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activation-energy-estimation-workflow

A workflow to estimate activation free energy for a protein structure obtained from a coarse-grained simulation

alan

Alignment viewer for linux terminal

alignmentviewer

Multiple sequence alignment visualizer

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_singularity

Open source code for AlphaFold.

alphapulldown

an-introduction-to-applied-bioinformatics

Interactive lessons in bioinformatics.

ancestralseq

Python framework for doing ancestral sequence reconstruction

art-of-command-line

Master the command line, in one page

bibliography

bios1140.github.io

pop gen tutes

bokeh-notebooks

Interactive Web Plotting with Bokeh in IPython notebook

bookdown-demo

A minimal book example using bookdown

cg_simtk_protein_folding

A toolkit for building CG model of protein/ribosome and MD simulation protocols for protein co- and post-translational folding

code_snippets

computational_biology_lectures

course material

data-science-from-scratch

code for Data Science From Scratch book

deepfolding

Protein contacts prediction using deep learning models

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.

foundationsofstatisticsfordatasci

data for the book 'foundations of statistics for data scientists with R and python'

gene-cluster-search-pipeline

A pipeline for constructing a list of genome sequences that are candidates for containing a user-specified gene cluster of interest. This pipeline utilizes Python scripts, NCBI E-utilities and the NCBI Identical Protein Groups database to convert the results of BLASTp searches (proteins) to the corresponding genome sequences. This pipeline was des

genetic_ancestors

Scripts to generate simulations and plots used in blog posts on genetic and genealogical ancestry gcbias.org/category/genetic-genealogy/ . These scripts were written over a couple of afternoons and are by no means optimal ways of constructing these quantities. Hopefully they will be of use.

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.

hello-world

Just another depository

hgdp_tgp

Human genome resource and tutorials

hugo-papermod-fork

A fast, clean, responsive Hugo theme.