An interactive pipetting-volume calculator for MoClo Golden Gate digestion–ligation reactions, with a searchable library of acceptor vectors, L0 parts, and end linkers so you don’t need to dig through a spreadsheet to find a sequence.
Software
Software I develop and use for analysis and discovery is (when possible) shared in public github repositories.
Open hardware and firmware for continuous, networked gas monitoring in biological growth chambers. CO₂ and O₂ sensing, local touchscreen display, web interface, SD logging, and Grafana Cloud integration. Find the full documentation here
Fast Linker Identification Pipeline for Pyrenoids (FLIPPer) was built to identify functional analogs of canonical pyrenoid Linker proteins based on shared feature with EPYC1. This was used to identify the Chlorella sorokiniana Linker protein (CsLinker).
SEC_Fit is an open-source Python tool designed for the quantitative analysis of analytical Size-Exclusion Chromatography (SEC) data. It allows users to easily fit interactive Gaussian models to overlapping chromatographic peaks, estimate molecular weights based on column calibration standards, and calculate relative species abundance and stoichiometry directly from ÄKTA CSV exports.
OxySolve is a Python-based tool designed to streamline the analysis of oxygen evolution data collected from Hansatech oxygen electrodes.
RubiCon (Rubisco Condensation) was designed to analyze and quantify phase separation in LAMMPS molecular dynamics simulations of Rubisco and linker proteins. It provides a robust pipeline for detecting condensates, Calculating phase-specific properties (concentration, volume and analyzing dynamics (diffusion).