From 98acba53059e9f1d558bc1063f9b74a0b1ae1e48 Mon Sep 17 00:00:00 2001 From: Suchen ZHENG Date: Mon, 27 Jan 2025 02:45:48 -0500 Subject: [PATCH] Update syllabus.md --- syllabus.md | 77 +++++++++++++++++++++++++++-------------------------- 1 file changed, 39 insertions(+), 38 deletions(-) diff --git a/syllabus.md b/syllabus.md index 365fda3..19a84e3 100755 --- a/syllabus.md +++ b/syllabus.md @@ -8,42 +8,42 @@ layout: page Please see [last year's syllabus](http://cbb752b23.gersteinlab.org/syllabus) (with slide packs at the bottom) for previews for this year’s lectures, which will be slightly different. For this year, an updated slide pack will be posted after the lecture. (If it is substantially different from '22, an updated video will also be posted.) Video recordings for this year's lectures can be found in the Media Library tab in Canvas. -| | Topic | 2025 Spring's Lecture | [2023 Spring's Lecture](https://cbb752b23.gersteinlab.org/syllabus) | Comment | Lecture Summary | -| ---- | -------------------------------------------------------------------------- | --------------------- | ------------------------------------------------------------------------ | ------- | --------------- | -| 1/13 | \*YALE\* Spring term classes begin, 8.20 a.m. | | | | | -| | | | | | | -| 1/13 | Introduction | 25i1-25i2a | 23i1, 23i2a | | | -| 1/15 | DATA - Proteomics I | | 23d3 | | | -| 1/22 | DATA - Proteomics II | | 23d4 | | | -| 1/27 | DATA - Genomics I | | 23d1 | | | -| 1/29 | DATA - Genomics II | | 23d2 | | | -| 2/3 | DATA - Knowledge Representation & Databases | | 23d5 | | | -| 2/5 | MINING - Personal Genomes + Seq. Comparison + Multi-seq Alignment | | 23i2b,23m3, 23m4 | | | -| 2/10 | MINING - Fast Alignment + Variant Calling (incl. a focused section on SVs) | | 23m5,23m6a | | | -| 2/12 | MINING - Basic Multi-Omics + Supervised Mining #1 | | 23m6b,23m7,23m8a | | | -| 2/17 | Quiz on 1st Half | | | | | -| 2/19 | MINING - Supervised Mining #2 + Deep Learning Fundamentals #1 | | 23m8b,23m8c | | | -| 2/24 | MINING - Deep Learning Fundamentals #2 + Unsupervised Mining #1 | | 23m9a,23m9c | | | -| 2/26 | MINING - Unsupervised Mining #2 + Single-Cell Analysis #1 | | 23m9d, 23m9e | | | -| 3/3 | MINING - Single-Cell Analysis #2 + Biomedical Image Analysis | | 23t1 | | | -| 3/5 | MINING - Network Analysis | | 23m10a, 23m10b, 23m10c, 23m10d, 23m10e | | | -| | | | | | | -| | | | | | | -| 3/7 | Spring break begins | | | | | -| | | | | | | -| 3/24 | MINING - Privacy | | 23m11a, 23m11b | | | -| 3/26 | MINING/MODELING - Deep Learning Advanced I | | 23m12a | | | -| 3/31 | MINING/MODELING - Deep Learning Advanced II | | 23m12b | | | -| 4/2 | SIMULATION - Protein Simulation I | | 23s1 | | | -| 4/7 | SIMULATION - Protein Simulation II | | 23s2 | | | -| 4/9 | SIMULATION - Protein Simulation III | | 23s3 | | | -| 4/14 | SIMULATION - Protein Simulation IV | | 23s4 | | | -| 4/16 | SIMULATION - Protein Simulation V | | 23s5 | | | -| 4/21 | Quiz on 2nd Half | | | | | -| 4/23 | Final Presentations | | | | | -| 4/25 | \*YALE\* Classes end; Reading period begins | | | | | -| 5/1 | \*YALE\* Final examinations begin | | | | | -| 5/7 | \*YALE\* Final examinations end | | | | +| | Topic | 2025 Spring's Lecture | [2023 Spring's Lecture](https://cbb752b23.gersteinlab.org/syllabus) | Comment | Lecture Summary | +| ---- | -------------------------------------------------------------------------- | --------------------- | ------------------------------------------------------------------------ | ----------------------------------------------------------------------------------------------------------------------- | --------------- | +| 1/13 | \*YALE\* Spring term classes begin, 8.20 a.m. | | | | | +| | | | | | | +| 1/13 | Introduction | 25i1-25i2a | 23i1, 23i2a | | | +| 1/15 | DATA - Proteomics I | 25d3 | 23d3 | [Suggested Reading](https://files.gersteinlab.org/public-docs/2025/01.23/Proteomics-suggested-reading&study-guide.docx) | | +| 1/22 | DATA - Proteomics II | 25d4 | 23d4 | [Suggested