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CMPyMOL

CMPyMOL is an add-on software to molecular visualization program PyMOL. It combines the protein 3D visualization capabilities of PyMOL and the protein's 2D contact map with an interactive interface for scientific analysis. This software is freely distributed under the MIT license for Windows, Linux and Mac OS X platforms.

DEEPN

A Bioinformatics software workflow to process data generated by Illumina next-gen sequencing technique.

gromacs-gamd

Gaussian Accelerated Molecular Dynamics Implementation in Gromacs

GridMAT-MD-parallel

A parallel algorithm to calculate area per lipid headgroup (APL) and bilayer thickness in molecular simulations of lipid bilayers. Originally developed by Bevan Lab at Virginia Tech

Gyration_tensor

This PyMOL plugin calculates and visualizes the gyration tensors for each chain of a given protein. (based on geometry)

kaggle-rsna2018

Team ChallengePneumo Solution for RSNA Pneumonia Detection Challenge

MAPster

A front-end GUI to map NGS DNA sequencing data using HISAT backend tool. This software offers robust seamless queueing of the mapping operations along with parameter memory for quick and easy customization.

DeepCount

Deep Neural Network trained to count single-molecule photobleaching steps.

deepncli

Interlink

A tool to identify intra-protein crosslinks using non-canonical amino acids and mass spectroscopy

MALTA

A Calculator for Easy Estimation of Coverage with shRNA, CRISPR, and cDNA libraries

Autoclick

A tool for repeated automatic clicking of screen locations.

Awesome-CGM

List of CGM datasets

blastquery

Codon_optimization

Methodology to optimize codons for efficient expression in a non-native expression system

DeepGene

Experiments with gene sequences and neural networks

Fytt

Fit fluorescence spectra by linear combination of its components

Glimpse

Gelles Labrotory microscopy program

Lambda2

Control Software in LabVIEW to operate Lambda2 single-molecule TIRF microscope at Dr. Janice Robertson's laboratory in University of Iowa

Photobleaching-Step-Detection

Matlab script to autodetect photobleaching steps from single-molecule trajectories

PyInterlink

A tool to identify intra-protein crosslinks using non-canonical amino acids and mass spectroscopy

R-FCN.pytorch

A Pytorch Implementation of R-FCN/CoupleNet

Rasbase

Ras-GTPase Interactome Database

stable-baselines

A fork of OpenAI Baselines, implementations of reinforcement learning algorithms

statmaker

Dynamic enrichment for evaluation of protein networks

Stop-Codon-Identification

Testing

uwsgi-nginx-docker

Docker image with uWSGI and Nginx for applications in Python (as Flask) in a single container. Optionally with Alpine Linux.

yadsa

Yet Another Data Structure and Algorithms library