Python De-novo-protein-design Resources

Predicting lncRNA–protein interactions based on graph autoencoders and collaborative training Code for our paper "Predicting lncRNA–protein interactio

Towards the D-Optimal Online Experiment Design for Recommender Selection (KDD 2021) Contact [email protected] or [email protected] for questions

Dependencies are Python 3, a recent PyTorch, numpy/scipy, tqdm, future and tensorboard. Plotting with Matplotlib. Implementation of the neural network

peptides.py Physicochemical properties and indices for amino-acid sequences. 🗺️ Overview peptides.py is a pure-Python package to compute common descr

IIRNet Direct design of biquad filter cascades with deep learning by sampling random polynomials. Usage git clone https://github.com/csteinmetz1/IIRNe

Non-destructive, node-based 2D image graphics editor written in Python, focused on simplicity, speed, elegance, and usability

PsychoPy is an open-source package for creating experiments in behavioral science. It aims to provide a single package that is: precise enoug

What is Dependency Injector? Dependency Injector is a dependency injection framework for Python. It helps implementing the dependency injection princi

PyChemia, Python Framework for Materials Discovery and Design PyChemia is an open-source Python Library for materials structural search. The purpose o

MONAI Deploy App SDK offers a framework and associated tools to design, develop and verify AI-driven applications in the healthcare imaging domain.

IIRNet Direct design of biquad filter cascades with deep learning by sampling random polynomials. Usage git clone https://github.com/csteinmetz1/IIRNe

Grokking the Object Oriented Design Interview

An addin for Autodesk Fusion 360 that lets you view your design in a Looking Glass Portrait 3D display

A graph neural network (GNN) model to predict protein-protein interactions (PPI) with no sample features

A geometric deep learning pipeline for predicting protein interface contacts.

hardware design of the 250mm drone

DeepCAD This repository provides source code for our paper: DeepCAD: A Deep Generative Network for Computer-Aided Design Models Rundi Wu, Chang Xiao,

CNN (InceptionV1) + STFT based Whale Detection Algorithm So, this repository is my PyTorch solution for the Kaggle whale-detection challenge. The obje

The first comprehensive Robustness investigation benchmark on large-scale dataset ImageNet regarding ARchitecture design and Training techniques towards diverse noises.

RGN2-Replica (WIP) To eventually become an unofficial working Pytorch implementation of RGN2, an state of the art model for MSA-less Protein Folding f

Lightning Network Fee Siphoning Attack LN-fee-siphoning is a collection of scripts to subtract BTC from Lightning Network enabled custodial services b

Lightning Network Fee Siphoning Attack LN-fee-siphoning is a collection of scripts to subtract BTC from Lightning Network enabled custodial services b

Django Material Material design for Django. Django-Material 1.7.x compatible with Django 1.11/2.0/2.1/2.2/3.0/3.1 Django-Material 1.6.x compatible wit

System Design course at HSE (2021) Wiki-страница курса Структура репозитория: slides - директория с презентациями с занятий tasks - материалы для выпо

- Este processo já foi concluído. Obrigado pelo seu interesse! Processo Seletivo para a bolsa de migração de conteúdo de Design de Software Primeirame

Decentralized Reinforcement Learning This is the code complementing the paper Decentralized Reinforcment Learning: Global Decision-Making via Local Ec

nmigen-tool command line tool for frequent nmigen tasks (generate sources, show design) Usage: generate verilog: nmigen generate verilog nmigen_librar

Python Patterns Help the project financially: Donate: https://smartlegion.github.io/donate/ Yandex Money: https://yoomoney.ru/to/4100115206129186 PayP

My Jetson Nano Baseboard This basic baseboard gives the user the foundation and the flexibility to design their own baseboard for the Jetson Nano. It

NEWLY ADDED A3G A NEW GPU/CPU ARCHITECTURE OF A3C FOR SUBSTANTIALLY ACCELERATED TRAINING!! RL A3C Pytorch NEWLY ADDED A3G!! New implementation of A3C

Using a predicted aligned error matrix corresponding to an AlphaFold2 model , returns a series of lists of residue indices, where each list corresponds to a set of residues clustering together into a pseudo-rigid domain.

keebapp-backend An app about keyboards, originating from the design of u/Sonnenschirm Setup Firstly, ensure that the environment for python is install

