James Lingford's repositories
alphafill
AlphaFill is an algorithm based on sequence and structure similarity that “transplants” missing compounds to the AlphaFold models. By adding the molecular context to the protein structures, the models can be more easily appreciated in terms of function and structure integrity.
alphafold
Open source code for AlphaFold.
ancestralSeq
Python framework for doing ancestral sequence reconstruction
art-of-command-line
Master the command line, in one page
bokeh-notebooks
Interactive Web Plotting with Bokeh in IPython notebook
cg_simtk_protein_folding
A toolkit for building CG model of protein/ribosome and MD simulation protocols for protein co- and post-translational folding
computational_biology_lectures
course material
data-science-from-scratch
code for Data Science From Scratch book
dotfiles
My dot files and config settings
esm
Evolutionary Scale Modeling (esm): Pretrained language models for proteins
foldseek
Foldseek enables fast and sensitive comparisons of large structure sets.
graphein
Protein Graph Library
handson-ml2
A series of Jupyter notebooks that walk you through the fundamentals of Machine Learning and Deep Learning in Python using Scikit-Learn, Keras and TensorFlow 2.
hgdp_tgp
Human genome resource and tutorials
localcolabfold
ColabFold on your local PC
manim
Animation engine for explanatory math videos
MelBioInf_tutorials
Melbourne Bioinformatics documentation in markdown format
MolecularNodes
Toolbox for molecular animations in Blender & Geometry Nodes.
openfold
Trainable, memory-efficient, and GPU-friendly PyTorch reproduction of AlphaFold 2
openVectorEditor
Teselagen's Open Source Vector/Plasmid Editor Component
pandas_exercises
Practice your pandas skills!
pydata-book
Materials and IPython notebooks for "Python for Data Analysis" by Wes McKinney, published by O'Reilly Media
python-basics
📚 Playground and cheatsheet for learning Python. Collection of Python scripts that are split by topics and contain code examples with explanations.
Python-programming-exercises
100+ Python challenging programming exercises
python-tutorials
Python tutorials
PythonDataScienceHandbook
Python Data Science Handbook: full text in Jupyter Notebooks
RFdiffusion
Code for running RFdiffusion
rifdock
Rifdock Library for Conformational Search
tiny_python_projects
Code for Tiny Python Projects (Manning, 2020, ISBN 1617297518). Learning Python through test-driven development of games and puzzles.