Overview

Teaching: min
Exercises: 420 min

Objectives

• Develop a conceptual pipeline of analysis

• Define a hypothesis based on your research question

• Choose one or more papers for inspiration

• Create a flow diagram (workflow or pipeline)

• Plan to end your project with an ecological hypothesis

To close off this course, we would like to give you the opportunity to design your own research project. Viromics is a new field, the virosphere is huge, and there is a LOT of data, so there are more unanswered than answered questions. We thought of three projects, all inspired by the experiments done in the wet lab in the module “Viromics - Virome isolation and sequencing”:

How does the addition of the target phage and host impact:

• the outcome of the community at the last time point?
• the host range of the target phage?
• the time dynamics of the target phage/host?

Each student should choose one of the topics above and work on their project individually. Organize yourselves so that you do not choose the same topic. Take the topic above as inspiration and refine the ideas by searching the literature and discussing with your colleagues and the teachers. It is important to have a clear hypothesis at the start of your project.

How to make a clear, data-driven hypothesis? Start with a specific question, which is neither too broad, now too narrow. For example: how does adding a target phage and host affect the virome community? This is a singular question that can be answered by comparing two datasets - one with the target phage/host and another without the target phage/host. It is crucial to manage your time in the set up and execution of your research project. After creating the hypothesis, you should also do some literature search. Then, make a workflow describing the methods (programs, databases), inputs, outputs and required statistics. An example of a workflow can be seen here. Always discuss your ideas with one of the teachers.

Documentation

Do not forget to document the development of the project in your lab book. Write down your hypothesis, any relevant papers, methods, databases, etc. Below are points that should be included in your documentation:

• A brief background on the topic
• A workflow for the steps you plan to take
• What will be the inputs and outputs?
• Which programs do you plan to use?

Presentation

The points below are what we expect to see in your final presentation:

• Background on the topic that lead to the research question (1-2 slides)
• Hypothesis and brief overview of the literature
• Workflow figure to describe the analysis
• A rationale for why you choose those methods
• What are the inputs?
• What do you expect to get as output?
• Which result would confirm and which result would refute the initial hypothesis?
• Things you found particularly interesting

Exercise

1. Create a clear, data-driven hypothesis, and discuss it with teachers and fellow students. Often your initial idea can be further refined based on discussions with others.
2. Make sure you check the literature Find at least one paper that is closely related to your project, and use it/them to refine your question.
3. Methods: Make a plan for tackling your question(s) in the form of a workflow. Think about data sources, bioinformatic methods, possible outcomes, expectations, backup/follow-up plans, hypotheses, and possible interpretation.

Key Points