Python Computational-biology Resources

Computational Xmas Tree This repo contains the code for the computational illumination of a Christmas Tree! It is based on the work by Matt Parker fro

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

ICLR Computational Geometry & Topology Challenge 2022 Welcome to the ICLR 2022 Computational Geometry & Topology challenge 2022 --- by the ICLR 2022 W

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

NATURAL-LANGUAGE-PROCESSING-AND-COMPUTATIONAL-LAB-II DLO8012: NLP & CSL804: CL-II [SEMESTER VIII] Syllabus NLP - Reference Books THE WALL MEGA SATISH

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

Self-Supervised Vision Transformers Learn Visual Concepts in Histopathology Self-Supervised Vision Transformers Learn Visual Concepts in Histopatholog

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.

Table of Contents The general idea How these scripts work? Loading data Needed modules and global variables Parsing the arrays in dataset Extracting a

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

WikiPron WikiPron is a command-line tool and Python API for mining multilingual pronunciation data from Wiktionary, as well as a database of pronuncia

POTHER: Patch-Voted Deep Learning-based Chest X-ray Bias Analysis for COVID-19 Detection Source code related to the article submitted to the Internati

CSPML (crystal structure prediction with machine learning-based element substitution) CSPML is a unique methodology for the crystal structure predicti

HistoKT: Cross Knowledge Transfer in Computational Pathology Exciting News! HistoKT has been accepted to ICASSP 2022. HistoKT: Cross Knowledge Transfe

A310 Computational Neuroscience - Okinawa Institute of Science and Technology, 2022 This repository contains modeling practice materials and homework

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

TensorDebugger (TDB) is a visual debugger for deep learning. It extends TensorFlow (Google's Deep Learning framework) with breakpoints + real-time visualization of the data flowing through the computational graph.

Computational Optimal Transport for Machine Learning Reading Group Over the last few years, optimal transport (OT) has quickly become a central topic

Python implementation of 3D facial mesh exaggeration using the techniques described in the paper: Computational Caricaturization of Surfaces.

A computational optimization project towards the goal of gerrymandering the results of a hypothetical election in the UK.

TIA Toolbox Computational Pathology Toolbox developed at the TIA Centre Getting Started All Users This package is for those interested in digital path

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Computational Design and Dynamics of Soft Systems · This is a repository that contains the source code for generating the lecture notes, handouts, exe

MothPruning Scientific Overview Originally inspired by biological nervous systems, deep neural networks (DNNs) are powerful computational tools for mo

PyCharge PyCharge is an open-source computational electrodynamics Python simulator that can calculate the electromagnetic fields and potentials genera

pyiron pyiron - an integrated development environment (IDE) for computational materials science. It combines several tools in a common platform: Atomi

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

The neural architecture of language: Integrative modeling converges on predictive processing Code accompanying the paper The neural architecture of la

OctaDist Octahedral distortion calculator: A tool for calculating distortion parameters in coordination complexes. https://octadist.github.io/ Registe

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

Computational Methods for Physics & Astronomy Book version at: https://restrepo.github.io/ComputationalMethods by: Sebastian Bustamante 2014/2015 Dieg

Cross-Camera Convolutional Color Constancy, ICCV 2021 (Oral) Mahmoud Afifi1,2, Jonathan T. Barron2, Chloe LeGendre2, Yun-Ta Tsai2, and Francois Bleibe

Illumination_Decomposition Code for TIP 2017 paper --- Illumination Decomposition for Photograph with Multiple Light Sources. This code implements the

Computational modelling of ray propagation through optical elements using the principles of geometric optics (Ray Tracer) Introduction By applying the

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.

