diff --git a/.github/workflows/notebook-pr.yaml b/.github/workflows/notebook-pr.yaml index 3edd478585..9a2845c9bb 100644 --- a/.github/workflows/notebook-pr.yaml +++ b/.github/workflows/notebook-pr.yaml @@ -64,6 +64,7 @@ jobs: - name: Install dependencies if: "!contains(env.COMMIT_MESSAGE, 'skip ci')" run: | + sudo apt-get update sudo apt-get install python3-opencv -y python -m pip install --upgrade pip wheel pip install -r requirements.txt diff --git a/projects/docs/project_guidance.md b/projects/docs/project_guidance.md index 309ff2d197..32d8ccaeaf 100644 --- a/projects/docs/project_guidance.md +++ b/projects/docs/project_guidance.md @@ -37,12 +37,12 @@ You will have a couple of scheduled meetings with a project mentor throughout th ## Week 1: Getting started -### W1D1 +### 🗓️ W1D1 * Split into groups. We recommend intentionally creating groups with diverse skillsets. Groups should have both students who are very confident in Python and those who are just learning. Through the project, students can work together to strengthen each other's skills. We want to make sure that all members of each group get a chance to do all parts of the project. We ask that folks who are good with Python share what they know and handoff tasks to peers who are learning so they can improve their skills. -* Introductions (15 min = 1 min/student): say a few things about yourself, then about your research area or research interests. What are you really curious about, that you might explore in your NMA project? +* **(⏱️ 15 min = 1 min/student)** Introductions: say a few things about yourself, then about your research area or research interests. What are you really curious about, that you might explore in your NMA project? * Listen carefully as others talk about their interests. -* Individual reading time (20 min): browse the projects booklet which includes this guide (skim the entire thing) + project templates with slides and code + dataset videos + docs with further ideas and datasets -* Now brainstorm within your group (60 min). Choose a topic and start thinking about concrete questions if you can. Make sure the topic you choose is well suited for answering the broad range of questions you are interested in. Try to come up with one or a few topics of interest, either by yourselves or directly from the booklet (i.e. project templates). +* **(⏱️ 20 min)** Individual reading time: browse the projects booklet which includes this guide (skim the entire thing) + project templates with slides and code + dataset videos + docs with further ideas and datasets +* **(⏱️ 60 min)** Now brainstorm within your group: Choose a topic and start thinking about concrete questions if you can. Make sure the topic you choose is well suited for answering the broad range of questions you are interested in. Try to come up with one or a few topics of interest, either by yourselves or directly from the booklet (i.e. project templates). Tips: * No need to have a very concrete project after this day. You will determine the feasibility of your questions in the next few days, and you will likely change your question completely. That’s how research works! @@ -80,17 +80,18 @@ Be on the lookout for interesting hypotheses. You might notice something unexpec * There are many complex clustering models like the Leiden/Louvain algorithms, hdbscan and spectral clustering, but those tend to be unstable for high-dimensional data and difficult to interpret. You will have to carefully try different parameters, and think through what the clusters mean. * You can still use nonlinear models very well as a *hypothesis* about what the brain is doing. For example, neural networks configured and trained in specific ways can resemble neural activity in the brain. -### W1D5 -- Looking ahead to the first project day (W2D1) +### 🗓️ W1D5 -- Looking ahead to the first project day (W2D1) -(30) -- Spend the last 30 minutes of today reflecting on the data analysis that you've done and the questions you're considering. Read through the guidance below for the first project day and identify a question (of your own or from the project template) that your group would like to use during the W2D1 project tutorial and to guide your abstract writing. +**(⏱️ 30 min)** -- Spend the last 30 minutes of today reflecting on the data analysis that you've done and the questions you're considering. Read through the guidance below for the first project day and identify a question (of your own or from the project template) that your group would like to use during the W2D1 project tutorial and to guide your abstract writing. ## Week 2: Reading, Writing, Models, and Data Analysis. Week 2 is when projects really start to ramp up. -### W2D1: Project Half Day +### 🗓️ W2D1: Project Half Day Today's project tutorial will introduce a set of general strategies to help you focus and refine your projects. You will also complete a literature review today and work on your project proposal. We have also designed an [LLM-based app](https://nma-project-planner.vercel.app/) to provide feedback to