DockStream Description DockStream is a docking wrapper providing access to a collection of ligand embedders and docking backends. Docking execution an

-Nyokong. Drug design and development team HackBio internship is a virtual bioinformatics program that introduces students and professional to advance

JANUS: Parallel Tempered Genetic Algorithm Guided by Deep Neural Networks for Inverse Molecular Design This repository contains code for the paper: JA

DeepCAD This repository provides source code for our paper: DeepCAD: A Deep Generative Network for Computer-Aided Design Models Rundi Wu, Chang Xiao,

Triangle Multiplicative Module - Pytorch Implementation of the Triangle Multiplicative module, used in Alphafold2 as an efficient way to mix rows or c

Transparency-by-Design networks (TbD-nets) This repository contains code for replicating the experiments and visualizations from the paper Transparenc

Invariant Point Attention - Pytorch Implementation of Invariant Point Attention as a standalone module, which was used in the structure module of Alph

DiffHand This repository contains the implementation for the paper An End-to-End Differentiable Framework for Contact-Aware Robot Design (RSS 2021). I

Distance-encoding for GNN design This repository is the official PyTorch implementation of the DEGNN and DEAGNN framework reported in the paper: Dista

ProGen - (wip) Implementation and replication of ProGen, Language Modeling for Protein Generation, in Pytorch and Jax (the weights will be made easily

Here is my Senior Design Project that I implemented to graduate from Computer Engineering. It is a chatbot made in RASA and helps the user to plan their vacation in the Turkish language. In order to plan the user's vacation, it provides reservations by asking various questions for hotel, flight, or event.

A data preprocessing package for time series data. Design for machine learning and deep learning.

GLRBaseDesigner A program to design your planet for Galaxy Life Reborn game. Description Do you want to share your base design with friends? Now it's

kaggle-hpa-2021-7th-place-solution Code for 7th place solution of Human Protein Atlas - Single Cell Classification on Kaggle. A description of the met

This project is based on RIFE and aims to make RIFE more practical for users by adding various features and design new models. Because improving the PSNR index is not compatible with subjective effects, we hope this part of work and our academic research are independent of each other.

SegFormer: Simple and Efficient Design for Semantic Segmentation with Transformers Figure 1: Performance of SegFormer-B0 to SegFormer-B5. Project page

Denoising Diffusion Probabilistic Model for Proteins Implementation of Denoising Diffusion Probabilistic Model in Pytorch. It is a new approach to gen

GTA-5-Lane-detection Just a script for detecting the lanes in any car game (not just gta 5) with specific resolution and road design ( very basic and

[TensorFlow] Protein Interface Prediction using Graph Convolutional Networks Unofficial TensorFlow implementation of Protein Interface Prediction usin

ProteinLM We pretrain protein language model based on Megatron-LM framework, and then evaluate the pretrained model results on TAPE (Tasks Assessing P

QLUSTER is a relative orbit design tool for formation flying satellite missions and space rendezvous scenarios, that I wrote in Python 3 for my own research and visualisation. It is currently unfinished (95%) but the core algorithm and app works. Here's an example snippet of the GUI where four deputy satellites are orbiting a single chief in LEO.

Implementation of paper DeepTag: A General Framework for Fiducial Marker Design and Detection. Project page: https://herohuyongtao.github.io/research/

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

ProteinBERT - Pytorch (wip) Implementation of ProteinBERT in Pytorch. Original Repository Install $ pip install protein-bert-pytorch Usage import torc

ProteinBERT is a universal protein language model pretrained on ~106M proteins from the UniRef90 dataset. Through its Python API, the pretrained model can be fine-tuned on any protein-related task in a matter of minutes. Based on our experiments with a wide range of benchmarks, ProteinBERT usually achieves state-of-the-art performance. ProteinBERT is built on TenforFlow/Keras.

DeepFRI Deep functional residue identification Citing @article {Gligorijevic2019, author = {Gligorijevic, Vladimir and Renfrew, P. Douglas and Koscio

Deep Learning Visuals contains 215 unique images divided in 23 categories (some images may appear in more than one category). All the images were originally published in my book "Deep Learning with PyTorch Step-by-Step: A Beginner's Guide".