Reading](https://files.gersteinlab.org/public-docs/2025/01.23/Proteomics-suggested-reading&study-guide.docx) | | +| 1/27 | DATA - Genomics I | 25d1 | 23d1 | | | +| 1/29 | DATA - Genomics II | | 23d2 | | | +| 2/3 | DATA - Knowledge Representation & Databases | | 23d5 | | | +| 2/5 | MINING - Personal Genomes + Seq. Comparison + Multi-seq Alignment | | 23i2b,23m3, 23m4 | | | +| 2/10 | MINING - Fast Alignment + Variant Calling (incl. a focused section on SVs) | | 23m5,23m6a | | | +| 2/12 | MINING - Basic Multi-Omics + Supervised Mining #1 | | 23m6b,23m7,23m8a | | | +| 2/17 | Quiz on 1st Half | | | | | +| 2/19 | MINING - Supervised Mining #2 + Deep Learning Fundamentals #1 | | 23m8b,23m8c | | | +| 2/24 | MINING - Deep Learning Fundamentals #2 + Unsupervised Mining #1 | | 23m9a,23m9c | | | +| 2/26 | MINING - Unsupervised Mining #2 + Single-Cell Analysis #1 | | 23m9d, 23m9e | | | +| 3/3 | MINING - Single-Cell Analysis #2 + Biomedical Image Analysis | | 23t1 | | | +| 3/5 | MINING - Network Analysis | | 23m10a, 23m10b, 23m10c, 23m10d, 23m10e | | | +| | | | | | | +| | | | | | | +| 3/7 | Spring break begins | | | | | +| | | | | | | +| 3/24 | MINING - Privacy | | 23m11a, 23m11b | | | +| 3/26 | MINING/MODELING - Deep Learning Advanced I | | 23m12a | | | +| 3/31 | MINING/MODELING - Deep Learning Advanced II | | 23m12b | | | +| 4/2 | SIMULATION - Protein Simulation I | | 23s1 | | | +| 4/7 | SIMULATION - Protein Simulation II | | 23s2 | | | +| 4/9 | SIMULATION - Protein Simulation III | | 23s3 | | | +| 4/14 | SIMULATION - Protein Simulation IV | | 23s4 | | | +| 4/16 | SIMULATION - Protein Simulation V | | 23s5 | | | +| 4/21 | Quiz on 2nd Half | | | | | +| 4/23 | Final Presentations | | | | | +| 4/25 | \*YALE\* Classes end; Reading period begins | | | | | +| 5/1 | \*YALE\* Final examinations begin | | | | | +| 5/7 | \*YALE\* Final examinations end | | | | ### Lecture Slide Pack @@ -55,8 +55,8 @@ Please see [last year's syllabus](http://cbb752b23.gersteinlab.org/syllabus) (wi | 25i2a | Introduction to Personal Genomes | | | [](https://youtu.be/K_Q-17uWlxo)[I2a](https://youtu.be/K_Q-17uWlxo) | | | 25i2b | An Individual's Perspective on Personal Genomes | | | [](https://youtu.be/0qDgfrPY180)[I2b](https://youtu.be/0qDgfrPY180) | [](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_Lecture_default_cbb752b21_24feb21_Carl_Zimmer_Personal_Genome.mp4)[i2b](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_Lecture_default_cbb752b21_24feb21_Carl_Zimmer_Personal_Genome.mp4) | | | | | | | | -| 23d3 | DATA - Proteomics I - Proteins | | | D3 | | -| 23d4 | DATA - Proteomics II - Structure | | | D4 | | +| 23d3 | DATA - Proteomics I - Proteins | [25d3](https://files.gersteinlab.org/public-docs/2025/01.23/CBB752-25d3-Proteins.pdf) | | D3 | | +| 23d4 | DATA - Proteomics II - Structure | [25d4](https://files.gersteinlab.org/public-docs/2025/01.23/CBB752-25d4-Structure.pdf) | | D4 | | | | | | | | | | 25d1 | DATA - Genomics I | | | [](https://www.youtube.com/watch?v=1Ns--G_v4pY&t=3359s)[D1](https://www.youtube.com/watch?v=1Ns--G_v4pY&t=3359s) | [](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_0203.mp4)[D1](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_0203.mp4) | | 25d2 | DATA - Genomics II | | | [](https://www.youtube.com/watch?v=XYxxfF1O0Y4)[D2](https://www.youtube.com/watch?v=XYxxfF1O0Y4) | [](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_0208.mp4)[D2](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_0208.mp4) | @@ -107,4 +107,5 @@ Please see [last year's syllabus](http://cbb752b23.gersteinlab.org/syllabus) (wi | 25s4 | Intrinsically Disordered Proteins | | | [](https://youtu.be/Ar-Nu7lNX0A)[S4](https://youtu.be/Ar-Nu7lNX0A) | [](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_0426.mp4)[S4](http://files.gersteinlab.org/media/videos/BioDataSciMiningModeling_0426.mp4) | | 25s5 | Simulation | | | | + See lab [permissions statement](https://sites.gersteinlab.org/permissions/) in relation to resusing any of the above material.