the different categories of a project proposal (question, hypothesis, dataset etc). -(1h) Complete the intro/tutorial/outro for W2D1: +#### TUTORIAL BLOCK TASKS +**(⏱️ 1 hour)** Complete the intro/tutorial/outro for W2D1: * This intro/tutorial/intro will introduce the first four steps for modelling applied to a hypothetical project based on the train illusion. * Step 1: Finding a phenomenon and a question to ask about it * Step 2: Understanding the state of the art & background @@ -101,27 +102,31 @@ Today's project tutorial will introduce a set of general strategies to help you * The first hypothetical project is illustrated in the videos, where a group of students identifies a research question and forms a basic plan for how to approach the question. The second project will be discussed between members of your group, and is a data analysis version of the train illusion project. * The original 10 step modeling paper is available [here](https://www.eneuro.org/content/eneuro/7/1/ENEURO.0352-19.2019.full.pdf). Note we stop after 4 steps. Beyond that, we will be using the project planner app [here](https://nma-project-planner.vercel.app/). -(1h) - -[The app](https://nma-project-planner.vercel.app/): getting familiar with Konrad's project planner. +**(⏱️ 1 hour)** [The app](https://nma-project-planner.vercel.app/): getting familiar with Konrad's project planner. At the end of the tutorial we introduced a project planner app that can provide feedback for the different steps and sections of a project. You will use this app to develop your own project plan. There are multiple sections in the app (question, audience, related etc.). Feel free to go through these in any order. Research is rarely "prescriptive", and different steps may be followed in different order by different types of projects. What is important is that at the end, all projects have all these sections completed out. So familiarize yourself with the sections, and start making progress wherever you can! You are encouraged to explore the app freely for the rest of the summer school. -(2h) +**(⏱️ 2.5 hours)** Literature review: identify interesting papers +The goal of this literature review is to situate your question in context and help you acquire some keywords that you will use in your proposal today. (The suggested timeline for the literature review is below). +* **(⏱️ 30 min)** 🔍 On your own, start doing a literature review using [google scholar searches](https://scholar.google.com/) and only look at abstracts to select 2-3 promising ones. +* **(⏱️ 10 min)** 🗣️ Report to the whole group what papers you found and pool them together. Use the "Related" section of the online planner app [here](https://nma-project-planner.vercel.app/) to get feedback on the papers you found and determine if you need to find other types of papers (contradictory papers for example). +* **(⏱️ 10 min)** from the pooled papers, assign one to each member of the group to read more carefully. +* **(⏱️ 60 min)** ✍️ on your own, read the paper that was assigned to you. Make notes in a common google doc shared with your group, and especially write down important keywords or concepts which you might use in your proposal later today. If you are not connected to an .edu domain or a VPN, try to find full versions of papers on preprint servers like arXiv / bioRxiv. You could also ask your TA to get it for you (and they might in turn ask someone who has access to a university VPN). There might be other options too. You may or may not have extensive experience reading journal articles. Below are a series of questions that you could try to answer after reading a paper. These are meant as a guide. If you can answer them, then you probably have a pretty good understanding of the paper. + 1. What is the research question(s) posed in the paper? Do the authors have hypotheses about what they expect to find? What are the hypotheses? + 1. Describe the design and methodology of the study. + 1. What were the results of the study? How do the results support or not support the authors’ hypotheses? + 1. Do you find the results/method significant, unexpected, and/or exciting? And why? + 1. What do you view as the key point/message the authors want to convey? + 1. What do you think is the most interesting open question from this paper? What follow-up research question would you address and would you pursue it? + +* **(⏱️ 60min)** 🗣️ report back to the group, and try to tell them as much as you understood about the paper. Get into details, using your own words. Don’t just read to them whole sections from the paper. Ask the other students questions about the papers they are presenting to understand them better. -(2.5h) Literature review: identify interesting papers -The goal of this literature review is to situate your question in context and help you acquire some keywords that you will use in your proposal today. -* (30min) on your own, start doing a literature review using [google scholar searches](https://scholar.google.com/) and only look at abstracts to select 2-3 