Bios 8366 is taught using Python and the Scientific Stack, a set of core scientific computing packages written and maintained by various third parties.
The use of version control systems is essential for effective scientific computing. In Bios 8366, we make extensive use of Git, which is one of several widely-used versioning systems.
To install Git, you can either download an installer from the Git website, or if you are on a UNIX-based computer, install it via your system’s package manager (recommended). On Mac OS X, you can easily install a variety of software packages using Homebrew. To obtain Git, simply type:
brew install git
On Linux, you can issue a similar command with
yum, depending on which Linux distribution you are using.
Git can also be installed using the
conda tool described below.
In addition to installing Git locally, we will be using GitHub to remotely store and share our code and documents. If you do not already have a GitHub account of your own, you can request an educational account that will allow you to create private repositories that you can use for your course work.
The first step is to install Python on your computer. I will be teaching this course based on Python 3.6. Perhaps the easiest way to get a feature-complete version of Python on your system is to install the Anaconda distribution. Anaconda is a completely free Python environment that includes includes almost 200 of the best Python packages for science and data analysis. Its simply a matter of downloading the installer (either graphical or command line), and running it on your system.
Be sure to download the Python 3.6 installer, by following the Python 3.6 link
In addition to Python itself, we will be making use of several packages in the scientific stack. These include the following:
We will install everything you require for Bios 8366 in one operation, described in the next section.
git clone https://github.com/fonnesbeck/Bios8366.git
If you are not familiar with Git and GitHub, you can simply download the zip file of the repository at the top of the main repository page.
Then, move to the directory created by the clone/zip file:
and install everything using
conda env create -f environment.yml
This will create an environment called
bios8366 that includes the packages required for the course.
If you are not using the Anaconda Python distribution, you will need to manually install the packages listed in
Which you probably don’t want to do.
So install Anaconda.
To use the environment, you may type:
conda activate bios8366
For preparing assignments and final projects, students may select from a variety of document preparation tools. Each of these facilitate scientific reporting by being able to embed code and typeset mathematical equations.
The use of traditional word processing software, such as Microsoft Word or OpenOffice is not permitted in Bios 8366.