View source for Bi/BE/CS 183, Winter 2024

{{Course
|Course number=Bi/BE/CS 183
|Course title=Introduction to Computational Biology and Bioinformatics
|Year=2024
|Term=Winter
|Lecture schedule=MWF 11-11:55a, room TBD
|Instructors=Tara Chari, Meichen Fang, TBD
|Instructor office hours=TBD
}}
This course closely follows the [[http:github.com/pachterlab/BI-BE-CS-183-2023|Winter 2023 course]].

=== Catalog Description ===

'''Bi/BE/CS 183. Introduction to Computational Biology and Bioinformatics.''' 9 units (3-0-6): second term. Prerequisites: Bi 8, CS 2, Ma 3; or BE/Bi 103 a; or instructor's permission. 

Biology is becoming an increasingly data-intensive science. Many of the data challenges in the biological sciences are distinct from other scientific disciplines because of the complexity involved. This course will introduce key computational, probabilistic, and statistical methods that are common in computational biology and bioinformatics. We will integrate these theoretical aspects to discuss solutions to common challenges that reoccur throughout bioinformatics including algorithms and heuristics for tackling DNA sequence alignments, phylogenetic reconstructions, evolutionary analysis, and population and human genetics. We will discuss these topics in conjunction with common applications including the analysis of high throughput DNA sequencing data sets and analysis of gene expression from RNA-Seq data sets.

=== Lecture Schedule ===

{| class="mw-collapsible wikitable" width=100% border=1 cellpadding=5
|-
| '''Date'''
| '''Topic'''
| '''Reading'''
| '''Homework'''

|- valign=top
| '''Week 1'''<br>
3 Jan <br>  5 Jan <br>
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
** [[http:docs.google.com/presentation/d/1-Bo7yaaaxbf8ul_2gacZIII_pggd6JmSVXEF4Zwqekg|Lecture 1]]: Introduction to computational biology of single-cell RNA-seq
** [[http:docs.google.com/presentation/d/1tpeNHSONBunT7TwZSlwm42VknPVNeufdY7A4rzqMhkI|Lecture 2]]: Single-cell RNA-seq technology
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->

|- valign=top
| '''Week 2'''<br>
8 Jan <br>  10 Jan <br> 12 Jan
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->

|- valign=top
| '''Week 3'''<br>
<s>15 Jan</s> <br>  17 Jan <br> 19 Jan
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->

|- valign=top
| '''Week 4'''<br>
22 Jan <br>  24 Jan <br> 26 Jan*
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->


|- valign=top
| '''Week 5'''<br>
29 Jan <br>  31 Jan <br> 2 Feb
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->


|- valign=top
| '''Week 6'''<br>
5 Feb <br>  7 Feb <br> 9 Feb
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->


|- valign=top
| '''Week 7'''<br>
12 Feb <br>  14 Feb <br> 16 Feb
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->

|- valign=top
| '''Week 8'''<br>
<s>19 Feb</s> <br> 21&nbsp;Feb <br> 23 Feb*
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->


|- valign=top
| '''Week 9'''<br>
26 Feb <br>  28 Feb <br> 1 Mar
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->

|- valign=top
| '''Week&nbsp;10'''<br>
4 Mar <br>  6 Mar <br> 8 Mar
| This week's overall topic
* Math topic to be covered
* Math topic to be covered
* Application topic to be covered
| 
* Wi 2024 lecture slides: Mon, Wed, Fri
* Wi 2023 lecture slides: 
* Jupyter notebooks: {{Bi/BE/CS 183 public|example.ipynb}}
* Optional reading:
| {{Bi/BE/CS 183 public|hw1-wi2024.pdf|HW #1}}
Out: 3 Jan <br>
Due: 10 Jan <br>
<!-- {{Bi/BE/CS 183 public|caltech/hw1-wi2024_solns.pdf|Solns}}&nbsp;(Caltech&nbsp;only) -->

|}

=== Grading ===
The final grade will be based on homework sets and a final exam: 

*''Homework (70%):'' Homework sets will be handed out weekly and due on Wednesdays by 11 am using GradeScope.  Each student is allowed up to two extensions of no more than 2 days each over the course of the term.  Homework turned in after Friday at 11 am or after the two extensions are exhausted will not be accepted without a note from the health center or the Dean.  Python code is considered part of your solution and should be printed and turned in with the problem set (whether the problem asks for it or not).

:The lowest homework set grade will be dropped when computing your final grade.

* ''Final exam (30%):''  The final exam will be handed out on the last day of class (8 Mar) and due at the end of finals week. It will be an open book exam and computers will be allowed.

=== Collaboration Policy ===

Collaboration on homework assignments is encouraged. You may consult outside reference materials, other students, the TA, or the instructor, but you cannot consult homework solutions from prior years and you must cite any use of material from outside references. All solutions that are handed in should be written up individually and should reflect your own understanding of the subject matter at the time of writing.  Any computer code that is used to solve homework problems is considered part of your writeup and should be done individually (you can share ideas, but not code).

No collaboration is allowed on the final exam.

=== Course Text and References ===

There is no course textbook, but the slides from the prior year's course serve as a reference for much of the material in the course:

* <span id="Pachter_2023">[Pac23]</span> L. Pachter, [[http:|Caltech BI/BE/CSS 183: Introduction to Computational Biology and Bioinformatics]], Winter 2023.

The following additional references may also be useful:

* TBD
* TBD

Note: the only sources listed here are those that allow free access to online versions.  Additional textbooks that are not freely available can be obtained from the library.

[[Category: Courses]]