This repository holds all the files (source code, LaTeX, etc.) for my thesis project, "Evaluating Languages for Bioinformatics: Performance, Expressiveness and Energy".
This project performs comparisons of five langauges: C, C++, Perl, Python and Rust. Measurements are taken on relative performance, expressiveness and energy usage. A variety of string-matching algorithms are implemented and applied to simulated DNA sequence data.
The directory src contains all the program source code for all languages and
for the harness utility used to run the experiments.
The directory thesis contains all the LaTeX source for the thesis, as well as
image files used for some of the diagrams.
In addition, the following files are also present in this top-level directory:
- compression-20221111.txt - Snapshot of the compression data
- cyclomatic-20221111.csv
- cyclomatic-20221111.json
- cyclomatic-20221111.yaml - Snapshot of the cyclomatic complexity data
- draft-20221116.pdf - The draft as submitted to the thesis committee on 2022-11-16
- experiments-data-20221111.yml
- experiments-data-20221120.yml
- experiments-data-20221124.yml - Preserved data from full experiments runs. The 2022-11-11 data was used for all tables and diagrams in the thesis. The others are subsequent full runs of the experiments for comparison purposes.
- sloc-20221111.csv - Snapshot of the SLOC data