updates

app.py

@@ -55,7 +55,7 @@ else:
 # Streamlit app layout
 
 # Set the page to wide or centered mode
-st.set_page_config(layout="wide")
+st.set_page_config(layout="wide", initial_sidebar_state="collapsed")
 
 # Load the terms file into a DataFrame
 df = pd.read_csv(config.default_terms_csv)
@@ -158,7 +158,7 @@ selected_term = st.selectbox('**SELECT FROM THE DROPDOWN MENU**', term_list)
 if selected_term:
     # If a new term is selected (including first time selection), reset or show the message
     if selected_term != st.session_state.old_term:
-        user_message = f"What is one thing you know about '{selected_term}'? What do you want to know about it? This could include a definition, examples, misconceptions, associations with other course terms, opinions, etc."
+        user_message = f"What is one thing you know or want to know about '{selected_term}'? Let's have a conversation!"
         st.session_state["display_messages"].append({"role": "user", "content": user_message})
         # Update old_term in session state
         st.session_state.old_term = selected_term

config.py

@@ -10,7 +10,7 @@
 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
+temperature = 0.5
 
 # 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
@@ -19,7 +19,7 @@ max_tokens = 1000
 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
+presence_penalty = 0.7
 
 # 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.
 
@@ -52,9 +52,10 @@ The goal of this app is to help you learn and and assess your knowledge of core
 ---
 **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" 'I want you to provide me with R code to create and print a ggplot object that has a common syntax error and challenge me to fix the bug.'
+- Ask the chatbot: 'Create a scenario where I have to solve a quantitative problem using this term. Make the problem challenging.'
 - 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!**
+- **Get creative! Play around and see what happens! Remember, deep learning occurs the more we scrimmage with the information**
 '''
 
 # The title of the sidebar
@@ -65,7 +66,7 @@ sidebar_instructions = "Do you have your own terms to study? If so, download the
 
 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."
+app_repo_license_message = "It can be found at [https://huggingface.co/spaces/keefereuther/Schema_Study_HF](https://huggingface.co/spaces/keefereuther/Schema_Study_HF) 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. Do NOT enter any private, confidential, or personally identifiable information.**"
 
@@ -83,40 +84,59 @@ def term_prompt(selected_term, selected_context, term_list):
 
 **Guidelines:**
 
-- **Communication Style:**
+#### **Communication Style:**
   - Use clear, simple language and avoid unnecessary jargon.
   - Be succinct but make sure to respond to all statements made by the user.
   - Be approachable and professional.
   - Provide information step-by-step to manage cognitive load.
-  - Use culturally inclusive examples and analogies.
+  - Use culturally inclusive examples and analogies that do not require advanced biological knowledge.
 
-- **Feedback and Encouragement:**
+#### **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:**
+#### **Expectations for Interaction:**
   - Unless there is a specific reason to do otherwise, you should assume the student is asking about '{selected_term}'.
 
-- **Context-Driven Support:**
+#### **Context-Driven Support:**
   - 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.
+  - 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. 
+#### **Critical Thinking and Engagement:**
+  - Assess and help build the student's understanding of the term '{selected_term}'
   - Ask me questions to determine my comprehension. Adapt to my responses, asking easier questions if responses are incorrect or poor and asking progressively harder questions if responses are good.
   - Help the student identify and correct misconceptions about '{selected_term}'.
   
-- **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.
+#### **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:**
+#### **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.
+  - Do NOT answer multiple-choice, fill-in-the-blank, or true/false questions. These are not allowed. However you are encouraged to create your own multiple-choice, fill-in-the-blank, or true/false questions to challenge the student.
+
+---
+
+### Additional Code Usage Guidelines
+
+Assume the student is using R and the tidyverse and has little to no command line experience.
+
+#### **Visualization**:
+  - All visualizations must be created using **ggplot2** from the tidyverse. Avoid any other plotting libraries.
+
+#### **Code Style**:
+  - Write all examples using **tidyverse** conventions for data manipulation and ggplot2 for visualizations.
+  - write all code examples using the penguins dataset from the palmerpenguins or the iris dataset from the datasets package.
+  - Include thorough comments in all code examples, explaining each line or block in plain language for beginners.
+
+#### **Encouraging Understanding**:
+  - Do not provide direct solutions to assignment-style questions. Instead, reframe questions to demonstrate generalizable concepts and guide students to apply these concepts themselves.
+
+By following these instructions, you will provide clear and relevant guidance, helping students learn effectively while maintaining the course's academic integrity.
 """
 
+
 ############################################################################################################
 
 ### RESOURCES

terms.csv

@@ -4,12 +4,12 @@ Sexual Selection,"Associated lectures: Week 3 Monday; Associated Assessments: Qu
 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"
+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. 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
+Research Experience for Undergraduates (REU),You can give this information comprehensively without socratic questioning; refer students to this URL: https://www.nsf.gov/funding/initiatives/reu
+Making a figure in R using ggplot2,use the example of the palmer penguins 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.
-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."
+tidy data,use the example of the palmer penguins dataset to explain what tidy data is
+Week 1 Learning Objectives,"You can give this information comprehensively without socratic questioning;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,You can give this information comprehensively without socratic questioning; 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.
+Effective study techniques,"You can give this information comprehensively without socratic questioning;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."