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Biomathhh is a Python package designed to efficiently provide common mathematical calculations used in biological research and analysis. This package provides life science researchers with easy-to-use functions for population dynamics, laboratory calculations, chemical properties, and biodiversity metrics. By consolidating these frequently-used formulas into a single package, Biomathhh aims to reduce repetitive coding and improve reproducibility in biological data analysis.
Biomathhh occupies a niche space in the Python ecosystem by focusing specifically on fundamental biological calculations that are frequently needed but not necessarily available in one package.
While comprehensive scientific computing packages like NumPy and SciPy provide the underlying mathematical operations, they do not offer biology-specific implementations. Packages like Biopython focus primarily on molecular biology, sequence analysis, and bioinformatics rather than general biological mathematics. Ecological analysis packages such as scikit-bio do include diversity indices, but lack the laboratory calculation functions that bench scientists use daily.
Related packages:
- NumPy - General numerical computing
- SciPy - Scientific computing and statistics
- Biopython - Molecular biology and bioinformatics tools
- scikit-bio - Bioinformatics and diversity metrics
Biomathhh fills the gap by providing a focused toolkit for the everyday mathematical needs of biologists across multiple subfields.
-
exponential_growth: Calculates exponential growth or decay over time using the continuous growth model
$$N(t) = N_0 e^{rt}$$
Useful for modeling population growth, bacterial culture expansion, radioactive decay, etc. -
calculate_dilution: Performs dilution and concentration calculations using the standard laboratory equation
$$C_1 V_1 = C_2 V_2$$
Helps researchers determine volumes and concentrations needed for preparing solutions, dilutions, and experimental reagents. -
calculate_pH: Converts between hydrogen ion concentration and pH using
$$\text{pH} = -\log_{10}([H^+])$$ -
sw_diversity_index: Computes the Shannon–Wiener Diversity Index
$$H' = -\sum_{i=1}^{S} p_i \ln(p_i)$$
where (p_i) is the proportion of individuals belonging to species (i).
You can install this package into your preferred Python environment using pip:
$ pip install git+https://github.com/UBC-MDS/DSCI_524_group27_biomathhh.gitFor more examples on how to use Biomathhh, use cases can be found in the package documentation here.
Below are working examples for each function in Biomathhh.
from biomathhh.dilution import calculate_dilution
final_conc = calculate_dilution(
stock_concentration=5.0,
stock_volume=1.0,
final_volume=5.0
)
print(final_conc)Output:
1.0
from biomathhh.exponential_growth import exponential_growth
value = exponential_growth(100, 0.05, 10)
print(round(value, 6))Output:
164.872127
from biomathhh.pH_scale import calculate_pH
ph_value = calculate_pH(1e-4)
print(ph_value)Output:
4.0
from biomathhh.sw_diversity_index import sw_diversity_index
species_counts = [50, 30, 20]
diversity_index = sw_diversity_index(species_counts)
print(round(diversity_index, 4))Output:
1.0297
Interested in contributing? Please check out the contributing guidelines for this project. Note that this project is released with a code of conduct and by contributing you agree to abide by its terms.
- Copyright © 2026 Diana Dadkhah Tirani Victoria Farkas Gurveer Madurai Zhihao Xie .
- Free software distributed under the MIT License.
LLMs (Gemini, Claude, ChatGPT) were used to format docstrings/documentation and with assistance in debugging workflow errors.