Toolbox for molecular animations in Blender, powered by Geometry Nodes.

COBRApy is a package for constraint-based modeling of metabolic networks.

Ribbon diagrams of proteins in #golang.

Scientific Computing for Chemists text for teaching basic computing skills to chemistry students using Python, Jupyter notebooks, and the SciPy stack. This text makes use of a variety of packages including NumPy, SciPy, matplotlib, pandas, seaborn, NMRglue, SymPy, scikit-image, and scikit-learn.

COPASI is a software application for simulation and analysis of biochemical networks and their dynamics.

Computational synthetic biology: Predicting DNA edits for bioengineering

Python package to study microbial communities using metabolic modeling.

Analysis of non-covalent interactions in MD trajectories

Experimental tech-demo for PhD thesis in Scientific Markdown; official:

Contact map analysis for biomolecules; based on MDTraj

Files and methodology pertaining to the sequencing and analysis of SARS-CoV-2, causative agent of COVID-19.

An implementation of genome-scale model reconstruction using Cost Optimization Reaction Dependency Assessment by Schultz et. al

A python package to analyse qPCR data for single-use or high-throughput application

A Python parser for the BRENDA database

Community-curated resources for research at the intersection of AI and molecular sciences

genomics, biochemistry, biotechnology, cell biology, biophysics, ecology

A VR app which allows creation and manipulation of dynamic models of polypeptides. Focus is fun and learning.

Wetlab Calculator

A List of Papers on Theoretical Foundations of Graph Neural Networks

AutoML system for building trustworthy peptide bioactivity predictors