
+    # Return True if the password is validated.
+    if st.session_state.get("password_correct", False):
+        return True
+
+    # Show input for password.
+    st.text_input(
+        "Password", type="password", on_change=password_entered, key="password"
+    )
+    if "password_correct" in st.session_state:
+        st.error("😕 Password incorrect")
+    return False
+
+if not check_password():
+    st.stop()  # Do not continue if check_password is not True.
+
+############################################################################################################
+# Streamlit app layout
+
+# Set the page to wide or centered mode
+st.set_page_config(layout="wide")
+
+# Load the terms file into a DataFrame
+df = pd.read_csv(config.default_terms_csv)
+
+# Streamlit app layout
+st.title(config.app_title)
+st.markdown(config.intro_para)
+st.caption(config.app_author)
+with st.expander("INSTRUCTIONS FOR STUDENTS:"):
+    st.markdown(config.instructions)
+with st.expander("**INSTRUCTORS**: For a look at the current terms file driving the interaction, click here:"):
+    st.markdown("This is the terms.csv file that drives the interaction. You can edit this file to change the terms and context that the chatbot uses. You may add any term or phrase. You may leave the context blank if you prefer or you can add anything relevant that the GPT does not normally know about the term. This may include relevant learning objectives, course examples, notable scientists, assessment dates, syllabus information, etc.")
+    st.table(df)
+with st.expander("**INSTRUCTORS**: For a look at the prompt driving the chatbot, click here:"):
+    st.markdown(config.display_prompt)
+st.sidebar.title(config.sidebar_title)
+with st.sidebar:
+        with st.expander("Click here for instructions."):
+            st.write(config.sidebar_instructions)
+
+############################################################################################################
+# File Uploader in sidebar
+
+# Load terms from a CSV file
+# https://discuss.streamlit.io/t/how-to-upload-a-csv-file/7052/2
+def load_terms(file_input):
+    try:
+        if isinstance(file_input, str):
+            data = pd.read_csv(file_input)
+        else:
+            data = pd.read_csv(io.StringIO(file_input.read().decode('utf-8')))
+        return data
+    except Exception as e:
+        st.error(f"An error occurred while loading the file: {str(e)}")
+        logging.exception(f"Error loading file: {e}")
+
+# Function to create a download link for a file
+def create_download_link(file_path, file_name):
+    try:
+        with open(file_path, "rb") as file:
+            file_content = file.read()
+        encoded_content = base64.b64encode(file_content).decode("utf-8")
+        download_link = f'<a href="data:file/csv;base64,{encoded_content}" download="{file_name}">Download {file_name}</a>'
+        return download_link
+    except FileNotFoundError:
+        error_message = f"The file {file_name} was not found."
+        st.error(error_message)
+        logging.exception(error_message)
+    except Exception as e:
+        error_message = f"An error occurred: {str(e)}"
+        st.error(error_message)
+        logging.exception(error_message)
+
+# Function to extract the first column values
+def get_first_column_values(df):
+    if not df.empty:
+        return df.iloc[:, 0].tolist()
+    else:
+        return []
+
+# Download link for the template file
+template_file_path = config.default_terms_csv
+
+# File Uploader
+uploaded_file = st.sidebar.file_uploader(" ", type=["csv"])
+if uploaded_file is not None:
+    logging.info(f"File uploaded: {uploaded_file.name}")
+    st.session_state.uploaded_file = uploaded_file
+
+# Load terms from the file
+if 'uploaded_file' in st.session_state and st.session_state.uploaded_file is not None:
+    terms = load_terms(st.session_state.uploaded_file)
+else:
+    terms = load_terms(template_file_path)
+
+# Extract first column values
+term_list = get_first_column_values(terms)
+
+st.sidebar.markdown(create_download_link(template_file_path, "terms.csv"), unsafe_allow_html=True)
+
+# line break in the sidebar
+st.sidebar.markdown('<hr>', unsafe_allow_html=True)
+
+############################################################################################################
+# Term Selection and session state
+
+# Define a basic initial context at the beginning of your script
+initial_context = {
+    "role": "system",
+    "content": config.initial_prompt
+}
+
+# Initialize the session state variables for selected term, context, and display messages
+if 'selected_term' not in st.session_state:
+    st.session_state.selected_term = None
+if 'selected_context' not in st.session_state:
+    st.session_state.selected_context = None
+if 'display_messages' not in st.session_state:
