Hekstra Lab
GitHub of the Hekstra Lab. Note: Careless and Reciprocal Spaceship have migrated to https://github.com/rs-station
Harvard University
Pinned Repositories
colav
Calculate protein structural representations (dihedral angles, CA pairwise distances, and strain analysis) for downstream analysis (e.g., PCA, t-SNE, or UMAP).
east
Scripts for Finding Crystal Orientation
laue-index-assigner
A robust algorithm for assigning miller indices to Laue data from approximate indexing solutions.
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
Hekstra Lab's Repositories
Hekstra-Lab/mdtools
Tools for running MD simulations in OpenMM
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/SFcalculator
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/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/SFcalculator_torch
Differentiable pipeline connecting protein atomic models and crystallography structure factors
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/envs
conda environment repository
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/scramble
A tool for disambiguating serial laue data
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