promising ones. -* (10min) report to the whole group what papers you found and pool them together. Use the "Related" section of the online planner app [here](https://nma-project-planner.vercel.app/) to get feedback on the papers you found and determine if you need to find other types of papers (contradictory papers for example). -* (10 min) from the pooled papers, assign one to each member of the group to read more carefully. -* (1h) on your own, read the paper that was assigned to you. Make notes in a common google doc shared with your group, and especially write down important keywords or concepts which you might use in your proposal later today. If you are not connected to an .edu domain or a VPN, try to find full versions of papers on preprint servers like arXiv / bioRxiv. You could also ask your TA to get it for you (and they might in turn ask someone who has access to a university VPN). There might be other options too. -* (1h) report back to the group, and try to tell them as much as you understood about the paper. Get into details, using your own words. Don’t just read to them whole sections from the paper. Ask the other students questions about the papers they are presenting to understand them better. +⏸️ **BREAK TIME!!** ⏸️ -BREAK TIME!! -Project block task: -(3h) Project proposal -* Try to write a proposal for this project based on the way you understand it now. This should reuse some of the text you wrote down for the four steps, and should include keywords and concepts that you identified in your literature review. Don’t worry too much about the structure of this paragraph! The goal is to get as many words (200-300) on paper as possible. Note that this is not an abstract. You have the entire day 10 to learn how to write a well structured scientific abstract. +#### PROJECT BLOCK TASKS +**(⏱️ 3 hours)** Project proposal +* Try to write a proposal for this project based on the way you understand it now. This should reuse some of the text you have written into the project planner, and should include keywords and concepts that you identified in your literature review. Don’t worry too much about the structure of this paragraph! The goal is to get as many words (200-300) on paper as possible. Note that this is not an abstract. You have the entire day 10 to write a structured scientific abstract for your project. * It is important to include the concepts which you identified as relevant, and the keywords that go with them. * When you are ready, please submit your proposal [here](https://airtable.com/shrcYuFYMPh4jGIng). This is not mandatory and can be submitted at any time. We won't evaluate this, but we will use it to keep track of the overall progress of the groups. * Use the project planner to get feedback on any of the sections you want to include in the proposal. @@ -132,7 +137,7 @@ You should now have a sense of the data, and you have probably refined your hypo Keep working on analyses, making sure to relate what you do back to the project plan you created. -### W2D5: Abstract Writing Day! +### 🗓️ W2D5: Abstract Writing Day! One of the best ways to understand your own research is to try to write about it. You should write early and often, not just at the end when you are trying to write a paper or your thesis. Science conferences are a great way to present your intermediate work, and they give you a chance to write an abstract. However, you do not have to wait so long to write your project abstract, you will do it today! If you have preliminary results that is great, but it is not required. Most of the components of an abstract do not in fact require results. The goal for this day is to workshop your abstract with your group, and then present this to your entire pod. You can also think of it as a much more refined version of the project proposal you submitted originally. @@ -142,22 +147,23 @@ The starting point for workshopping your abstract should be the [NMA project pla Note: the timings for this day are just suggestions. You can spend more or less time on different parts depending on how much work you think your abstract needs. -With your group -* (30 min) use the ABC...G questions from the example [model](https://compneuro.neuromatch.io/projects/modelingsteps/TrainIllusionModel.html#summary)/[data](https://compneuro.neuromatch.io/projects/modelingsteps/TrainIllusionDataProject.html#summary) projects to write your own answers and build a first version of your abstract. -* (30 min) by yourself, skim the [Ten simple rules for structuring papers](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619). Pay close attention to figure 1, and how it specifies the same overall structure for the abstract, for each paragraph in the paper, and for the paper as a whole. -* (1h) workshop your abstract together as a group. Say what you like and what you do not like about it. Try to refer back to the principles from the "Ten simple rules" paper in order to find problems with your abstract and follow the recommended solutions from the paper. +#### WITH YOUR GROUP +* **(⏱️ 30 min)** use