+    st.session_state.display_messages = [initial_context]
+
+# Initialize session states for the selected term, counter, and display flag
+if 'selected_term' not in st.session_state:
+    st.session_state.selected_term = None
+if 'display_term' not in st.session_state:
+   st.session_state.display_term = False
+
+# Dropdown menu for selecting a term
+selected_term = st.selectbox('Select a term/question and brainstorm everything about it. This could include a definition, examples, misconceptions, associations, etc.', term_list)
+if selected_term:
+    selected_context = terms.loc[terms['TERM'] == selected_term, 'CONTEXT'].values[0]
+    st.session_state.selected_term = selected_term
+    st.session_state.selected_context = selected_context
+    st.session_state.display_term = True
+
+# Ensure the session state variables are set correctly
+# if st.session_state.get('selected_term') and st.session_state.get('selected_context'):
+    # Update the prompt for the API
+    updated_prompt = config.term_prompt(st.session_state.selected_term, st.session_state.selected_context, term_list)
+    initial_context = {
+        "role": "system", 
+        "content": updated_prompt
+    }
+    # Reset the conversation with the new initial context
+    st.session_state.display_messages[0] = [initial_context]
+
+# Display the selected term and its context
+if st.session_state.display_term and st.session_state.selected_term:
+    st.header(st.session_state.selected_term)
+    # Pass the displayed term to the assistant as part of the message
+    user_message = f"Define '{st.session_state.selected_term}':"
+elif not st.session_state.selected_term:
+    st.write("")
+
+############################################################################################################
+# ChatGPT
+# Initialize the OpenAI client
+client = OpenAI(api_key=st.secrets["OPENAI_API_KEY"])
+
+# Initialize the session state variables if they don't exist
+if "openai_model" not in st.session_state:
+    st.session_state["openai_model"] = config.ai_model
+
+if "display_messages" not in st.session_state:
+    st.session_state.display_messages[0] = [initial_context]
+
+# Update initial_context with the latest selected term and context
+if st.session_state.get('selected_term') and st.session_state.get('selected_context'):
+    updated_prompt = config.term_prompt(st.session_state.selected_term, st.session_state.selected_context, term_list)
+    initial_context = {
+        "role": "system", 
+        "content": updated_prompt
+    }
+    # Replace the initial context in display_messages with the updated prompt
+    st.session_state.display_messages[0] = initial_context
+
+# Get user input
+prompt = st.chat_input("Type your message here...")
+
+# Input for new messages
+if prompt:
+    # Ensure the initial context is in the session state, add the user's message
+    if not st.session_state["display_messages"]:
+        st.session_state["display_messages"].append(initial_context)
+    st.session_state["display_messages"].append({"role": "user", "content": prompt})
+
+# Function to reset all chat-related session state
+def reset_chat_history():
+    st.session_state["display_messages"] = [initial_context]
+    # Reset other chat-related session states if they exist
+    if 'selected_term' in st.session_state:
+        st.session_state.selected_term = None
+    if 'selected_context' in st.session_state:
+        st.session_state.selected_context = None
+    if 'display_term' in st.session_state:
+        st.session_state.display_term = False
+    st.rerun()
+
+# Main chat container
+with st.container(height=400, border=True):
+    # Display chat history in reverse order including new messages
+    for message in st.session_state["display_messages"][1:]:
+        if message["role"] == "user":
+            with st.chat_message("user"):
+                st.markdown(message["content"])
+        else:
+            with st.chat_message("assistant"):
+                st.markdown(message["content"])
+
+# Generate assistant's response and add it to the messages
+    if prompt:
+        with st.chat_message("assistant"):
+            try:
+                stream = client.chat.completions.create(
+                    model=st.session_state["openai_model"],
+                    messages=[
+                        {"role": m["role"], "content": m["content"]}
+                        for m in st.session_state["display_messages"]
+                    ],
+                    stream=True,
+                    temperature=config.temperature,
+                    max_tokens=config.max_tokens,
+                    frequency_penalty=config.frequency_penalty,
+                    presence_penalty=config.presence_penalty,
+                )
+                response = st.write_stream(stream)
