Python Structural-biology Resources

Molecular Docking integrated in Jupyter Notebooks Description | Citation | Installation | Examples | Limitations | License Table of content Descriptio

Drug Interaction Prediction with Tigerlily Documentation | Example Notebook | Youtube Video | Project Report Tigerlily is a TigerGraph based system de

GeoDiff: a Geometric Diffusion Model for Molecular Conformation Generation [OpenReview] [arXiv] [Code] The official implementation of GeoDiff: A Geome

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

SBINN: Systems-biology informed neural network The source code for the paper M. Daneker, Z. Zhang, G. E. Karniadakis, & L. Lu. Systems biology: Identi

Reverse engineering the dengue virus (under development 🚧 ) What is dengue? Dengue is a viral infection transmitted to humans through the bite of inf

This repository contains the code for TABS, a 3D CNN-Transformer hybrid automated brain tissue segmentation algorithm using T1w structural MRI scans. TABS relies on a Res-Unet backbone, with a Vision Transformer embedded between the encoder and decoder layers.

package tests docs license stats support This repository contains FEDOT - an open-source framework for automated modeling and machine learning (AutoML

BioPy is a collection (in-progress) of biologically-inspired algorithms written in Python. Some of the algorithms included are mor

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

A collection of graph classification methods, covering embedding, deep learning, graph kernel and factorization papers

NeoDTI NeoDTI: Neural integration of neighbor information from a heterogeneous network for discovering new drug-target interactions (Bioinformatics).

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

script-SV-genotyping These are the scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel stru

pyscreener A pythonic interface to high-throughput virtual screening software Overview This repository contains the source of pyscreener, both a libra

Documentation | External Resources | Datasets | Examples ChemicalX is a deep learning library for drug-drug interaction, polypharmacy side effect and

Full Spectrum Bioinformatics is a free online text designed to introduce key topics in Bioinformatics using the Python programming language. The text is written in interactive Jupyter Notebooks, which allow you to try out and modify example code and analyses.

An easy to use elastic 3D structural engineering finite element analysis library for Python.

CCasGNN A new framework, collaborative cascade prediction based on graph neural networks (CCasGNN) to jointly utilize the structural characteristics,

slientruss3d : Python for stable truss analysis tool Desciption slientruss3d is a python package which can solve the resistances, internal forces and

Structural Guidance for Transformer Language Models This repository accompanies the paper, Structural Guidance for Transformer Language Models, publis

structural-probes Codebase for testing whether hidden states of neural networks encode discrete structures. Based on the paper A Structural Probe for

LexPOS_ko Generating Korean Slogans with phonetic and structural repetition Generating Slogans with Linguistic Features LexPOS is a sequence-to-sequen

Welcome MICOM is a Python package for metabolic modeling of microbial communities currently developed in the Gibbons Lab at the Institute for Systems

Cellpose | A generalist algorithm for cell and nucleus segmentation. Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Cel

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

===================================== README: Inpainting based PatchMatch ===================================== @Author: Younesse ANDAM @Conta

tree-SNE t-SNE and hierarchical clustering are popular methods of exploratory data analysis, particularly in biology. Building on recent advances in s

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

Python Causal Impact Causal inference using Bayesian structural time-series models. This package aims at defining a python equivalent of the R CausalI

3DFEM Python 3D finite element code This python code allows for solving 3D structural problems using the finite element method. New features will be a

Cellpose | A generalist algorithm for cell and nucleus segmentation. Cellpose was written by Carsen Stringer and Marius Pachitariu. To learn about Cel

AlphaFold Analyser This program produces high quality visualisations of predicted structures produced by AlphaFold. These visualisations allow the use

ToeholdTools Category Status Repository Package Build Quality A library for the analysis of toehold switch riboregulators created by the iGEM team Cit

Structural Constraints on Information Content in Human Brain States Code accompanying the paper "The information content of brain states is explained

xtbreak estimating and testing for many known and unknown structural breaks in time series and panel data. For an overview of xtbreak test see xtbreak

pcnaDeep-napari A customized interface for single cell track visualisation based on pcnaDeep and napari. 👀 Under construction You can get test image

Kaggle: Cell Instance Segmentation The goal of this challenge is to detect cells in microscope images. with simple view on how many cels have been ann

Role-based network embedding via structural features reconstruction with degree-regularized constraint Train python main.py --dataset brazil-flights

Graph Neural Networks with Learnable Structural and Positional Representations Source code for the paper "Graph Neural Networks with Learnable Structu

PurNet Project for the TIP 2021 Paper "Salient Object Detection with Purificatory Mechanism and Structural Similarity Loss" Abstract Image-based salie

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

pcnaDeep: a deep-learning based single-cell cycle profiler with PCNA signal Welcome! pcnaDeep integrates cutting-edge detection techniques with tracki

MangaLineExtraction_PyTorch The (Official) PyTorch Implementation of the paper "Deep Extraction of Manga Structural Lines" Usage model_torch.py [sourc

StructDepth PyTorch implementation of our ICCV2021 paper: StructDepth: Leveraging the structural regularities for self-supervised indoor depth estimat

DIML Created by Wenliang Zhao*, Yongming Rao*, Ziyi Wang, Jiwen Lu, Jie Zhou This repository contains PyTorch implementation for paper Towards Interpr

Hello 🤟 #Team-Greider The team of 20 people for HackBio'2021 Virtual Bioinformatics Internship 💝 🖨️ 👨‍💻 HackBio: https://thehackbio.com 💬 Ask us

Attention Walk ⠀⠀ A PyTorch Implementation of Watch Your Step: Learning Node Embeddings via Graph Attention (NIPS 2018). Abstract Graph embedding meth

GAM ⠀⠀ A PyTorch implementation of Graph Classification Using Structural Attention (KDD 2018). Abstract Graph classification is a problem with practic

Visual-Reasoning-eXplanation [CVPR 2021 A Peek Into the Reasoning of Neural Networks: Interpreting with Structural Visual Concepts] Project Page | Vid

This repository contains FEDOT - an open-source framework for automated modeling and machine learning (AutoML). It can build custom modeling pipelines for different real-world processes in an automated way using an evolutionary approach. FEDOT supports classification (binary and multiclass), regression, clustering, and time series prediction tasks.

Learning Structural Edits via Incremental Tree Transformations Code for "Learning Structural Edits via Incremental Tree Transformations" (ICLR'21) 1.

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

Commonsense Knowledge Base Completion with Structural and Semantic Context Code for the paper Commonsense Knowledge Base Completion with Structural an

SLM: Structural Language Models of Code This is an official implementation of the model described in: "Structural Language Models of Code" [PDF] To ap

Awesome Pattern Matching (apm) for Python pip install awesome-pattern-matching Simple Powerful Extensible Composable Functional Python 3.7+, PyPy3.7+

Documentation: https://raamana.github.io/neuropredict/ News As of v0.6, neuropredict now supports regression applications i.e. predicting continuous t