the ABC...G questions from the example [model](https://compneuro.neuromatch.io/projects/modelingsteps/TrainIllusionModel.html#summary)/[data](https://compneuro.neuromatch.io/projects/modelingsteps/TrainIllusionDataProject.html#summary) projects to write your own answers and build a first version of your abstract. +* **(⏱️ 30 min)** by yourself, skim the [Ten simple rules for structuring papers](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005619). Pay close attention to figure 1, and how it specifies the same overall structure for the abstract, for each paragraph in the paper, and for the paper as a whole. +* **(⏱️ 1 hour)** workshop your abstract together as a group. Say what you like and what you do not like about it. Try to refer back to the principles from the "Ten simple rules" paper in order to find problems with your abstract and follow the recommended solutions from the paper. -1h break +⏸️ **1 hour break** ⏸️ -* (30-60 min) Edit the abstract individually in your own google doc. At this stage, it is also important to control the flow of the abstract, in addition to keeping the structure from the 10 rules-paper. The flow relates to the “writing style”, which is generally no different for scientists than for other writers. Most importantly, make sure each sentence continues from where the previous one left, and do not use jargon without defining it first. Check out this book about writing if you have time ([book](https://sites.duke.edu/niou/files/2014/07/WilliamsJosephM1990StyleTowardClarityandGrace.pdf), especially chapter 3 about "cohesion" and flow. -* (30 min) You should now have as many copies of your abstract as there are students in your group. Put them all into the same google doc, and try to see what you all did the same / differently. What sounds better? Pick and choose different sentences from different abstracts. +* **(⏱️ 45 min)** Edit the abstract individually in your own google doc. At this stage, it is also important to control the flow of the abstract, in addition to keeping the structure from the 10 rules-paper. The flow relates to the “writing style”, which is generally no different for scientists than for other writers. Most importantly, make sure each sentence continues from where the previous one left, and do not use jargon without defining it first. Check out this book about writing if you have time ([book](https://sites.duke.edu/niou/files/2014/07/WilliamsJosephM1990StyleTowardClarityandGrace.pdf), especially chapter 3 about "cohesion" and flow. +* **(⏱️ 30 min)** You should now have as many copies of your abstract as there are students in your group. Put them all into the same google doc, and try to see what you all did the same / differently. What sounds better? Pick and choose different sentences from different abstracts. -* (30-60min) Meet with your Project TA, show them your abstract. Try to get explicit feedback and edit the abstract together in a google doc. +* **(⏱️ 45 min)** Meet with your Project TA, show them your abstract. Try to get explicit feedback and edit the abstract together in a google doc. (Note that this will depend on your Project TAs schedule and may need to be shorter or happen at a different time). -* (30min / group = 1h) With your pod: present your research to the other group in your pod. Take turns in your pod to read each other’s abstracts and provide feedback on them. Tell the other group what you understand and what you do not from their research project. Give detailed writing feedback if you can (use "suggestion mode" in google docs). If there is no other project group in your pod, ask your TA to reach out to other pods to find a group you can workshop your abstract with. +#### WITH YOUR POD +* **(⏱️ 30min / group = 1h)** With your pod: present your research to the other group in your pod. Take turns in your pod to read each other’s abstracts and provide feedback on them. Tell the other group what you understand and what you do not from their research project. Give detailed writing feedback if you can (use "suggestion mode" in google docs). If there is no other project group in your pod, ask your TA to reach out to other pods to find a group you can workshop your abstract with. -Back in your group -* (1-2h) Has the abstract refined or changed your question? Use the rest of this day to make a concrete plan for the final week of your project. If you already answered your question, then you will need to plan for control analyses, maybe including some simulated data that you need to also generate yourself. +#### BACK IN YOUR GROUP +* **(⏱️ 1-2h)** Has the abstract refined or changed your question? Use the rest of this day to make a concrete plan for the final week of your project. If you already answered your question, then you will need to plan for control analyses, maybe including some simulated data that you need to also generate yourself. Once you are done, please submit the abstract [here](https://airtable.com/app1MtChyjyKEDzAt/shr0ozNAhXq6K1p8o). We will not use this for further matching or evaluation, but