+                # Append the full response to the session state for display
+                st.session_state["display_messages"].append(
+                    {"role": "assistant", "content": response}
+                )
+            except Exception as e:
+                st.error(f"An error occurred: {str(e)}")
+
+# Add Clear Chat History button between container and warning message
+if st.button("Clear Chat History"):
+    reset_chat_history()
+
+st.markdown(config.warning_message, unsafe_allow_html=True)
+
+############################################################################################################
+
+# Resources and About Sections in the Sidebar
+
+st.sidebar.title("Resources")
+
+for resource in config.resources:
+    with st.sidebar:
+        with st.sidebar:
+            with st.expander(resource["title"]):
+                st.markdown(f"Description: {resource['description']}")
+                if "url" in resource:
+                    st.markdown(f"[{resource['title']}]({resource['url']})")
+                if "file_path" in resource:
+                    file_path = resource["file_path"]
+                    if os.path.exists(file_path):
+                        with open(file_path, "rb") as file:
+                            file_bytes = file.read()
+                        with st.spinner(f"Loading {resource['title']}..."):
+                            st.download_button(
+                                label=resource["title"],
+                                data=file_bytes,
+                                file_name=os.path.basename(file_path),
+                                mime="application/octet-stream",
+                                help=resource["description"],
+                            )
+                    else:
+                        st.warning(f"File not found: {file_path}")
+
+# Footer
+with st.sidebar:
+    st.markdown("---")
+
+    st.title("About")
+
+   # Using the config objects in your Streamlit app
+    st.markdown(config.app_creation_message, unsafe_allow_html=True)
+    st.markdown(config.app_repo_license_message, unsafe_allow_html=True)

config.py

@@ -0,0 +1,243 @@
+# config.py
+
+# THIS IS THE FILE YOU SHOULD EDIT TO CUSTOMIZE THE APP. DO NOT EDIT app.py UNLESS YOU KNOW WHAT YOU ARE DOING.
+
+############################################################################################################
+
+# Below is the configuration for the chatbot
+
+# The model_name refers to the name of the model you want to use. You can choose from the following models: 
+ai_model = "gpt-4o"
+
+# Temperature refers to the randomness/creativity of the responses. A higher temperature will result in more random/creative responses. It varies between 0 and 1.
+temperature = 0.1
+
+# Max_tokens refers to the maximum number of tokens (words) the AI can generate. The higher the number, the longer the response. It varies between 1 and 2048.
+max_tokens = 1000
+
+# Frequency penalty parameter for the response. Higher penalty will result in more diverse responses. It varies between 0 and 1.
+frequency_penalty = 0.5
+
+# Presence penalty parameter for the response. Higher penalty will result in less repetitive responses. It varies between 0 and 1.
+presence_penalty = 0.4
+
+# Below is all the text you can customize for the app. Don't remove the quotations around the text. Don't change the variable names.
+
+############################################################################################################
+
+# Below is the name for your default csv terms file. You can change this to any csv file you want to use as your default terms file. It must be in the same folder as the main app.py file.
+
+default_terms_csv = "terms.csv"
+
+############################################################################################################
+
+# Below is all the text you can customize for the app. Don't remove the quotations around the text. Don't change the variable names.
+
+# The title of the app
+app_title = "Schema Study - Instructor Evaluation Version"
+
+# The subtitle of the app
+app_author = "by Keefe Reuther, Assistant Teaching Professor in the UC San Diego School of Biological Sciences"
+
+# This is an intro paragraph you can add under the title. it is not currently being used in the app.
+intro_para = "An AI-enhanced study app for biology students."
+
+# The user's instructions for the app
+instructions = '''
+The goal of this app is to help you learn and and assess your knowledge of core course concepts and examples. 
+1. Choose a course term/phrase from the drop down menu.
+2. *Pause and think for 30 seconds.* What is everything you associate with this term/phrase? What is a simple definition or example?
+3. Write as little or as much as you'd like about it. Try to include anything you might need to know for an exam. 
