University of Florida Homepage


ZOO 4926/6927: Special Topics

Computational Tools for Research

MWF 2nd Period (8:30-9:20)

Instructor: Matt Gitzendanner

Increasingly, knowledge of scripting, database management, and advanced computing skills are critical for academic researchers

Topics covered:

  • Linux Command Line and Bash scripting
  • Python scripting
  • Using High-Performance computer clusters
  • Databases for research


This course will survey areas where high performance computing, large-scale data access and integration, informatics tools and software, and multi-disciplinary collaboration have had high impact on research as a foundation for computationally-enabled research.

The course is divided into three main topics, each addressing broadly applicable computational tools for modern research. The first topic covers basic Linux command-line skills and usage of the university’s HiPerGator computer cluster. These skills open the door the running analysis on a top 500 super computer, enabling student’s computational research. The second section introduces the Python scripting language, introducing students to core computer programming concepts and structure. Throughout this module, while the focus is on Python, we will emphasize how all computer languages share fundamental similarities and how students can transfer their Python skills to other languages and tasks. The final topic introduces databases, focusing on simple database design and administration as well as how to access data from databases using Python.

These topics provide the computational skills enabling students to continue learning and applying informatics tools in their research and careers.

The course will cover basic concepts that will provide the ability for students to apply new technologies to a wide array of research questions. A foundation in information management concepts opens doors for well-trained scientists and allows them to work in multidisciplinary research domains that are becoming increasingly essential.

Textbook: This course will use free open-source texts and materials.

Computer: Participants will be expected to bring a computer with internet access to each class

Draft Syllabus: CompToolsRes.2018.Syllabus