we will keep a record of it to help us track the progress of all groups. If you really need/want to, the abstract can also be submitted on Monday. @@ -206,16 +212,16 @@ This is the day where you present your project to other groups. The groups will At the end of your last project block, you should also submit your slides via this [Airtable link](https://airtable.com/shrvoz2N9UulAVqqU). -### Schedule +### 🗓️ Final Presentation Schedule -* 10 minutes of meet & greet. Do a round of introductions (one TA calls out names from the zoom list). Everyone says their name, pod name, position, university and subject of study, as well as one interesting fact about themselves "Hi, I'm Jonny from the wiggly caterpillars and I am a PhD student at University of Notre Dame in Paris. I do neuroscience experiments in flies, and in my free time I like to go on long bike rides". +* **(⏱️ 10 min)** Meet & Greet: Do a round of introductions (one TA calls out names from the zoom list). Everyone says their name, pod name, position, university and subject of study, as well as one interesting fact about themselves "Hi, I'm Jonny from the wiggly caterpillars and I am a PhD student at University of Notre Dame in Paris. I do neuroscience experiments in flies, and in my free time I like to go on long bike rides". -* 30-40 minutes of presentations, including questions. Each group should speak for approx 5 minutes (1 minute per person + 2 minutes of intro/discussion), and then take questions for 1-2 minutes. Try not to waste too much time on logistics: join the zoom link and go to the appropriate breakout room quickly. Then the student groups can start presenting in any order. +* **(⏱️ 30-40 min)** Presentations, including questions. Each group should speak for approx **(⏱️ 5 min)** (1 minute per person + 2 minutes of intro/discussion, and then take questions for 1-2 minutes). Try not to waste too much time on logistics: join the zoom link and go to the appropriate breakout room quickly. Then the student groups can start presenting in any order. -* 10-20 minutes of general discussion. Here are some ideas for questions you could ask: +* **(⏱️ 10-20 minutes)** General Discussion. Here are some ideas for questions you could ask: * What was missing in the dataset that you would have really liked to have? * Does anyone plan to continue working on this project in the future? Perhaps a few students from the multiple groups would like to continue together? - * Which one of the 10 steps to modeling/research was hardest and why? + * Which of the steps to modeling/research was hardest and why? * Based on your experience with the NMA project, what project would you most like to do next? Make up your own, or pick from the NMA projects (a different dataset or project template which you did not use). * What surprised you the most about the process of doing a project? In what way was this project most different from other projects you have done in the past. * What technique did you learn at NMA which you think you can immediately apply to your own project (if you are currently doing research)? diff --git a/tutorials/W2D1_ModelingPractice/W2D1_Intro.ipynb b/tutorials/W2D1_ModelingPractice/W2D1_Intro.ipynb index 57ffa51946..f8698239ef 100644 --- a/tutorials/W2D1_ModelingPractice/W2D1_Intro.ipynb +++ b/tutorials/W2D1_ModelingPractice/W2D1_Intro.ipynb @@ -34,9 +34,9 @@ "source": [ "## Overview\n", "\n", - "During the first day, you learned that different models can answer different questions. That means that depending on your question, goals, and hypotheses, you will need to develop different kinds of models. How to best approach this is the goal of today. We will use this as an opportunity to kick off your group projects simultaneously. To do so, we will start walking you through a step-by-step guide of how-to-model. Today, we will start with the following steps: how to develop a good question and goal, how to do a literature review, how to determine what ingredients you need, and what hypotheses you would like to evaluate.\n", + "During the first day, you learned that different models can answer different questions. That means that depending on your question, goals, and hypotheses, you will need to develop different kinds of models. Our goal today will be to examine how to best approach developing a model based on the details of a specific project.