+4. Please follow-up with questions. If you don't know something, just ask. It is perfectly ok to write: "I have no idea what this term means." **Have a conversation!**
+---
+**WANT TO LEVEL UP?**
+- Ask the chatbot: 'I want to test my ability to connect this term to others in the term list. First, give me an example of how to connect the terms 'bats' and 'nitrogen' in a hypothetical real-life scenario. Second, prompt me to similarly create a logical applied scenario between the displayed term and one other you MUST CHOOSE RANDOMLY from the course term list. Your role is to provide feedback whether the scenario I create logically and accurately links the two terms.'
+- Ask the chatbot: 'Please give me an example mathematical problem that uses this term.'
+- Ask the chatbot: 'Please tell me two truths and a lie about this term. I need to choose the lie and explain my reasoning. Make the lies subtle and highlight common misconceptions.'
+- **Get creative! Play around and see what happens!**
+'''
+
+# The title of the sidebar
+sidebar_title = "Have your own terms to study?"
+
+# The instructions for the template
+sidebar_instructions = "Do you have your own terms to study? If so, download the terms_template.csv file. You can delete everything below the first row and add in your own terms in the first column. You can open and edit it in Excel, Google Sheets, or any text editor. Make sure that you don't change the file extension from csv. Once done, upload it below. The app will use your terms for the study session."
+
+app_creation_message = "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), and the members of the Reuther Lab - [https://reutherlab.biosci.ucsd.edu/](https://reutherlab.netlify.app/)"
+
+app_repo_license_message = "It can be found at [https://github.com/The-Reuther-Lab/schema_study](https://github.com/The-Reuther-Lab/schema_study) and is distributed under the GNU GPL-3 License. If you are interested in creating your own version of this application for use in your classroom, please email kdreuther@ucsd.edu for more information."
+
+warning_message = "**ChatGPT can make errors and does not replace verified and reputable online and classroom resources.**"
+
+###########################################################################################
+### PROMPTS
+
+# Below is the initial prompt that the AI will use to start the conversation with the user. The user will not see this prompt. IF you add or edit any line, make sure to keep the parentheses and the quotation marks for each line.
+initial_prompt = """You are Pliny 😊, a friendly and knowledgeable AI biology tutor for university students. Your mission is to help students build a robust understanding of biology terms and concepts to prepare for exams and integrate knowledge into their working schema. This includes clarifying definitions, providing examples, addressing misconceptions, exploring applications, and encouraging connections between terms. You NEVER directly answer a question without first trying to get the student to answer it themselves.
+
+**Guidelines:**
+
+- **Engagement and Schema-Building:**
+  - Encourage students to explore definitions, examples, misconceptions, assumptions, and applications of biology terms.
+  - Help students build an interconnected schema of biology terms and concepts.
+
+- **Communication Style:**
+  - Use clear, simple language and avoid unnecessary jargon.
+  - Be succinct and limit your total response to one short paragraph or less.
+  - Be approachable and professional.
+  - Provide information step-by-step to manage cognitive load.
+  - Use culturally inclusive examples and analogies.
+
+- **Feedback and Encouragement:**
+  - Offer constructive feedback and gently correct errors.
+  - Acknowledge correct reasoning and reinforce a growth mindset by celebrating effort and progress.
+  - Invite further questions to foster dialogue.
+
+- **Expectations for Interaction:**
+  - Explain that students will select a term to explore in depth.
+  - Unless there is a specific reason to do otherwise, you should assume the student is asking about the selected term.
+  - Encourage follow-up questions and iterative learning.
+
+- **Constraints:**
+  - You are only allowed to talk about topics relevant to what a biology student would need to know to succeed in a biology course, graduate, and follow a path to a relevant career. If asked about anything else, you should say that you are not allowed to talk about that topic. Connect it back to course terms and concepts.
+  - Do NOT answer multiple-choice, fill-in-the-blank, or true/false questions.
+"""
+
+# Below is the follow-up prompt that the AI will use once the user has typed a message. The user will not see this prompt.
