Python Biological-sciences Resources

Large-Scale Computing for the Social Sciences Spring 2022 - MACS 30123/MAPS 30123/PLSC 30123 Instructor Information TA Information TA Information Cour

Adversarially-Robust-Periphery Code + Data from the paper "Finding Biological Plausibility for Adversarially Robust Features via Metameric Tasks" by A

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

First steps with Python in Life Sciences This course material is part of the "First Steps with Python in Life Science" three-day course of SIB-trainin

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

BioThings SDK Quick Summary BioThings SDK provides a Python-based toolkit to build high-performance data APIs (or web services) from a single data sou

jBrain Software associated with the AAAI 2022 paper Francesco D'Amore, Daniel Mitropolsky, Pierluigi Crescenzi, Emanuele Natale, Christos H. Papadimit

SeqLike - flexible biological sequence objects in Python Introduction A single object API that makes working with biological sequences in Python more

Self-Supervised Learning (SimCLR) with Biological Plausible Image Augmentations Official code base for the poster "On the use of Cortical Magnificatio

Python-bioformats is a Python wrapper for Bio-Formats, a standalone Java library for reading and writing life sciences image file formats. Bio-Formats

Read and write TIFF files Tifffile is a Python library to store numpy arrays in TIFF (Tagged Image File Format) files, and read image and metadata fro

Knowledge Graph Embeddings and Chemical Effect Prediction, 2020. Scripts and outputs related to the paper Prediction of Adverse Biological Effects of

PyCellID (building...) Functions to analyze Cell-ID single-cell cytometry data using python language. Dependecies for this project. attrs(=21.1.0) fo

BEAR Overview This repository contains code associated with the preprint A generative nonparametric Bayesian model for whole genomes (2021), which pro

geo_calcs A Python package for caclulations and visualizations in geological sciences. Free software: MIT license Documentation: https://geo-calcs.rea

DiffuseAnimals: Reaction-Diffusion Models for the Generation of Biological Patterns Introduction Reaction-diffusion equations can be utilized in order

RBSRICNN: Raw Burst Super-Resolution through Iterative Convolutional Neural Network An official PyTorch implementation of the RBSRICNN network as desc

What is autoRICEWQ? This project aims to be a handler for input creation and running of multiple RICEWQ simulations. What is RICEWQ? From the descript

Python based Wikidata framework for easy dataframe extraction wikirepo is a Python package that provides a framework to easily source and leverage sta

U_analysis Universal data analysis tools for atmospheric sciences Script written in python 3. This file defines multiple functions that can be used fo

Neural Distance Embeddings for Biological Sequences Official implementation of Neural Distance Embeddings for Biological Sequences (NeuroSEED) in PyTo

Selene is a Python library and command line interface for training deep neural networks from biological sequence data such as genomes.

GANs for Biological Image Synthesis This codes implements the ICCV-2017 paper "GANs for Biological Image Synthesis". The paper and its supplementary m

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

CellProfiler is a free open-source software designed to enable biologists without training in computer vision or programming to quantitatively measure