CMSC6950 Computer Based Research Tools and Applications

Memorial University of Newfoundland

Spring 2021

Instructor:

  • James Munroe

  • jmunroe@mun.ca

  • Meeting times: Mondays and Thursdays, 1 pm - 4 pm (meeting remotely)
  • Course website: https://cmsc6950.github.io

Teaching Assistant

  • TBD

Description:

Using computers in research computing requires a diverse set of skills and tools for the research to be effective and efficient. The goal of this practical six-week intersession course is to increase your level of proficiency with using computers to do research in science.

Computing in research often gets applied with one of two approaches. Some researchers develop new code and have to consider the technical details of numerical analysis and software engineering. Other researchers use proven applications that provide a predefined user interface and have established work flows. This course sits at the interface between those approaches and will cover how to build new programs from other software and libraries. It will also develop automation of research work flows for passing data between different software applications.

Textbook: Anthony Scopatz, Kathryn D. Huff. Effective Computation in Physics: Field Guide to Research with Python. O’Reilly Media, 2015.

Evaluation:

  • Participation: 10%
  • Assignments: 50%
  • Project: 40%

Topics:

1: Command line and scripting

  • The Bourne Shell (bash)
  • Bash scripting
  • Regular expressions
  • Editors and IDEs

2: Python

  • Basic Python
  • Jupyter notebooks
  • numpy, scipy, matplotlib

3: Software development

  • Revision control (git and GitHub)
  • Building software (make)
  • Unit testing
  • Test-driven development
  • Debugging, profiling and code optimization
  • Code documentation

4: Working with data and visualization

  • Data structures
  • Files and formats
  • Databases

5: Other topics

  • Other 2D and 3D visualization tools
  • Animations and movies
  • High performance computing

Memorial University Policies:

Accommodations for Students with Disabilities http://www.mun.ca/blundon/accommodations/

Student Code of Conduct http://www.mun.ca/student/conduct/

Exemptions From Parts of the Evaluation http://www.mun.ca/regoff/calendar/sectionNo=REGS-0601#REGS-1949

Academic Misconduct http://www.mun.ca/regoff/calendar/sectionNo=REGS-0748

Binder