Software

11 packages published to the Python Package Index · 322,901 downloads · source on GitHub

I write open-source scientific Python: optimization and metabolic-modeling tools for microbial communities, GPU-accelerated sequence alignment, and cheminformatics utilities for water treatment and reaction kinetics. Several of these packages are the computational basis of my publications, and every one of them still records installations each week.

Downloads

Download counts from pepy.tech, which tallies every PyPI download event — automated mirrors and continuous-integration installs included. Refreshed by update_package_stats.py; last updated October 2026.

Metabolic modeling & microbial ecology

ModelSEEDpy-freiburgermsu

• My release channel of ModelSEEDpy — the toolkit for reconstructing and analyzing genome-scale metabolic models with ModelSEED, where I am a core developer.
• Publishing it under my own name lets collaborators pip install my working branch directly, rather than wait upon an upstream release.

dFBApy

• An API that simulates dynamic Flux Balance Analysis (dFBA) of BiGG models, which propagates metabolite concentrations through time instead of resolving a single steady state.
• The module consumes the enzyme kinetics that are assembled by the BiGG-SABIO module.

CommScores

• An API that quantifies the metabolic interactions between members of a microbial community, which distinguishes syntrophy from competition for the same resources.
• I am the lead developer of this module, which consolidates extant interaction metrics into a single operable package, and which builds upon the ModelSEEDpy and COBRApy packages.

BiGG-SABIO

• An API that scrapes SABIO-RK for the enzyme kinetics of every reaction in a given BiGG model.
• The resulting kinetics tables parameterize the dFBA simulations of the dFBApy module.

OptlangHelper

• An API that constructs Linear Programming models for Optlang, which is the solver-agnostic optimization interface that underlies COBRApy and ModelSEED.
• Variables, constraints, and objectives are defined as named tuples, which removes the boilerplate of assembling each new optimization problem by hand.

Genomics & sequence analysis

Codons

• An API that conducts the central dogma of biology — the transcription and translation of an arbitrary genetic sequence — and executes BLAST results for protein and genetic sequences.
• The module exports FASTA-formatted files of the processed sequences, and interfaces with BLAST databases to identify them.

gpusw

• An API that scores Smith-Waterman (local) and Needleman-Wunsch (global) sequence alignments on the GPU, with BLOSUM substitution matrices, from a kernel that is compiled at runtime.
• The runtime kernel compiles through CUDA (CuPy/NVRTC) on NVIDIA hardware and through Metal (PyObjC) on Apple Silicon, so neither nvcc nor Xcode must be installed beforehand.
• The module requires Python 3.10 or newer.

Chemistry, water treatment & kinetics

ChemW

• An API that precisely calculates the MW from any chemical formula, including inorganic complexations and decimal stoichiometry, to the appropriate significant digits.
• The module also accepts protein sequences of one- or three-letter codes, and common chemical names that are recognized by PubChem.
• The module further offers the ability to refine PHREEQC databases into programmable JSON files.
• The aforementioned use-cases of ChemW were applied in the ROSSpy module.

ROSSpy

• An API and UI that simulates the geochemical reactive transport of Reverse Osmosis desalination.
• The module importantly predicts mineral precipitation, which causes scaling and module destruction.

hillfit

• An API that calculates regression according to the biochemical Hill-equation for a set of data, co-authored with Hiroaki Imoto.
• The module exports a regression plot with the R², a TXT file of the equation and parameter values, and provides API access to all components of the equation.
• The module was critically applied in refining the predictions of the PDIpy module.

PDIpy

• An API and UI that predicts the log-reduction of a bacterial solution or biofilm colony from Photodynamic inactivation.
• The module applies chemical kinetics to fundamentally model membrane oxidation over the course of time, and with the parameterized experimental conditions.