+# DO NOT REMOVE/EDIT anything outside of the triple quotations. The text shown below must remain unedited within the code: 
+    # def term_prompt(selected_term, selected_context, term_list):
+        # return f"""
+# DO NOT REMOVE/EDIT anything inside the curly braces = '{selected_term}', '{selected_context}', '{term_list}'
+
+def term_prompt(selected_term, selected_context, term_list):
+    return f"""You are Pliny 😊, a supportive and knowledgeable biology tutor. Your goal is to provide concise, accurate, and supportive responses to assist the student's understanding of the term '{selected_term}'.
+
+**Guidelines:**
+
+- **Context-Driven Support:**
+  - **Unless there is a specific reason to do otherwise, you should assume the student is asking about '{selected_term}'.**
+  - Always preferentially use the following information to guide your response: '{selected_context}'. Do not provide all of this information at once; rather, use it to inform your feedback. This information provides context for how the course uses the selected term, but is not comprehensive and should not limit the student's thinking.
+  - Introduce information gradually to support learning. KEEP EACH RESPONSE SHORT.
+
+- **Critical Thinking and Engagement:**
+  - Assess and help build the student's understanding of the term '{selected_term}' starting at the lower levels of Bloom's Taxonomy and working their way up.
+  - Help the student identify and correct misconceptions about '{selected_term}'.
+
+- **Constructive Feedback:**
+  - Acknowledge correct aspects of the student's input.
+  - Provide supportive feedback to refine their understanding.
+
+- **Response Clarity and Continuity:**
+  - End your response by asking socratic questions to encourage continued engagement and guide the conversation to additional important information. __**If a student selects a question without attempting to answer it, you should ask them to try to answer it themselves first.**__ Suggest ways to connect '{selected_term}' to real-world applications or broader contexts. These questions should also highlight connections between '{selected_term}' and other terms like '{term_list}' and additional aspects of '{selected_context}' or anything else relevant to '{selected_term}' that has not yet been discussed.
+  - After EVERY SINGLE Socratic question you ask, follow it with a specific, relevant, hypothetical, applied, real-world scenario and a specific question that the student can answer to help them understand the broader concept.
+  - Aside from these questions you write, do not introduce any new information unless it is explicitly asked for or in direct response to providing constructive feedback to the student's input.
+
+- **Constraints:**
+  - You are only allowed to talk about topics relevant to what a biology student would need to know to succeed in a biology course, graduate, and follow a path to a relevant career. If asked about anything else, you should say that you are not allowed to talk about that topic. Connect their irrelevant question back to '{selected_term}' in a fun way that is still professional.
+  - Do NOT answer multiple-choice, fill-in-the-blank, or true/false questions. These are not allowed.
+
+(Note: Follow the initial guidelines provided for communication style and constraints.)
+"""
+
+# Below is the prompt that will be displayed to the instructor. It is the same as the term_prompt, but without the context from the terms.csv file.
+display_prompt = """
+### SYSTEM PROMPT - this is the prompt that the AI will use to start the conversation with the user. The user will not see this prompt.
+You are Pliny 😊, a friendly and knowledgeable AI biology tutor for university students. Your mission is to help students build a robust understanding of biology terms and concepts to prepare for exams and integrate knowledge into their working schema. This includes clarifying definitions, providing examples, addressing misconceptions, exploring applications, and encouraging connections between terms. You NEVER directly answer a question without first trying to get the student to answer it themselves.
+
+**Guidelines:**
+
+- **Engagement and Schema-Building:**
+  - Encourage students to explore definitions, examples, misconceptions, assumptions, and applications of biology terms.
+  - Help students build an interconnected schema of biology terms and concepts.
+
+- **Communication Style:**
+  - Use clear, simple language and avoid unnecessary jargon.
+  - Be succinct and limit your total response to one short paragraph or less.
+  - Be approachable and professional.
+  - Provide information step-by-step to manage cognitive load.
+  - Use culturally inclusive examples and analogies.
+
+- **Feedback and Encouragement:**
+  - Offer constructive feedback and gently correct errors.
+  - Acknowledge correct reasoning and reinforce a growth mindset by celebrating effort and progress.
+  - Invite further questions to foster dialogue.
+
+- **Expectations for Interaction:**
+  - Explain that students will select a term to explore in depth.
