Final Project
Introduction
- enough background for non-experts to understand the significance of the work
- goal of the project clearly stated
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Methods
- data description: where it came from, size, characteristics
- for every step in the pipeline, you include
- name of the software
- reference
- short description of the method
- short description of strengths (why chosen?)
- short description of weaknesses/limitations
- short description of the main assumptions of the method
- user choices (parameters that you had to choose and how)
- Not enough to write: “we used X, Y, and Z”
- Better to write: “We used X (reference) which [short description of the methodology]. We chose X because [short description of strengths]. We know that X has the following limitations [short description of weaknesses] and that it has the main following assumptions [short description of the assumptions]. The software X requires the user to input the following parameters: [parameter/user choices selected]”
- Use the Methods section in Yi et al (2021) as a template of how to write the Methods section in your project
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Advice
Read the software paper of the software you are citing and create a cheatsheet for yourself with the above items: description, strengths, weaknesses, assumptions, user choices
Example: RAxML
- Description: performs maximum likelihood estimation of a phylogenetic tree from aligned sequences
- Strengths: accurate estimation and statistically consistent
- Weaknesses: not scalable for large datasets and potential model misspecification error
- Assumptions: the substitution model and other model choices are correct and the optimization algorithm has converged to the maximum
- User choices: User needs to specify the substitution model and other model characteristics (e.g. rate variation); user can select starting tree but if it is not selected by the user, RAxML choose 5 starting trees based on parsimony
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Class dynamic: Project Q&A
Options:
- Stay in the class for questions
- Log off and use the time to work on your project
Before leaving, please fill out a checkup poll!