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ama-parser

Takes 96-well plate reader data, converts to pandas dataframe, and allows for analysis/plotting of bacterial growth curves

asr-protocol

Protocol and scripts for doing ancestral sequence reconstruction

bcmap

map barcodes to full sequences from a high-throughput mapping experiment

dataprob

Library for fitting models using a likelihood framework.

docker-jupyter-teaching

Temporary Jupyter Notebooks for scientific computing demos.

eee

ensemble epistasis engine

ellipticbn

tool for measuring ellipticity of cucurbituril macrocycles

ensemble_epistasis

epistasis

A Python API for estimating statistical high-order epistasis in genotype-phenotype maps.

epistasis-notebooks

Tutorial notebooks for the epistasis package hosted on Binder.

examl-tree-ancestor

pipeline stitching together fasttree, examl, and lazarus/paml for phylogenetics and ancestral sequence reconstruction

experimental-ensemble-epistasis

Scripts and data for reproducing the analysis in "An experimental demonstration of ensemble epistasis in the lac repressor"

fast_dbscan

fast, lightweight dbscan implementation for peptide strings

flowsym

A Python API for simulating flow cytometry data.

gelquant

Simple SDS-PAGE/western blot gel quantification software.

genotype-phenotype-maps

A curated list of experimental genotype-phenotype maps from published literature in JSON format

gmx-template

template for setting up MD simulations in the Harms lab.

gpgraph

NetworkX for genotype-phenotype maps

gpmap

A Python API for managing genotype-phenotype map data

gpseer

A tool to predict missing data in sparsely sampled genotype-phenotype maps

gpvolve

A Python API for computing evolutionary paths across genotype-phenotype maps and clustering of genotype-phenotype maps.

hops

Use machine learning to find rules for peptide binding

hops_enrich

software for processing phage display data for machine learning with peplearn

jupyterhub

Multi-user server for Jupyter notebooks

latticegpm

Python package for building fitness landscapes from protein lattice models

latticeproteins

2d protein lattice model simulator in Python

library_simulator

python package for simulating random libraries made by an error-prone polymerase

linkage

package for fitting thermodynamic linkage models to experimental data

m63f-biophysics

scripts and data to reproduce biophysical investigation of S100A9/M63F

networkviewer

Interactive Network Graph Viewer using D3.js