Computational Genomics (KIZ, Fall 2024): Difference between revisions

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[[File:Banner-comp-genomics.png|800px|center]]
[[File:Banner-comp-genomics.png|800px|center]]
<center>Sept, Oct & Nov of 2024</center>
<center>Thursdays 8:30-11:30am, Oct 10 - Dec 10, 2024</center>
<center>'''Guest Instructor:''' Weigang Qiu, Ph.D.<br>Professor, Department of Biological Sciences, City University of New York, Hunter College & Graduate Center<br>Adjunct Faculty, Department of Physiology and Biophysics,
<center>'''Guest Instructor:''' Weigang Qiu, Ph.D.<br>Professor, Department of Biological Sciences, City University of New York, Hunter College & Graduate Center<br>Adjunct Faculty, Department of Physiology and Biophysics,
Institute for Computational Biomedicine, Weil Cornell Medical College</center>
Institute for Computational Biomedicine, Weil Cornell Medical College</center>
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<center>'''Lab Website:''' https://wiki.genometracker.org</center>
<center>'''Lab Website:''' https://wiki.genometracker.org</center>
<br>
<br>
<center>'''Assistants''': Mr Bei Liu & Dr Charles Adeola</center>
<center>'''Host''': Dr Yun Gao, Ph.D.<br>[http://english.kiz.cas.cn/ Kunming Institute of Zoology (KIZ)]</center>
<center>'''Host''': Dr Yun Gao, Ph.D.<br>[http://english.kiz.cas.cn/ Kunming Institute of Zoology (KIZ)]</center>
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===Week 1, Thursday, Oct 10, 2024===
===Week 1, Thursday, Oct 10, 2024===
* Introudction. Lecture slides: [[File:QiuLab-CUNY-Hunter.pdf|thumb]]
* Introudction. Lecture slides: [[File:QiuLab-CUNY-Hunter.pdf|thumb]]
* Computer setup: gitee accounts (for course management)
* Computer setup: gitee accounts (for course management). [https://edu.gitee.com/huntercollege/courses/3030/noticeboard Course link on gitee]
* <span style="color: blue">Survey 1: Genomics & Data Science</span> PDF file: [[File:KIZ-survey-1.pdf|thumb]]
* <span style="color: blue">Survey 1: Genomics & Data Science</span> PDF file: [[File:KIZ-survey-1.pdf|thumb]]
* <span style="color: blue">Survey 2: Tree-thinking Skills</span> PDF file: [[File:Pretest-1.pdf|thumb]]
* <span style="color: blue">Survey 2: Tree-thinking Skills</span> PDF file: [[File:Pretest-1.pdf|thumb]]
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===Week 2, Thursday, Oct 17, 2024===
===Week 2, Thursday, Oct 17, 2024===
* <span style="color: green">Linux Tutorial: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)</span>
* Git usages (by Mr Liu)
* Assignment 1
** Demo: homework submission using Gitee
** Download the course repository: <code>git clone https://gitee.com/huntercollege/comp-genomics-kiz.git</code>  
* Linux Tutorial I. [[File:Intro-unix-KIZ.pdf|thumb]]
* Phylogenetics lecture: [[File:Part-1-tree-thinking.pdf|thumb]]
** Tree manipulations: reroot & tree distances
** Gene tree vs Species tree; orthologous and paralogous genes; tree pruning & collapsing
 
===Week 3, Thursday, Oct 24, 2024===
===Week 3, Thursday, Oct 24, 2024===
* <span style="color: red">Quiz #1</span>
* Review: Tree manipulations
* <span style="color: green">Python Tutorial I: Advanced Python</span>
* <span style="color: red">Quiz #1. tree terms & tree manipulations</span> (20 pts); open-book; 9-10am, in-class
* Assignment 2
* <span style="color: green">Linux Tutorial II: BpWrapper Toolkit (https://github.com/bioperl/p5-bpwrapper)</span> Updated sldies: [[File:Intro-unix-KIZ.pdf|thumb]]
 
===Week 4, Thursday, Oct 31, 2024===
===Week 4, Thursday, Oct 31, 2024===
* <span style="color: green">Python Tutorial II: Regular expression & scientific computing with Python</span>
* <span style="color: red">Quiz #2. Linux commands & BpWrappper toolkits</span>: 20 pts, 9-10:30am
* Assignment 3
* <span style="color: orange">AFSV Genomics I </span>: Download and align genomes.
** Fork a copy of [https://edu.gitee.com/huntercollege/projects/696311/repos/huntercollege/afsv-genomics/sources the ASFV project repository].
** Instructions to fork a repository (prepared by Mr Liu): https://zwmqn249t3y.feishu.cn/wiki/OVdEwB00ciNx9Xkxvxsc7lJEncc?from=from_copylink
** Project overview: Lecture slides: [[File:Afsv-project-kiz.pdf|thumb]]
 
===Week 5, Thursday, Nov 7, 2024===
===Week 5, Thursday, Nov 7, 2024===
* <span style="color: red">Quiz #2</span>
* ASFV project:
* Computer setup: R & RStudio
** <code> git clone https://gitee.com/huntercollege/asfv-genomics.git </code>
* <span style="color: orange">R Tutorial 1: Basic R</span>
** Align genomes: protocol-1
* Assignment 4
** SNP calls; quality check by Ts/Tv ratio (Protocol 1)
** Annotate SNPs: Protocol 2
** IQ-tree to get genome tree: Protocol-3
* Trait evolution and comparative analysis [[File:Trait-evolution-KIZ.pdf|thumb]]
* Assignment: Pre-test 2


