1 Syllabus

1.1 General syllabus

Note: click on this, and actually read it; it’s part of the syllabus:
../../SyllabusGeneral.html

1.2 Course description

The course will familiarize students with the application of computational methods to the biological sciences broadly, as viewed from both perspectives. We will introduce problems in molecular, structural, morphological, neurological, epidemiological, biomedical, and biodiversity informatics. We will explore principles, algorithms, tools, and software to address those problems.

1.2.1 Pre-requisites

• A grade of “C” or better in both one of Bio Sci 1113 or Bio Sci 1213, and one of Comp Sci 1570 / 1580 or Comp Sci 1971 / 1981.
  • Despite these minimal official pre-requisites, intro programming, data structures, intro biology, and genetics are highly recommended before enrolling. This course can be the culminating course of the Bioinformatics minor: https://catalog.mst.edu/undergraduate/degreeprogramsandcourses/bioinformaticsminor/ If you interested the minor, get in touch with me!

1.3 Textbooks and resources

1.3.1 Required (free/open)

1. Introduction to Applied Bioinformatics - Greg Caporaso
   • https://readiab.org/introduction.html
   • Cost: Free and open
2. Genomes, 2nd edition. Terence A Brown.
   • https://www.ncbi.nlm.nih.gov/books/NBK21128/
   • Cost: Free and open
3. Network Science - Albert-László Barabási
   • http://networksciencebook.com
   • Cost: Free and open

1.3.2 Optional (not free)

4. Bio-star Handbook (Bio* Handbook) - Istvan Albert
   • Optional (better for Biologists who would like to learn some practical tools)
   • https://www.biostarhandbook.com/
   • Cost: $25 for student edition

1.4 Which virtual machine / OS for this class?

Fedora latest running within VirtualBox is recommended,
but if you run any Linux bare-metal,
then we can likely make that work.

1.5 Which programming language for this class?

Mostly Python, and a hint of Bash