Hekstra Lab

colav

Calculate protein structural representations (dihedral angles, CA pairwise distances, and strain analysis) for downstream analysis (e.g., PCA, t-SNE, or UMAP).

integrator

Proof of concept profile fitting and integration with neural nets

mdtools

Tools for running MD simulations in OpenMM

microutil

Python utils for working microscopy datasets

napari-labeller

nesm-python

Notebooks for the python workshop at the New England Society for Microscopy Spring 2021 Meeting

phase-retrieval

A small library implementing phase retrieval algorithms for 2D images.

scientific-python-bootcamp

Notebooks from a three day introduction to scientific computing in python at Harvard University.

SFcalculator

SFcalculator_torch

Differentiable pipeline connecting protein atomic models and crystallography structure factors

Hekstra-Lab/colav

Calculate protein structural representations (dihedral angles, CA pairwise distances, and strain analysis) for downstream analysis (e.g., PCA, t-SNE, or UMAP).

Hekstra-Lab/mdtools

Tools for running MD simulations in OpenMM

Hekstra-Lab/SFcalculator

Hekstra-Lab/integrator

Proof of concept profile fitting and integration with neural nets

Hekstra-Lab/laue-index-assigner

A robust algorithm for assigning miller indices to Laue data from approximate indexing solutions.

Hekstra-Lab/microutil

Python utils for working microscopy datasets

Hekstra-Lab/napari-labeller

Hekstra-Lab/SFcalculator_torch

Differentiable pipeline connecting protein atomic models and crystallography structure factors

Hekstra-Lab/EF-X-crystal-MD

Setup and analysis of MD simulations mimicking the application of an external electric field to a protein crystal.

Hekstra-Lab/raman-analysis

Spontaneous Raman analysis library

Hekstra-Lab/scramble

A tool for disambiguating serial laue data

Hekstra-Lab/Devices_Optics

Code to collect and analyze data using the spectroscopic setup & data collected

Hekstra-Lab/disco

Generate feasible Laue Bragg spots from randomly oriented crystals

Hekstra-Lab/marccd

Read, write, and manipulate diffraction images that use the MarCCD format

Hekstra-Lab/SFcalculator_jax

Hekstra-Lab/cog

Wrapper for Precognition to simplify Laue data reduction

Hekstra-Lab/dw

jupyter notebooks exploring the double-Wilson model

Hekstra-Lab/dw-examples

Examples of merging crystallographic intensities with a bivariate prior

Hekstra-Lab/fasrc-ood-jupyter

OnDemand app for serving Jupyter notebooks out of your local path

Hekstra-Lab/fast-overlap

meep meep

Hekstra-Lab/hadamuxer

Demultiplex Hadamard-encoded diffraction images.

Hekstra-Lab/hekstra-lab.github.io

Essentially a custom 404 in case anyone tries this URL

Hekstra-Lab/landfill

Machine learning tools to estimate spatiotemporally resolved background intentensities

Hekstra-Lab/regroup

Determine new space groups for analyzing pump-probe crystallography experiments

Hekstra-Lab/room-of-requirement

Useful Lab Utilities

Hekstra-Lab/russell-thesis

Jupyter notebooks that were used for data analysis and figure making for John Russell's Ph.D. Thesis.

Hekstra-Lab/SFcalculator_tf

Hekstra-Lab/spectra-baseline

Fast implementations of baseline subtraction for raman spectra

Hekstra-Lab/tape

Tasks Assessing Protein Embeddings (TAPE), a set of five biologically relevant semi-supervised learning tasks spread across different domains of protein biology.

Hekstra-Lab/yeast-mrcnn

Another implementation of mask-rcnn for detecting budding yeast cells in microscopy images