Update 2.3.1_research_question.md

Author: waltercostamb

_episodes/2.3.1_research_question.md

@@ -27,60 +27,57 @@ 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 one type of project
+# Choose a type of project
 
-Choose one type of project that better fits your interests:  
+To start, choose one type of project that better fits your interests:  
 
 - 1. Go into detail into analyses  
 - 2. Build a broader research proposal  
 
-1. 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?". Here are our expactations from you if you choose this type of project:
+## Detailed analyses
 
+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?".   
+
+The following points should be clear in your final presentation and in your lab book:
+
+- 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?
+- Which data to use
+- Which programs will/do you use
 
-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. Here are our expactations from you if you choose this type of project:
+Note that hypotheses do not need be proven. We want to see from you as results:
 
-- what is the question
-- what informed the question
-- is it testable? and how
-- Complexity of the problem  
+- 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  
 
+## Research proposal
 
-Results:  
+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.  
 
-- 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)
+The following points should be clear in your final presentation and in your lab book:
 
-Presentation  
+- 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?
 
-- comprehensive
-- has to connect back to hypothesis
+# Presentation  
 
-# Exercise
+Document your project 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.
 
+# 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?
->    Find the three papers that are the most closely related to your project, and use them to refine 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.
 > 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.
 > {: .source}
 {: .challenge}
 
 Here, you can find [ideas for projects](https://mgxlab.github.io/Viromics2024/ideas_projects/index.html).  
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