Image Crop Analysis This is a repo for the code used for reproducing our Image Crop Analysis paper as shared on our blog post. If you plan to use this

ShineOn: Illuminating Design Choices for Practical Video-based Virtual Clothing Try-on [ Paper ] [ Project Page ] This repository contains the code fo

Graph-Based Protein Design This repo contains code for Generative Models for Graph-Based Protein Design by John Ingraham, Vikas Garg, Regina Barzilay

Django Material Administration Quick start pip install django-material-admin Add material.admin and material.admin.default to your INSTALLED_APPS sett

Twins: Revisiting the Design of Spatial Attention in Vision Transformers Very recently, a variety of vision transformer architectures for dense predic

Datamol is a python library to work with molecules. It's a layer built on top of RDKit and aims to be as light as possible.

Structural basis for solubility in protein expression systems Large-scale protein production for biotechnology and biopharmaceutical applications rely

Smart Flip Clock 3D printed smart clock that puts a new twist on old technology. Making The Smart Flip Clock The first thing that must be done for thi

Datamol is a python library to work with molecules. It's a layer built on top of RDKit and aims to be as light as possible.

Tired of playing with font sizes and other matplotlib parameters every time you start a new project or write a new plotting function? Want all you plots have the same style? Use matplotlib configuration files!

The dataTap Python library is the primary interface for using dataTap's rich data management tools. Create datasets, stream annotations, and analyze model performance all with one library.

AutoOED is an optimal experiment design platform powered with automated machine learning to accelerate the discovery of optimal solutions. Our platform solves multi-objective optimization problems and automatically guides the design of experiment to be evaluated.

Script-server is a Web UI for scripts. As an administrator, you add your existing scripts into Script server and other users would be ab

Disclaimer This project is stable and being incubated for long-term support. It may contain new experimental code, for which APIs are subject to chang

CDFI (Compression-Driven-Frame-Interpolation) [Paper] (Coming soon...) | [arXiv] Tianyu Ding*, Luming Liang*, Zhihui Zhu, Ilya Zharkov IEEE Conference

yacv: Yet Another Compiler Visualizer yacv is a tool for visualizing various aspects of typical LL(1) and LR parsers. Check out demo on YouTube to see

QKeras github.com/google/qkeras QKeras 0.8 highlights: Automatic quantization using QKeras; Stochastic behavior (including stochastic rouding) is disa

PI Zero W Audio Book Motivation and requirements My dad is practically blind and at 80 years has trouble hearing and operating tiny or more complicate

Differentiable molecular simulation of proteins with a coarse-grained potential This repository contains the learned potential, simulation scripts and

MatchZoo Facilitating the design, comparison and sharing of deep text matching models. MatchZoo 是一个通用的文本匹配工具包，它旨在方便大家快速的实现、比较、以及分享最新的深度文本匹配模型。 🔥 News

MatchZoo Facilitating the design, comparison and sharing of deep text matching models. MatchZoo 是一个通用的文本匹配工具包，它旨在方便大家快速的实现、比较、以及分享最新的深度文本匹配模型。 🔥 News

A Material Design theme for MkDocs Create a branded static site from a set of Markdown files to host the documentation of your Open Source or commerci

flake8-bugbear A plugin for Flake8 finding likely bugs and design problems in your program. Contains warnings that don't belong in pyflakes and pycode

trRosetta - Pytorch (wip) Implementation of trRosetta and trDesign for Pytorch, made into a convenient package

My-QR.Art This web app lets users design their own QR codes to any domain. It can be acessed on my-qr.art. You can find some more background info abou

StockBot is a Python application for designing and testing your own daily stock trading algorithms. Installation Use the

Geometric Vector Perceptron Implementation of Geometric Vector Perceptron, a simple circuit with 3d rotation equivariance for learning over large biom

Installation | Documentation | Gitter Chat | Google Group Bowtie Introduction Bowtie is a library for writing dashboards in Python. No need to know we

Neuraxle Pipelines Code Machine Learning Pipelines - The Right Way. Neuraxle is a Machine Learning (ML) library for building machine learning pipeline

python-patterns A collection of design patterns and idioms in Python. Current Patterns Creational Patterns: Pattern Description abstract_factory use a

PyPattyrn from pypattyrn.creational.singleton import Singleton class DummyClass(object, metaclass=Singleton): # DummyClass is now a Singleton!