\n", "\n", - "Today’s tutorial focuses on the first 4 steps of how-to-model by demonstrating the thought process based on a simple phenomenon known as the train illusion. We will first introduce the phenomenon and then provide a step-by-step guide on thinking about and developing the 4 first steps of framing your project. Groups will then think about their own projects and develop answers to each step’s questions. We will introduce an online project planner based on a large language model that can give you feedback to these answers, which you can use iteratively to develop the full plan of your project. Different types of projects will probably go through the steps in a different order, but at the end, all projects should complete all steps. \n", + "Today's tutorial will focus on the following steps: how to develop a good question and goal, how to do a literature review, how to determine what ingredients you need, and what hypotheses you would like to evaluate. We will demonstrate these steps using a project that is focused on a simple phenomenon known as the train illusion. We will first introduce the phenomenon and then provide a guide for each of the steps. Groups will then think about their own projects and develop answers to each step’s questions. We will introduce an online project planner based on a large language model that can give you feedback to these answers, which you can use iteratively to develop the full plan of your project. Different types of projects will probably go through the steps in a different order, but at the end, all projects should complete all steps. \n", "\n", "How to model is rarely, if ever, taught systematically. Our guide and project planner is not the only way to approach modeling, but it’s one way to ensure you don’t miss anything important. Going through all the steps also makes publication much easier because you have already explicitly thought about all the elements you will ultimately need to communicate (see Abstract section later for example). \n" ] @@ -98,7 +98,7 @@ "name": "python3" }, "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -116,5 +116,5 @@ } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 4 } diff --git a/tutorials/W2D1_ModelingPractice/W2D1_Tutorial1.ipynb b/tutorials/W2D1_ModelingPractice/W2D1_Tutorial1.ipynb index 9c24106ed7..f596d1ac88 100644 --- a/tutorials/W2D1_ModelingPractice/W2D1_Tutorial1.ipynb +++ b/tutorials/W2D1_ModelingPractice/W2D1_Tutorial1.ipynb @@ -1160,7 +1160,7 @@ "name": "python3" }, "kernelspec": { - "display_name": "cellpose", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1178,5 +1178,5 @@ } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 4 } diff --git a/tutorials/W2D1_ModelingPractice/instructor/W2D1_Intro.ipynb b/tutorials/W2D1_ModelingPractice/instructor/W2D1_Intro.ipynb index fcc66ad1a4..5f393bbd3b 100644 --- a/tutorials/W2D1_ModelingPractice/instructor/W2D1_Intro.ipynb +++ b/tutorials/W2D1_ModelingPractice/instructor/W2D1_Intro.ipynb @@ -34,9 +34,9 @@ "source": [ "## Overview\n", "\n", - "During the first day, you learned that different models can answer different questions. That means that depending on your question, goals, and hypotheses, you will need to develop different kinds of models. How to best approach this is the goal of today. We will use this as an opportunity to kick off your group projects simultaneously. To do so, we will start walking you through a step-by-step guide of how-to-model. Today, we will start with the following steps: how to develop a good question and goal, how to do a literature review, how to determine what ingredients you need, and what hypotheses you would like to evaluate.\n", + "During the first day, you learned that different models can answer different questions. That means that depending on your question, goals, and hypotheses, you will need to develop different kinds of models. Our goal today will be to examine how to best approach developing a model based on the details of a specific project.\n", "\n", - "Today’s tutorial focuses on the first 4 steps of how-to-model by demonstrating the thought process based on a simple phenomenon known as the train illusion. We will first introduce the phenomenon and then provide a step-by-step guide on thinking about and developing the 4 first steps of framing your project. Groups will then think about their own projects and develop answers to each step’s questions. We will introduce an online project planner based on a large language model that can give you feedback to these answers, which you can use iteratively to develop the full plan of your project. Different types of projects will probably go through the steps in a different order, but at the end, all projects should complete all steps. \n", + "Today's tutorial will focus on the following steps: how to develop a good question and goal, how to do a literature review, how to determine what ingredients you need, and what hypotheses you would like to evaluate. We will demonstrate these steps using a project that is focused on a simple phenomenon known as the train illusion. We will first introduce the phenomenon and then provide a guide for each of the steps. Groups will then think about their own projects and develop answers to each step’s questions. We will introduce an online project planner based on a large language model that can give you feedback to these answers, which you can use iteratively to develop the full plan of your project. Different types of projects will probably go through the steps in a different order, but at the end, all projects should complete all steps. \n", "\n", "How to model is rarely, if ever, taught systematically. Our guide and project planner is not the only way to approach modeling, but