MA579: Numerical Methods in the Biological Sciences

Instructor: Prof. Samuel A. Isaacson
Office: MCS 231
Email:
Time and Location: T/TH 11-12:20PM, CAS 324
Office Hours: T 3:30-4:30PM, W 3:00-4:00pm in my office.

Syllabus: web page, [pdf] (Subject to change.)


Notes:

Notes on feedback regulation of gene expression: [here].


Labs:

Lab 0 - Jupyter notebook to download: [here].
     Please also download and save this css file to the same folder: [here].
     Non-interactive html version of lab for online viewing: [here]

Lab 1 - Due by email at 5pm on 09/26, see submission instructions in notebook file.
     Jupyter notebook to download: [here].
     Please also download and save this css file to the same folder: [here].

Lab 2 - Due by email at 5pm on 10/06, see submission instructions in notebook file.
     Jupyter notebook to download: [here].
     Please also download and save this css file to the same folder: [here].

Lab 3 - Due by email at 5pm on 11/14, see submission instructions in notebook file.
     Jupyter notebook to download: [here].
     Please also download and save this css file to the same folder: [here].

Lab 4 - Due by email at 5pm on 12/12, see submission instructions in notebook file.
     Jupyter notebook to download: [here].
     Please also download and save this css file to the same folder: [here].
     Standalone ctrwSamp.py file: [here].


Homework Assignments:

Homework 1 (due 9/28 in class): [Jupyter notebook file], css file for notebook (put in same folder): [here].
Webpage version of the homework: [here].

Homework 2 (due 10/12 in class): Webpage version: [here].

Homework 3 (due 11/02 in class, NOTE this material is on the midterm!): [Jupyter notebook file],
     css file for notebook (put in same folder): [here].
     Webpage version: [here].

Homework 4 (due 11/09 in class): Webpage version: [here].

Homework 5 Part I (due 11/30 in class): Webpage version: [here].
     Python Notebook version: [here].
     css file for notebook (put in same folder): [here].

Homework 6 (due 12/12 in class, will be accepted through 12/14 at noon to my mailbox): Webpage version: [here].
     Python Notebook version: [here].
     css file for notebook (put in same folder): [here].
     Standalone ctrw3d.py file: [here].


Use of Python:

Python will be used for many of the course assignments. I recommend Anaconda Python, which you can download for free at: https://store.continuum.io/cshop/anaconda/. (Please use version 3.6 as your default install.)


Python Tutorials:

Python documentation at: https://www.python.org/doc/

NumPy / SciPy tutorials and documentation: http://www.scipy.org/getting-started.html

Google’s Online Python Tutorial: https://developers.google.com/edu/python/

The iPython-based notebook tutorials at: https://github.com/jakevdp/2014_fall_ASTR599

A tutorial for writing Markdown in Jupyter/iPython notebooks. (How to write formatted text.): here.


Latex Tutorials:

Here is a template you can use for homework assignments. It includes links to Latex resources. The ".tex" file is where you write your assignment, the ".pdf" file is the compiled document. I've included one image, which Latex compiles into the pdf. Files: [here].