Skip to content

Latest commit

 

History

History
149 lines (105 loc) · 5.28 KB

tutorial3.md

File metadata and controls

149 lines (105 loc) · 5.28 KB
Raw
title output
Lab11: Documentation
html_document

Preamble

Please mark the following boxes with an X as appropriate:

[ ] Completed the Request for Evaluation by Artem
[ ] Answers assisted with generative AI (please indicate where)

Lesson Feedback (2 minutes): Please share your feedback about this lecture to improve the course, and tailor it to your learning for the next lecture.

Link: https://forms.gle/XXXXXXXXXXXX

Tutorial Objectives:

"happiness only real when shared"
- Christopher McCandless

Like happiness, what we do as scientists only matters if we are able to share
it with those around us. Be it through scientific publications, presentations,
or even code documentation, our ability to explain and teach the next
generation of scientists is equally important to our ability to do the science
in the first place.

Here you will go into the wild and try a web-based bioinforamtics tool. Explore,
play, experiment and learn. You will then take those experiences and create
a "Tutorial" which will teach next-years MGY441's students to do Virus Discovery
better.

The VIRUSxDISCVRY Repository

We will collectively be building a public Virus Discovery repository which will collect and curate tutorials for web-tools which could be used as part of the MGY441 Assignment 3.

As for the previous assignments you're expected to submit your answers by the deadline to your MGY441 gitlab repository.

# Pull Lab 11
# (remember to replace UTORid with your actual UTORid)
git clone https://gitlab.XXXXXXXXXX/UTORid/Lab11

# Submitting your work
cd lab11
git commit -a -m "Completed Lab11"
git push

I highly encourage you to submit the tutorial you create as part of this tutorial, and the template markdown file for your Assignment 3 to the public VIRUSxDISCOVERY repository. Although, you are not obliged to do so.

Question 1 : Software Tutorial (10 points) --------------------------------

** Due 10PM Dec 1st. 2024 **

Q.: In the data/toolAssignment.csv you are assigned a web-based bioinformatics tool or resource. You are to create a wiki-style Tutorial for {Insert Your Tool Name}, using as the example the virus from your Assignment 3. If your tool/virus combination does not work, you may use any generic sequence/input to write the tutorial wiki.

For this, your audience is your MGY441 peers, who can use your tutorial and apply it to improve their Assignment 3 answers, and also next years MGY441 students. As such consider the emphasis of these tutorials to be on how the tools apply to Virus Discovery.

Note: If you wish to write a tutorial for another tool/resource which you have found useful as part of your project and that tool is not listed in the toolAssignment.csv, you have until end of day Wednesday to message Artem on Piazza/email with the name and link of the tool you would like to do.

2 points - Introduction section

7 points - Tutorial/walkthrough

1 point - Conclusion and useful links

Submitting your tool wiki to VIRUSxDISCVRY (OPTIONAL) -------------------

  1. Navigate to https://github.com/ababaian/VIRUSxDISCVRY

  2. Fork the VIRUSxDISCVRYto your own github account.

  3. Clone your copy of the repository to your local computer

# Pull Tutorial Repository
git clone https://github.com/<YOUR_GITHUB_ID>/VIRUSxDISCVRY.git
  1. Add your tutorial to your local repository.

This means add your {toolname.md} to the tools/ folder and link any data or image files into tools/img/{toolname}/figure1.png etc... as needed.

  1. Commit and Push your local changes to your version of the repository.
# Submitting your work
cd VIRUSxDISCVRY
git commit -a -m "Added mytool Tutorial and supporting data"

# This will push to YOUR "fork" of the repository, and you should
# see it online on your github version
git push
  1. Create Pull Request to merge your changes into the common VIRUSxDISCVRY

When you're ready to merge your own repository into the main public repository you will do this by opening a Pull Request.

On the GitHub page for your fork of the repository. At the top tabs, click on Pull Requests and then click on the green Nuew Pull Request button.

As the base repository select ababaian/VIRUSxDISCVRY and as the head repository select <YOURNAME>/VIRUSxDISCVRY and click "Create Pull Request".

Submitting your Virus Report to VIRUSxDISCVRY (OPTIONAL) --------------

** DUE 10PM Dec 4th, 2024 **

The work you've all done on Tutorial 2 has been amazing! I'd love to share each of these projects year after year and have students build on top of one another in terms of the class assignment.

For 3 bonus points on your Assignment 3, copy and paste your answers from Assignment 3 and Tutorial 2 as indicated in the virTemplate.md file.

Follow the same instructions as above for "Submitting your tool wiki" but instead submit the parsed version of your Assignment 3 to the VIRUSxDISCVRY repo.