Embedded Files
Slides & resources from the M.Sc. bootcamp
Bioinformatics
Roaslind Franklin's contributions in discovery of dna structure and Photo51
Amy Lu's excellent slides on AlphaFold
Modeling
Lecture 1 (bioinformatics session 1) - 31 August 2024
MIT EECS's missing semester resources, Missing semester youtube playlist
Scientific Computing From Scratch
(via Prof. Pratyush Tiwary, with links to lots of useful resources)
Shell & shell commands
https://missing.csail.mit.edu/2020/course-shell/
Install WSL (for windows laptops)
Follow instructions here
Lecture 2(bioinfo session2) - 07 Sep 2024
Pre-requisites(Will assume you have read/watch before coming to class on 07Sep2024
Lecture 2 will build on concepts in this prereq readings, they are *not* optional ) :
An introduction to sc RNA seq by Statquest
An ibiology introduction to sc RNA seq
Optional, but highly recommended (2 excellent videos by Mark Sanborn of @Sanbomics) :
Part 1 of Sanbomics sc(single cell) guide on RNA preprocessing & QC
Part 2 of Sanbomics sc(single cell) guide on RNA integration & annotation
Lecture-2-zoom-recordings :
Lecture 3
Pre-req readings for L3(14 September 2024)
Please read(in this sequence) before class on 14 September 2024 :
a. How to read a research paper (2pages), more details here
Graphical flow chart of the 3-pass algo on "How to Read a paper"
b. Read the Kinker_2020_NatureGenetics paper
c. Data for the paper is openly available at :
https://singlecell.broadinstitute.org/single_cell/study/SCP542/pan-cancer-cell-line-heterogeneity#study-download
Especially for folks not from a biology background,
i used google's very recent NotebookLM, to create an
ai-generated 2-person audio conversation, from the pdf of the paper !!!
In my opinion, it's quite good ! Check it out here !
Read all the points below carefully,
4. contains details of your assignment, due, on 21Sep2024
I will be adapting Dean Lee's brilliant F1L(Figure 1 Lab) pedagogy for the remaining bioinformatics portion of the course.
Read this F1L piece very carefully:
https://www.linkedin.com/pulse/week-1-f1l-internship-emulator-ksq-dean-lee-354ke/
F1L github repo : https://github.com/deanslee/FigureOneLab/
F1L contains a curated set of questions, data, and methods that you can use to build a strong compbio project:
1. Questions presented in the form of papers are sourced from the fields of cancer biology, immunology, neuroscience, stem cell biology. Figure 1 of these papers serve as our starting point. These papers address topics of broad scientific appeal to both academia and industry so you are working on problems that people actually care about.
Kinker_2020_NatureGenetics paper is a study of biological programs in commonly used cancer cell lines.
OR
Schmidt_2022_Science paper is a study of CRISPR-edited human T cells.
In class, we will mostly focus on the Kinker 2020 cancer cell lines paper.
2. Data accompanying these papers are open (not behind a paywall or in a restricted database), from human tissue, and multiomic.
3. Methods are well-documented Python packages.
4. It's not real if it's not written.
Write a short 2-3 page memo on the KSQ(Key Scientific Question) for the Kinker 2020 paper, in your own words
Due date : 21 September 2024
a. Ok to use claude.ai , perplexity.ai, ChatGPT, your fav LLM tool to understand the paper,
**but not to actually write the memo**
b. acknowledge clearly whatever LLM tools you use
c. properly cite all the resources or additional papers/resources, you use
Why write a memo :
As Dean articulates beautifully in the link above,
[
Memos Drive Clarity
Memos Drive Clarity
I am asking you to write a memo to yourself because compbio work is complex, and it is easy to get lost. I want the memo to be a tool that helps you clarify your understanding of the work as it unfolds in the coming weeks. When you leave work on Friday and come back on Monday, you should be able to skim through your memo and instantly know where you left off. If someone, such as your supervisor, asks you for a project update, you should be able to pull out your memo and give a concise update instantly. When you are lost in the weeds of data exploration, you should be able to refer back to your memo to get yourself back on track. As you work on your project in the coming weeks, you should update this memo to reflect your developing/changing understanding of the KSQ.
I cannot overstate the importance of having clarity when you work. This is true not just of compbio jobs in biotech/pharma; it's true of pretty much every job. Writing memos drives clarity.
I now share my favorite work mantra: It's not real if it's not written.
]
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