softbear

AMIDD

Introduction to Applied Mathematics and Informatics in Drug Discovery (AMIDD)

AMPL

The ATOM Modeling PipeLine (AMPL) is an open-source, modular, extensible software pipeline for building and sharing models to advance in silico drug discovery.

AutomatedStockTrading-DeepQ-Learning

Every day, millions of traders around the world are trying to make money by trading stocks. These days, physical traders are also being replaced by automated trading robots. Algorithmic trading market has experienced significant growth rate and large number of firms are using it. I have tried to build a Deep Q-learning reinforcement agent model to do automated stock trading.

Awesome_BigData_AI_DrugDiscovery

A collection of resources useful for leveraging big data and AI for drug discovery. It mainly serves as an orientation for new lab folks. It may be biased towards my lab interest.

boompow

BANANO's super official Proof of Work system (BoomPoW)

CloudCrunch

Script to run BOINC projects on jupyter notebooks

CloudRIC

testing RIC software compatibility with Jupyter

Drip-SWAI2018

deepchem

Democratizing Deep-Learning for Drug Discovery, Quantum Chemistry, Materials Science and Biology

drug-disovery-ML

Notebooks created as part of drug discovery ML research project during time as research associate at the Lewis Lab for Systems Biology and Cell Engineering

dynamo-release

Inclusive model of expression dynamics with scSLAM-seq and multiomics, vector field reconstruction and potential landscape mapping

Fiji-macro-scripts

Scripts to automate Fiji image analysis for personal use

genome-sketching

online notebooks for a review of genome sketching

Genomic-ULMFiT

ULMFiT for Genomic Sequence Data

GENTRL

Generative Tensorial Reinforcement Learning (GENTRL) model

icml18-jtnn

Junction Tree Variational Autoencoder for Molecular Graph Generation (ICML 2018)

ivado-mila-dl-school-2019

IVADO/ Mila's Summer Deep Learning School

MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

mais-202-coding-challenge-f2019

mais-bootcamp-w2019

Course content for MAIS 202 (Winter 2019) very loosely based off of Machine Learning UC Berkeley material: https://github.com/mlberkeley/Machine-Learning-Decal-Fall-2018

modelling-language-of-life

MONET

MONET : MOdularising NEtwork Toolbox - doi: https://doi.org/10.1101/611418

Nofinger-Inc

PharmaHacks 2019 Project - Reverse engineer a chemical structure with limited information

Pharmacogenomics_Prediction_Pipeline_P3

scgen-reproducibility

softbear.github.io

squidpy_notebooks

Tutorials for Squidpy

stock-analysis-engine

Backtest 1000s of minute-by-minute trading algorithms for training AI with automated pricing data from: IEX, Tradier and FinViz. Datasets and trading performance automatically published to S3 for building AI training datasets for teaching DNNs how to trade. Runs on Kubernetes and docker-compose. >150 million trading history rows generated from +5000 algorithms. Heads up: Yahoo's Finance API was disabled on 2019-01-03 https://developer.yahoo.com/yql/

The-Databases-for-Drug-Discovery

The Databases for Drug Discovery (DDD)

wstrade-api

A JavaScript WealthSimple Trade API Wrapper