Update 2.3.1_research_question.md

Author: vmkhot

_episodes/2.3.1_research_question.md

@@ -5,8 +5,9 @@ teaching:
 exercises: 480
 questions:
 objectives:
-- "Choose a type of project"
-- "Write down research questions and discuss them"
+- "Get acquainted with the state of the art of phage research"
+- "Choose one or more papers for inspiration"
+- "Write down 1 or 2 research questions"
 - "Make a plan on how to tackle the questions"
 keypoints:
 ---
@@ -26,51 +27,64 @@ Here are a few papers that caught our eye, maybe they inspire you (feel free to
 - [High viral abundance and low diversity are associated with increased CRISPR-Cas prevalence across microbial ecosystems](https://www.sciencedirect.com/science/article/pii/S0960982221014615), by Meaden *et al* (2022)
 - [Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats](https://www.nature.com/articles/s41564-023-01347-5), by Hwang *et al* (2023)
 
-# Choose a type of project
+# Choose one type of project
 
-To start, choose one type of project that better fits your interests:  
+Choose one type of project that better fits your interests:  
 
-- Go into detail into analyses  
-- Build a broader research proposal  
+1. Go into detail into analyses  
+2. Build a broader research proposal  
 
-Independently of which type of project you choose, document it in your lab book and final presentation in a comprehensive way. Make sure your methods and results connect back to your hypothesis/what you wanted to achieve.
+{:start='1'}
+1. This type of project is more hands-on. You might write your own script(s), run your own analyses and produce your own plots. The idea here would be to focus on one of the methods/analyses we covered in the course and to go deeper into the analysis. In any case, the question you want to address should be clearly defined.
 
-## Detailed analyses
+An example: "What are the differences between functional annotation done with Pharokka and Genomad?". 
 
-In this type of project, you should be more hands-on. Write your own script(s), run your own analysis, produce your own plots, etc. The focus is on the method rather than on the biological questions. In any case, whatever you want to achieve should be clear and straightforward. An example: "What are the differences between functional annotation done with Pharokka and Genomad?".   
+Below are what should be included in your documentation/presentation for project type 1
 
-The following points should be clear in your final presentation and in your lab book:
+- A brief background on the topic
+- A workflow for the steps you plan to take
+- A rationale for why you will take those steps
+- What will be the inputs and outputs?
+- Which programs will (do you plan to) use?
 
-- What you want to achieve
-- Steps to take (consider drawing a workflow)
-- Why you take these steps
-- Which data to use
-- Which programs will/do you use
+- What are your expected results?
+- 
 
-Note that hypotheses do not need be proven. We want to see from you as results:
+{:start='2'}
+2. This type of project is more in the style of a research proposal with a broader scope. You should focus on the biological questions and how to address them using viromics.
 
-- Output (a table or a figure)
-- Interpretation of the output: what does the data tell you? 
-- Does it answer your question? It does not have to. In a negative case, can you say what you might do differently next time  
+Your hypothesis and aims should be clear and backed-up by the literature.
 
-## Research proposal
+Below are what should be included in your documentation/presentation for project type 2
 
-In this type of project, you should focus on the biological questions and design it as if you were writing a research proposal. Your hypothesis and aims should be clear and backed-up by the literature.  
+- A brief background on the topic
+- Formulate your research question or hypothesis to test
+- What informed the question?
+- How would you address this question or test the hypothesis? (make a detailed plan)
+- Estimate the complexity of the problem  
 
-The following points should be clear in your final presentation and in your lab book:
 
-- What is the question
-- What is the state of the art (backed up by the literature)
-- What informed the question (cite your sources)
-- Is it testable? How?
+
+- expected results
+- Hypotheses don't need be proven - can be null hypothesis
+- If you choose to do the detailed analyses:
+    - Generate an output (a table or a figure)
+    - Interpretation of the output: what does the data tell you? 
+    - Does it answer your question? (It doesn't have to, you can say what you might do differently next time)
+
+Presentation  
+
+- comprehensive
+- has to connect back to hypothesis
 
 # Exercise
 
+
 > ## Exercise
 > 1. Once you have an idea of a research question, take some time to talk about your idea with your fellow students.
 >    Often your initial idea can be further refined based on discussions with others.
 > 2. Make sure you check the literature: are there any papers that do something related to your question?
->    For research proposal: find the three papers that are the most closely related to your project, and use them to refine your question.
+>    Find the three papers that are the most closely related to your project, and use them to refine your question.
 > 3. Make a plan for tackling your question(s).
 >    The more detail you can add, the better.
 >    Think about data sources, bioinformatic methods, possible outcomes, expectations, backup/follow-up plans, hypotheses, and interpretation.