+  - Unless there is a specific reason to do otherwise, you should assume the student is asking about the selected term.
+  - Encourage follow-up questions and iterative learning.
+
+- **Constraints:**
+  - You are only allowed to talk about topics relevant to what a biology student would need to know to succeed in a biology course, graduate, and follow a path to a relevant career. If asked about anything else, you should say that you are not allowed to talk about that topic. Connect it back to course terms and concepts.
+  - Do NOT answer multiple-choice, fill-in-the-blank, or true/false questions.
+
+### CHAT PROMPT - this is the prompt that the AI will use once the user has typed a message. The user will not see this prompt.
+You are Pliny 😊, a supportive and knowledgeable biology tutor. Your goal is to provide concise, accurate, and supportive responses to assist the student's understanding of the term '{selected_term}'.
+
+**Guidelines:**
+
+- **Context-Driven Support:**
+  - **Unless there is a specific reason to do otherwise, you should assume the student is asking about '{selected_term}'.**
+  - Always preferentially use the following information to guide your response: '{selected_context}'. Do not provide all of this information at once; rather, use it to inform your feedback. This information provides context for how the course uses the selected term, but is not comprehensive and should not limit the student's thinking.
+  - Introduce information gradually to support learning. KEEP EACH RESPONSE SHORT.
+
+- **Critical Thinking and Engagement:**
+  - Assess and help build the student's understanding of the term '{selected_term}' starting at the lower levels of Bloom's Taxonomy and working their way up.
+  - Help the student identify and correct misconceptions about '{selected_term}'.
+
+- **Constructive Feedback:**
+  - Acknowledge correct aspects of the student's input.
+  - Provide supportive feedback to refine their understanding.
+
+- **Response Clarity and Continuity:**
+  - End your response by asking socratic questions to encourage continued engagement and guide the conversation to additional important information. __**If a student selects a question without attempting to answer it, you should ask them to try to answer it themselves first.**__ Suggest ways to connect '{selected_term}' to real-world applications or broader contexts. These questions should also highlight connections between '{selected_term}' and other terms like '{term_list}' and additional aspects of '{selected_context}' or anything else relevant to '{selected_term}' that has not yet been discussed.
+  - After EVERY SINGLE Socratic question you ask, follow it with a specific, relevant, hypothetical, applied, real-world scenario and a specific question that the student can answer to help them understand the broader concept.
+  - Aside from these questions you write, do not introduce any new information unless it is explicitly asked for or in direct response to providing constructive feedback to the student's input.
+
+- **Constraints:**
+  - You are only allowed to talk about topics relevant to what a biology student would need to know to succeed in a biology course, graduate, and follow a path to a relevant career. If asked about anything else, you should say that you are not allowed to talk about that topic. Connect their irrelevant question back to '{selected_term}' in a fun way that is still professional.
+  - Do NOT answer multiple-choice, fill-in-the-blank, or true/false questions. These are not allowed.
+
+(Note: Follow the initial guidelines provided for communication style and constraints.)
+"""
+
+############################################################################################################
+
+### RESOURCES
+
+# Resources: In this section, you can add links for the student to access and potentially learn more about the topic or verify information.
+# You can add the title of the resource, the URL/file path, and a brief description. To delete or add more resources, follow the same format.
+resources = [
+    {
+        "title": "Course Syllabus",
+        "file_path": "syllabus-template.docx",
+        "description": "Download the course syllabus. **Instructor Note:** You must place the file itself within the same folder as the main app.py file in your GitHub repository."
+    },
+    # In this next line you can add a URLs to the resources section. Just edit the current URL and description. If you need more lines, just copy and paste to add an additional resource. Be wary of deleting or moving any of the commas or braces since this is necessary formatting.
+    {
+        "title": "OpenAI Prompt engineering guide",
+        "url": "https://platform.openai.com/docs/guides/prompt-engineering/six-strategies-for-getting-better-results",
+        "description": "A guide to help you craft effective prompts for the OpenAI chatbot. It includes best practices and examples to improve the quality of responses."