Flow Flow is a computational framework for deep RL and control experiments for traffic microsimulation. See our website for more information on the ap

How to apply? Create your config.ini file following the example provided in config.ini Choose one of the options below to run: Run with Python3 pip in

MDAnalysis Repository README [*] MDAnalysis is a Python library for the analysis of computer simulations of many-body systems at the molecular scale,

Machine Learning for Argument-Based Computational Persuasion This repo contains the source code and a benchmark for predicting user's utilities with M

A toolkit for computational pathology and machine learning. View documentation Please cite our paper Installation There are several ways to install Pa

LitMatter A template for rapid experimentation and scaling deep learning models on molecular and crystal graphs. How to use Clone this repository and

H2G-Net This repository contains the code relevant for the proposed design H2G-Net, which was introduced in the manuscript "Hybrid guiding: A multi-re

Few-shot Deep HDR Deghosting This repository contains code and pretrained models for our paper: Self-Gated Memory Recurrent Network for Efficient Scal

"Dataflow variables are spectacularly expressive in concurrent programming" Henri E. Bal , Jennifer G. Steiner , Andrew S. Tanenbaum Quick overview Ne

pyradiomics v3.0.1 Build Status Linux macOS Windows Radiomics feature extraction in Python This is an open-source python package for the extraction of

giotto-tda is a high-performance topological machine learning toolbox in Python built on top of scikit-learn and is distributed under the G

Factorisation-based Image Labelling Overview This is a scheme for training and applying the factorisation-based image labelling (FIL) framework. Some

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

BookNLP BookNLP is a natural language processing pipeline that scales to books and other long documents (in English), including: Part-of-speech taggin

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

Exposure: A White-Box Photo Post-Processing Framework ACM Transactions on Graphics (presented at SIGGRAPH 2018) Yuanming Hu1,2, Hao He1,2, Chenxi Xu1,

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

NoCodeSeg: Deep segmentation made easy! This is the official repository for the manuscript "Code-free development and deployment of deep segmentation

StackNet This repository contains StackNet Meta modelling methodology (and software) which is part of my work as a PhD Student in the computer science

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

Rotapy Purpose Generate Gaussian 09 input files for the rotamers of an input compound. Distance to the axis of rotation remains constant throughout th

freud Overview The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics

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

POS-Tagger This repository details the creation of a Part-of-Speech tagger using Trigram Hidden Markov Models to predict word tags in a word sequence.

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

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

Documentation redrawing Python package provinding tools for artistic interactive applications using AI Created by ReDrawing Campinas team for the Open

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

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

DQC: Differentiable Quantum Chemistry Differentiable quantum chemistry package. Currently only support differentiable density functional theory (DFT)

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

feature-set-comp Compares various time-series feature sets on computational performance, within-set structure, and between-set relationships. Reposito

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

pyHype: Computational Fluid Dynamics in Python pyHype is a Python framework for developing parallelized Computational Fluid Dynamics software to solve

MaD GUI Machine Learning and Data Analytics Graphical User Interface MaD GUI is a basis for graphical annotation and computational analysis of time se

MUSCO - Multimodal Descriptions of Social Concepts Automatic Modeling of (Highly Abstract) Social Concepts evoked by Art Images This project aims to i

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

CS 506 - Computational Tools for Data Science Code, slides, and notes for Boston University CS506 Fall 2021 The Final Project Repository can be found

bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo

nlcc Install pip install nlcc Must have Open-AI Codex key: export OPENAI_API_KEY=your key here then nlcc key bindings ctrl-w copy to clipboard (Note

MolEncoder Molecular AutoEncoder in PyTorch Install $ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder $ python setup.py insta

Contrastive Learning of Object Representations Supervisor: Prof. Dr. Gemma Roig Institutions: Goethe University CVAI - Computational Vision & Artifici

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

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

JittorVis - Visual understanding of deep learning model.

House-GAN++ Code and instructions for our paper: House-GAN++: Generative Adversarial Layout Refinement Network towards Intelligent Computational Agent

PICCL: Philosophical Integrator of Computational and Corpus Libraries PICCL offers a workflow for corpus building and builds on a variety of tools. Th

ReproZip ReproZip is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used comm

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

cochlea cochlea is a collection of inner ear models. All models are easily accessible as Python functions. They take sound signal as input and return

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

Colibri Core by Maarten van Gompel, [email protected], Radboud University Nijmegen Licensed under GPLv3 (See http://www.gnu.org/licenses/gpl-3.0.html

Ucto for Python This is a Python binding to the tokeniser Ucto. Tokenisation is one of the first step in almost any Natural Language Processing task,