After you have your group set, go to this link to accept the group project. Your team name should be your group name (Group 1 to Group 10). Note that this is an empty repository. You will fill it in. One of the group members will create a team and other members of the same group will join that team.

Key dates

Component Due Date
First part - report submission 15/11/2023 23:59
First part - presentations 17/11/2023 During Class Hours
Final report submission 30/12/2023 23:59
Final presentation 3-5/1/2024 During Class/Lab Hours

What to do?

First Part

  • You should prepare a list for potential mutations that might have caused the disease.
  • You can investigate the pipelines for “Whole Exome Sequencing”, eg. GATK pipeline
  • You will use the troya server. You can connect the server through ssh. The server DNS address and password information will be provided by your instructor.
  • Your user name will be your group name. The data us shared with you at /disk2/ens210/data. Please do not duplicate this data.
  • You can use conda to install the tools that you need.
  • If you need to install a software that is not available through conda, you should ask your TAs to install it for you.

Second Part

  • You will choose one of the most critical missense mutations from Patient X that might have made him/her sick.
  • After you get an approval from your advisor, you will perform an evolutionary analysis on the protein that has the mutation of your interest.
  • This evolutionary research will include the following tasks:
    • Homology search
    • Phylogenetic tree construction
    • Identification of paralogs and decide whether they have the “same” function with your protein of interest. If not, exclude them from MSA.
    • Perform conservation analysis on the refined MSA.
    • Write a report

Week 13

  • Complete the project.
  • Interpret the results as a group.
  • Write a report (see due date above).
  • Push your report.
  • Push your codes and plots.

Week 14

  • Make the final presentation.
  • Revise the report if asked by the instructor.
  • Push everything to the repository.

Report

Report should be submitted markdown format. The report should include the following sections.

  • Title
  • Introduction (½ page)
  • Results (2 pages)
  • Figures (min 4) with legends
  • Discussion (½ page)
  • Materials and Methods (½-1 page)
  • References

Consider one page as 500 words.

A markdown-formatted template is given below:

# Project Title

## Authors

## Introduction

* Introduce the data, the gene (protein), the disease

## Results

Figures should be embeded in this section.

## Discussion

* What are the limitations of this study? 
* What else would you do to confirm your mutation?

## Materials and Methods

* Explain your methids in detail, eg. what tools and parameters you used.

## References

First Presentation (17/11/2023)

  • 5 min presentation
  • One group member can present.

Final Presentation (3-5/1/2024)

  • 10 min presentation + 2 min QA ~ 12 min total.
  • It is recommended that each group member presents a part of the study.
  • The attendance will be taken and it will contribute to the final score on both days.

Method code and documentation on GitHub

All the code and steps should be given in an appropriate file such as python, bash. The code and steps should be documented in a markdown file such as method.md. The aim is to provide reproducible environment.

Grading

  • The first part will have 50% weight on your total score.
  • Report (20 points) Story flow, English, appropriate referencing
  • Depth of work (20 points)
  • GitHub documentation (20 points)
  • Presentation (20 points)
  • Individual contribution (20 points)
    • Work load will also be considered here. Group work load should be equally distributed.
    • Participation by asking questions to other groups will contribute to your score.

Notes on grading

  • Work load for each group member should be balanced. The work balance will be checked through the contributions of each member at GitHub repo. Each member should push their own work to the repository. The work load balance will be evaluated.

  • The group project will affect 10% of your total class score.

  • If you get 0 from any of the sections (see grading), the group will get 0 for the entire project.

  • Plagiarism will not be tolerated: the entire group will fail the project.