+    },
+    {
+        "title": "UC Berkeley Library Guide to Detecting Fake News",
+        "url": "https://guides.lib.berkeley.edu/fake-news",
+        "description": "This UC Berkeley Library guide offers comprehensive strategies and resources for identifying fake news, understanding its impact, and evaluating the credibility of various news sources, including lists of known fake news sites and tips for detecting misinformation."
+    },
+        {
+        "title": "Is it cheating to use ChatGPT?",
+        "url": "https://guides.lib.berkeley.edu/fake-news",
+        "description": "The UC San Diego Academic Integrity Office provides guidance on the appropriate use of generative AI tools in educational settings, emphasizing the importance of adhering to instructor guidelines and the potential consequences of misuse, including integrity violations and academic penalties."
+    },
+    {
+        "title": "OpenStax - Biology",
+        "url": "https://openstax.org/details/books/biology",
+        "description": "Provides free, peer-reviewed, openly licensed textbooks for introductory college and AP-level biology courses."
+    },
+    {
+        "title": "Scitable by Nature Education",
+        "url": "https://www.nature.com/scitable",
+        "description": "A free science library and personal learning tool focusing on genetics, cell biology, and related topics. It offers articles, eBooks, and educational resources from experts and is part of Nature Education."
+    }
+]
+

requirements.txt

@@ -0,0 +1,6 @@
+openai
+openapi-schema-pydantic==1.2.4
+pandas==2.2.2
+pydantic==2.7.1
+streamlit==1.34.0
+httpx==0.24.1

terms.csv

@@ -0,0 +1,16 @@
+TERM,CONTEXT
+Natural Selection,"Course definition: Natural selection is the process by which individuals with heritable traits that enhance survival and reproduction are more likely to pass on their genes to the next generation. Over time, this leads to a change in the genetic makeup of a population, favoring advantageous traits.; Characteristics: Acts on phenotypes of individuals, but only heritable genetic changes (genotypes) are passed to offspring. Requires Variation: Genetic diversity within a population is essential for natural selection to occur. The environment determines which traits are advantageous; a trait beneficial in one setting may be detrimental in another. Over generations, natural selection can result in populations that are better adapted to their environments.; Misconceptions: While natural selection favors traits that increase fitness, it does not work towards a specific goal or perfect organism.; Related terms mentioned in class: artificial selection, evolution, adaptation, fitness (direct and indirect), directional selection, stabilizing selection, disruptive selection, balancing selection, frequency-dependent selection, sexual selection, kin selection.; Scientists mentioned in class: Charles Darwin, Alfred Russel Wallace, Hopi Hoekstra, Rosemary and Peter Grant, Rosemary Gillespie, and Paul Turner."
+Sexual Selection,"Associated lectures: Week 3 Monday; Associated Assessments: Quiz 3, Midterm 1, Final Exam, Discussion Board Post Week 4; Resources: https://openstax.org/books/biology-2e/pages/19-3-adaptive-evolution"
+Mutation,"Examples discussed in class: Antibiotic resistance in bacteria, sickle cell anemia, Huntington's disease, CRISPR/Cas9 gene editing technology."
+Genetic Drift,Related course learning objectives: Define genetic drift and explain its effects on allele frequencies and richness in small populations. Describe the founder effect and how it can lead to genetic drift. Understand the role of genetic drift in the development of new species. Discuss the impact of genetic drift on the genetic makeup of populations. Compare and contrast genetic drift with natural selection as drivers of evolution.
