Update 2.3.1_research_question.md

Author: waltercostamb

_episodes/2.3.1_research_question.md

@@ -15,10 +15,10 @@ keypoints:
 To close off this course, we would like to give you the opportunity to design your own research project. 
 A research question does not have to be very profound, it can be simple. 
 Viromics is a new field, the virosphere is huge, and there is a LOT of data, so there are more unanswered than answered questions. 
-Looking back on the course, are there things you are wondering about? 
+Looking back on the course, are there things you are wondering about or want more time to work on? 
 You can also look in literature for inspiration. 
 
-Here are a few recent papers that caught our eye, maybe they inspire you (feel free to find other papers too): 
+Here are a few papers that caught our eye, maybe they inspire you (feel free to find other papers too): 
 
 - [A highly abundant bacteriophage discovered in the unknown sequences of human faecal metagenomes](https://www.nature.com/articles/ncomms5498), by Dutilh *et al* (2014)
 - [Bacteriophage evolution differs by host, lifestyle and genome](https://www.nature.com/articles/nmicrobiol2017112), by Mavrich and Hatfull (2017)
@@ -27,6 +27,45 @@ Here are a few recent papers that caught our eye, maybe they inspire you (feel f
 - [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 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:
+
+- Steps to take (consider drawing a workflow)
+- Why you take these steps
+- 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:
+
+- what is the question
+- what informed the question
+- is it testable? and how
+- Complexity of the problem  
+
+
+Results:  
+
+- 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.
@@ -38,4 +77,10 @@ Here are a few recent papers that caught our eye, maybe they inspire you (feel f
 > {: .source}
 {: .challenge}
 
-Here, you can find [ideas for projects](https://mgxlab.github.io/Viromics2024/draco/index.html).  
+Here, you can find [ideas for projects](https://mgxlab.github.io/Viromics2024/ideas_projects/index.html).  
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