it’s one way to ensure you don’t miss anything important. Going through all the steps also makes publication much easier because you have already explicitly thought about all the elements you will ultimately need to communicate (see Abstract section later for example). \n" ] @@ -98,7 +98,7 @@ "name": "python3" }, "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -116,5 +116,5 @@ } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 4 } diff --git a/tutorials/W2D1_ModelingPractice/instructor/W2D1_Tutorial1.ipynb b/tutorials/W2D1_ModelingPractice/instructor/W2D1_Tutorial1.ipynb index 357688f834..8e3131ca58 100644 --- a/tutorials/W2D1_ModelingPractice/instructor/W2D1_Tutorial1.ipynb +++ b/tutorials/W2D1_ModelingPractice/instructor/W2D1_Tutorial1.ipynb @@ -1160,7 +1160,7 @@ "name": "python3" }, "kernelspec": { - "display_name": "cellpose", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1178,5 +1178,5 @@ } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 4 } diff --git a/tutorials/W2D1_ModelingPractice/student/W2D1_Intro.ipynb b/tutorials/W2D1_ModelingPractice/student/W2D1_Intro.ipynb index dac5b793b8..186096af3e 100644 --- a/tutorials/W2D1_ModelingPractice/student/W2D1_Intro.ipynb +++ b/tutorials/W2D1_ModelingPractice/student/W2D1_Intro.ipynb @@ -34,9 +34,9 @@ "source": [ "## Overview\n", "\n", - "During the first day, you learned that different models can answer different questions. That means that depending on your question, goals, and hypotheses, you will need to develop different kinds of models. How to best approach this is the goal of today. We will use this as an opportunity to kick off your group projects simultaneously. To do so, we will start walking you through a step-by-step guide of how-to-model. Today, we will start with the following steps: how to develop a good question and goal, how to do a literature review, how to determine what ingredients you need, and what hypotheses you would like to evaluate.\n", + "During the first day, you learned that different models can answer different questions. That means that depending on your question, goals, and hypotheses, you will need to develop different kinds of models. Our goal today will be to examine how to best approach developing a model based on the details of a specific project.\n", "\n", - "Today’s tutorial focuses on the first 4 steps of how-to-model by demonstrating the thought process based on a simple phenomenon known as the train illusion. We will first introduce the phenomenon and then provide a step-by-step guide on thinking about and developing the 4 first steps of framing your project. Groups will then think about their own projects and develop answers to each step’s questions. We will introduce an online project planner based on a large language model that can give you feedback to these answers, which you can use iteratively to develop the full plan of your project. Different types of projects will probably go through the steps in a different order, but at the end, all projects should complete all steps. \n", + "Today's tutorial will focus on the following steps: how to develop a good question and goal, how to do a literature review, how to determine what ingredients you need, and what hypotheses you would like to evaluate. We will demonstrate these steps using a project that is focused on a simple phenomenon known as the train illusion. We will first introduce the phenomenon and then provide a guide for each of the steps. Groups will then think about their own projects and develop answers to each step’s questions. We will introduce an online project planner based on a large language model that can give you feedback to these answers, which you can use iteratively to develop the full plan of your project. Different types of projects will probably go through the steps in a different order, but at the end, all projects should complete all steps. \n", "\n", "How to model is rarely, if ever, taught systematically. Our guide and project planner is not the only way to approach modeling, but it’s one way to ensure you don’t miss anything important. Going through all the steps also makes publication much easier because you have already explicitly thought about all the elements you will ultimately need to communicate (see Abstract section later for example). \n" ] @@ -98,7 +98,7 @@ "name": "python3" }, "kernelspec": { - "display_name": "Python 3", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -116,5 +116,5 @@ } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 4 } diff --git a/tutorials/W2D1_ModelingPractice/student/W2D1_Tutorial1.ipynb b/tutorials/W2D1_ModelingPractice/student/W2D1_Tutorial1.ipynb index 44469a4a16..0d31162af1 100644 --- a/tutorials/W2D1_ModelingPractice/student/W2D1_Tutorial1.ipynb +++ b/tutorials/W2D1_ModelingPractice/student/W2D1_Tutorial1.ipynb @@ -1160,7 +1160,7 @@ "name": "python3" }, "kernelspec": { - "display_name": "cellpose", + "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, @@ -1178,5 +1178,5 @@ } }, "nbformat": 4, - "nbformat_minor": 0 + "nbformat_minor": 4 }