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Part I |
Data Science |
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| Sept 8 |
L0 |
Introduction and orientation |
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| Sept 10 |
L1 |
Information technology for managing science |
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| Sept 15 |
L2 |
Modern computing paradigms |
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| Sept 17 |
L3 |
Visualizing breast cancer transcriptomes |
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| Sept 22 |
L4 |
Representing & manipulating data |
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| Sept 24 |
L5 |
Transformations of breast cancer transcriptomes |
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| Sept 28 |
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Assignment 1 due |
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| Sept 29 |
L6 |
Exploratory data analysis of breast cancer transcriptomes |
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Part II |
Bioinformatics |
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| Oct 1 |
L7 |
The NCBI: a rich resource for the life sciences |
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| Oct 6 |
L8 |
How to wrangle with marine microbes |
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| Oct 8 |
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Midterm 1 (1hr; open book; Zoom) |
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| Oct 13 |
L9 |
Organzing the Tara Ocean’s data |
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| Oct 15 |
L10 |
Exploring microbial diversity across our oceans |
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| Oct 19 |
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Assignment 2 due |
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| Oct 20 |
L11 |
Representing genomes in R |
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| Oct 22 |
L12 |
Genome annotations |
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| Oct 22 |
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Quiz 2 |
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| Oct 22 |
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Project outline due for genomics diploma and grad students (1 page) |
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Part III |
Computational Biology |
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| Oct 27 |
L13 |
Transcription factor binding sites in Baker’s yeast |
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| Oct 26 |
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Quiz 3 |
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| Oct 29 |
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Midterm 2 (1hr, open book, Zoom) |
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| Nov 3 |
L14 |
Gene finding with Hidden Markov Models |
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| Nov 5 |
L15 |
Gene finding continued |
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| Nov 5 |
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Quiz 4 |
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| Nov 9 |
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Assignment 3 due |
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| Nov 10 |
L16 |
Models of sequence evolution |
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| Nov 12 |
L17 |
Phylogenies and alignments |
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| Nov 12 |
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Quiz 5 |
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| Nov 17 |
L18 |
Basics of machine learning |
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| Nov 19 |
L19 |
Discovery breast cancer subtypes: unsupervised analysis |
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| Nov 19 |
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Quiz 6 |
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| Nov 24 |
L20 |
Predicting breast cancer patient outcome from expression data: supervised analysis |
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| Nov 26 |
L21 |
Deep learning: proliferative index of a cancer cell with microscopy |
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| Nov 26 |
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Quiz 7 |
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| Nov 27 |
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Assignment 4 due |
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| Dec 1 |
L22 |
Computational challenges of single cell profiling |
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Part IV |
Reproducible Science and Communication |
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| Dec 3 |
L23 |
Reproducibility in life science research |
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| Dec 10 |
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Project due |
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| Dec TBA |
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Final (2hr, take home, open book) |
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