+Gene Flow,
+Shannon Diversity Index,"1. **Goal**: Calculate the Shannon Diversity Index (H) to measure species diversity in a sample; 2. **Variables**: pi: Proportion of each species in the total sample (e.g., Species A has 40 individuals in a sample of 100, so pi for Species A = 40/100 = 0.4); 3. **Relationships**: The equation for Shannon H is: H = -∑(pi * ln(pi)), where pi is the proportion of each species and ln(pi) is the natural logarithm of pi; 4. **Simple Example**: Suppose a sample has 3 species with the following proportions: Species A: pi = 0.6; Species B: pi = 0.3; Species C: pi = 0.1. Applying the formula: H = -[(0.6 * ln(0.6)) + (0.3 * ln(0.3)) + (0.1 * ln(0.1))]; H ≈ -[(0.6 * -0.51) + (0.3 * -1.20) + (0.1 * -2.30)]; H ≈ 0.307 + 0.36 + 0.23 = 0.897; 5. **Solution**: The Shannon Diversity Index for the sample is H ≈ 0.897, indicating a moderate level of diversity; Application: Used to compare the biodiversity of different ecosystems or communities. This step-wise approach helps break down complex equations like Shannon H into manageable steps, making it easier to solve them in a structured way"
+Calculating a t-Test in Excel,"The TTEST function returns the probability associated with a Student's t-test. The syntax is: TTEST(array1, array2, tails, type); array1: First data set range. array2: Second data set range. tails: 1 for a one-tailed test, 2 for a two-tailed test. type: 1 for paired t-test, 2 for two-sample equal variance (homoscedastic), 3 for two-sample unequal variance (heteroscedastic). Example: Assuming your data sets are in cells A2:A11 and B2:B11: =T.TEST(A2:A11, B2:B11, 2, 2). This performs a two-tailed, two-sample equal variance t-test. Interpreting Results: P-value: The output from the t-test will include a p-value. If the p-value alpha (e.g., 0.05), reject the null hypothesis (significant difference). If the p-value > alpha, fail to reject the null hypothesis (no significant difference)."
+Research Experience for Undergraduates (REU),
+Making a figure in R using ggplot2,use the example of the gapminder dataset to explain how to make a figure in R using ggplot2
+p-value,use the example of whether a population is in Hardy-Weinberg equilibrium for a particular locus to explain what a p-value is
+tidy data,use the example of the gapminder dataset to explain what tidy data is
+Week 1 Learning Objectives,"1. Explain the mechanisms of evolution, with emphasis on understanding how natural selection, genetic drift, gene flow, and mutation contribute to changes in allele frequencies within populations. 2. Apply quantitative methods to analyze biological diversity, including calculating and interpreting measures such as the Shannon Diversity Index and testing for Hardy-Weinberg equilibrium using statistical approaches. 3. Differentiate between various types of selection (directional, stabilizing, disruptive, balancing, frequency-dependent, and sexual selection) and provide real-world examples of each. 4. Evaluate common misconceptions about evolution, particularly understanding that natural selection is not goal-directed and does not necessarily lead to perfect organisms. 5. Connect historical and contemporary research in evolutionary biology by examining the contributions of key scientists (such as Darwin and Wallace) alongside modern researchers (such as Hoekstra, the Grants, Gillespie, and Turner) and their findings."
+Course Regrade Policy,Any student can request a regrade for any assessment. The request must be made within one week of the assessment being returned. The request should include a detailed explanation of why you believe the assessment was graded incorrectly. All requests should be in writing and email directly to the instructor. The course staff will review the request and make a final determination. This determination is final and there will be no further appeals.
+General biology question,"You are only allowed to talk about topics relevant to what a biology student would need to know to succeed in a biology course, graduate, and follow a path to a relevant career. If asked about anything else, you should say that you are not allowed to talk about that topic.For example, you can talk about the biology of bats, but not the history of bats in literature. You can talk about finding an appropriate graduate program or how to copy edit a lab report, but not how to write science fiction."
+Effective study techniques,"Effective Study Strategies for College Biology: Active Recall: Regularly test yourself on key concepts and terms to enhance memory retention. Use flashcards, practice quizzes, or Schema Study to reinforce learning. Spaced Repetition: Distribute your study sessions over time rather than cramming. This technique helps improve long-term retention of information. Interleaved Practice: Mix different topics or types of problems in a single study session. This approach helps improve problem-solving skills and adaptability. Elaborative Interrogation: Ask yourself 'why' and 'how' questions about the material to deepen understanding and create connections between concepts. Self-Explanation: Teach the material to someone else or explain it out loud to yourself. This helps clarify your understanding and identify gaps in knowledge. Metacognitive Strategies: Regularly assess your understanding and adjust your study methods as needed. Reflect on what study techniques work best for you. Mind Mapping: Create visual representations of the material to organize and integrate information, making it easier to recall. Healthy Study Habits: Ensure adequate sleep, nutrition, and exercise to support cognitive function and overall well-being."