11 projects
gpusw
GPU-accelerated Smith-Waterman / Needleman-Wunsch alignment scoring via a kernel compiled at runtime — CUDA (CuPy/NVRTC, no nvcc) on NVIDIA or Metal (PyObjC, no Xcode) on Apple Silicon
OptlangHelper
Python package for building Linear Programming models that are compatible with Optlang
ModelSEEDpy-freiburgermsu
Python package for building and analyzing models using ModelSEED
commscores
A Python package for quantifying microbial interactions
hillfit
Model for fitting data with the Hill equation, and exporting the contents
ChemW
Calculates the Molecular Weight, to the appropriate significant digits, from a string of an arbitrary chemical formula, a protein sequence of one- or three-letter codes, or chemical common names that are recognized by PubChem.
ROSSpy
Software for predicting the brine concentrations and scaling quantities after RO desalination.
dFBApy
Simulate dynamic Flux Balance Analysis (dFBA) of BiGG models, with compatibility to the BiGG-SABIO module.
Codons
Translates and transcribes an arbitrary genetic sequence, generates FASTA-formatted files, and interfaces with BLAST databases to identify genetic and protein sequences.
PDIpy
Simulate Photodynamic Inactivation (PDI) of from a kinetics model of membrane oxidation.
BiGG-SABIO
Scrapes SABIO-RK for enzyme kinetics data for given BiGG Model for dFBA simulation.