===Week 6, Thursday, Nov 14, 2024===
===Week 6, Thursday, Nov 14, 2024===
* <span style="color: orange">R Tutorial 2: Data visualization & basic statistics</span>
* Computer setup: R & RStudio; <span style="color: orange">R Tutorial Part 1: Basic R & Data manipulations</span>
* Assignment 5
* Lecture slides: [[File:R-tutorials-KIZ-part-1.pdf|thumb]]
* Assignment: Practice-1 & -2
 
===Week 7, Thursday, Nov 21, 2024===
===Week 7, Thursday, Nov 21, 2024===
* <span style="color: red">Quiz #3</span>
* R tutorials:
* <span style="color:  #33ff8a">Genomics Tutorial 1: Cluster analysis & scRNA analysis</span>
** part 2 (Visualization & Statistics). Slides: [[File:R-tutorials-KIZ-part-2.pdf|thumb]]
* Final report (draft 1: Background, Hypothesis, Significance, Material & Methods)
** Assignment: Practice-3 & -4
* Final project:
** Introduction to Ka/Ks analysis
** File distribution: each student is assigned 10 random genes; Run <code>git pull</code>; or if you haven't cloned the repository, run <code>git clone https://gitee.com/huntercollege/asfv-genomics.git</code>
** Follow the protocol in "doc/protocol-4-paml.txt"
 
===Week 8, Thursday, Nov 28, 2024===
===Week 8, Thursday, Nov 28, 2024===
* <span style="color: #33ff8a ">Genomics Tutorial 2. NGS data analysis</span>
* <span style="color: red">Quiz #3. R exercises</span>
* Final report (draft 2: Results & Discussion)
* Final project:
** Visualize tree with <code>ggtree</code>
** Plot Ka/Ks for genes
** Run IQ-TREE to obtain site-specific rates; Plot site-specific rates


===Week 9, Thursday, Dec 5, 2024===
===Week 9, Thursday, Dec 5, 2024===
* <span style="color:  #33ff8a ">Genomics Tutorial 3. Monte Carlo simulations of genome evolution</span>
* Final presentations
* Final report (draft 3: Conclusions, future directions, reference)
* <span style="color: red">Final report due Nov 26</span>


===Week 10, Thursday, Dec 10, 2024===
===Week 10, Thursday, Dec 10, 2024===
* Final presentation
* Final presentations

Latest revision as of 14:46, 19 November 2024

Banner-comp-genomics.png
Thursdays 8:30-11:30am, Oct 10 - Dec 10, 2024
Guest Instructor: Weigang Qiu, Ph.D.
Professor, Department of Biological Sciences, City University of New York, Hunter College & Graduate Center
Adjunct Faculty, Department of Physiology and Biophysics, Institute for Computational Biomedicine, Weil Cornell Medical College
Office: B402 Belfer Research Building, 413 East 69th Street, New York, NY 10021, USA
Email: wqiu@hunter.cuny.edu
Lab Website: https://wiki.genometracker.org


Assistants: Mr Bei Liu & Dr Charles Adeola
Host: Dr Yun Gao, Ph.D.
Kunming Institute of Zoology (KIZ)

Course Overview

Welcome to Computational Genomics, a 9-week computer workshop for graduate students. A genome is the total genetic content of an organism. Driven by breakthroughs such as the decoding of the first human genome and next-generation DNA -sequencing technologies, biomedical sciences are undergoing a rapid and irreversible transformation into a highly data-intensive field.

Genome information is revolutionizing virtually all aspects of life sciences including basic research, medicine, and agriculture. Meanwhile, use of genomic data requires life scientists to be familiar with concepts and skills in biology, computer science, as well as data analysis.

This workshop is designed to introduce computational analysis of genomic data through hands-on computational exercises, using published studies.

The pre-requisites of the course are college-level courses in molecular biology, cell biology, and genetics. Introductory courses in computer programming and statistics are preferred but not strictly required.

Learning goals

By the end of this course successful students will be able to:

  • Use Linux commands & compose simple shell scripts to automate a bioinformatics pipeline
  • Program in Python for parsing texts and simulating evolution
  • Visualize data and perform statistical analysis using R/RStudio
  • Compose a bioinformatics research report

Web Links

Assignments, Quizzes, and Final Report

Student performance will be evaluated by attendance, three (3) quizzes, six (6) assignments, and a final report:

  • Attendance & participation: 30 pts
  • Assignments: 6 x 10 = 60 pts
  • Open-Book Quizzes: 3 x 20 pts = 60 pts
  • Final presentation: 50 pts

Total: 200 pts

Course Schedule

Week 1, Thursday, Oct 10, 2024

Week 2, Thursday, Oct 17, 2024

Week 3, Thursday, Oct 24, 2024

Week 4, Thursday, Oct 31, 2024

Week 5, Thursday, Nov 7, 2024

Week 6, Thursday, Nov 14, 2024

Week 7, Thursday, Nov 21, 2024

Week 8, Thursday, Nov 28, 2024

  • Quiz #3. R exercises
  • Final project:
    • Visualize tree with ggtree
    • Plot Ka/Ks for genes
    • Run IQ-TREE to obtain site-specific rates; Plot site-specific rates

Week 9, Thursday, Dec 5, 2024

  • Final presentations

Week 10, Thursday, Dec 10, 2024

  • Final presentations
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