SOFTWARE

A full list of software tools developed in the Davis lab are linked from our lab’s Github. All software developed in the Davis lab is released open source, typically with a GPL-3.0 license. Note that trainees typically maintain their own Github repositories with the latest versions of these tools.

Electron microscopy software

CryoDRGN ❄🐉

Our machine learning based approach to uncover and resolve structural heterogeneity in single particle cryo-EM datasets developed by Ph.D. student Ellen Zhong. Learn more here, and download here.

MAVEN ❄🧮

 

Our model-based approach to analyze compositionally heterogeneous structural ensembles developed by Ph.D. student Laurel Kinman. Learn more about this approach to analyze subunit occupancy here, see a wonderful example application here, and download here.

SIREn ❄🚨

 

em_scripts ❄💻

 

cryoSRPNT ❄🐍

 

CALC_LEVELS ❄🧮

Our model-free approach to identify regions within an ensemble of 3D desnity maps that are heterogeneous. This tool was developed by Ph.D. students Laurel Kinman and Maria Carreira. Download SIREn here.

An ever growing repository of (potentially) useful helper scripts to munge electron microscopy data. Download here.

A tool to rapidly simulate cryoEM datasets for studies aimed at benchmarking other cryoEM analysis tools. We have developed much of the software in the Davis lab using this method developed by Ph.D. student Barrett Powell. See example applications here. Download cryoSRPNT here.

A tool developed by Ph.D. student Maria Carreira to calculate isosurface levels for 3D reconstructions from cryo-EM or cryo-ET data. This turns out to be incredibly useful for looking at large volume ensembles generated by tools such as cryoDRGN and tomoDRGN. Download here.

ELECTRON TOMOGRAPHY SOFTWARE

 

tomoDRGN 🌐🐉

Developed by Ph.D. student Barrett Powell, tomoDRGN is our machine-learning based approach to analyze structural heterogeneity in cryo-ET datasets. Read about its development here, and some early applications here.

MASS SPECTROMETRY SOFTWARE

pysodist ⚖️🧮

 

pyextractMS ⚖️⛏️

A Pythonic implementation of isodist that allows for accurate fitting and quantitation of complex isotopic mass distributions within mass spectra. Download here.

A repository of Python scripts to interact with mass spectrometry data stored in Thermo RAW format. Download here.

msDataSheet ⚖️✅

A tool to rapidly generate datasheets to QC the performance of a mass spectrometer. Download here.

TEACHING

 

cryoEM workshop ❄📖

Source material for an interactive workshop the Davis lab runs that teaches students with limited backgrounds in structural biology about cryoEM image processing and 3D reconstruction. View and download material here.