B

biology

ResponseOS is an open-source platform for reproducible clinical research analysis that re-examines medical studies to identify what truly drives patient outcomes. It aggregates and normalizes clinical trial data, applies Bayesian and meta-analytic methods to measure treatment effects against placebo signals, and highlights areas requiring further biological investigation. Designed for transparency and auditability, ResponseOS builds a continuously updated knowledge system where all analyses are versioned, reproducible, and open to scientific scrutiny under the AGPL-3.0+ license. https://roxanneardary.com/responseos/

The Uncertain Machine is an open-source, AI-powered scientific simulation platform where players learn by interacting directly with dynamic models of reality. Instead of memorizing facts, users explore physics, biology, chemistry, and complex systems through experimentation, curiosity, and play. Built for all ages and skill levels, it adapts explanations in real time, turning every interaction into a discoverable, replayable learning experience where science is something you do, not something you read.

BioFoundry is an open-source computational biology platform designed to streamline primer design, genome validation, and CRISPR-aware experiment planning. It combines traditional bioinformatics tools with modular, extensible architecture and AI-ready workflows to support researchers from raw DNA sequence input through to validated experimental design. Built under the AGPL-3.0+ license, it emphasizes transparency, reproducibility, and community-driven development — enabling collaborative innovation in modern genetic research.

Explore Animal Taxonomy

Remix of IO-Rodeo's colorimeter, reusing their cuvette holder and led-sensor hardware. This version runs on ESP32s, offering basic control through buttons, and advanced control through a web UI, websockets, and serial.

Firmwares and documents for the CubeSat electronics.

Approximation of eigenvalues ​​and eigenvectors.

AmpCheck investigates primer/probe - template matching and return amplicon related information.

https://dnarna.gitlab.io/ampcheck

SeqExtract searches annotated genomes for keywords and extract corresponding fasta records

A comprehensive Python toolkit for analyzing protein structures and small molecules using real datasets from RCSB PDB and FDA-approved drugs.

Paj web Haitian Scientific Society a.

A Flutter app for visualizing 3D molecular structures from CIF files in the PDB database.

RepeatGrower identify repeating k-mers in a genome and grows them until their occurrences decline.

This is the script for the bacterial FHN model that we reported in Startford et al., PNAS (2019). https://doi.org/10.1073/pnas.1901788116

Microscope Image Annotator (MIA) provides command-line driven microscope image annotation, including scales, labels and image post processing.

This script contains a collection of functions designed to put EthoVision tracks into a more usable format for further data analysis. This includes interpolating, smoothing, extracting data and metadata and writing them out as separate csv files.

Bioinformatics - Segmentation of biofilm images using OpenCV library.

A parametric design for a test rig for different combinations of LEE or Rosco gel filters allowing LEDs and photodetectors to be set up with different filter combinations and either a cuvette or capillary containing the sample.