Python Systems-biology-simulation Resources

KuaiRec: A Fully-observed Dataset for Recommender Systems (Density: Almost 100%) KuaiRec is a real-world dataset collected from the recommendation log

AutoTrader AutoTrader is Python-based platform intended to help in the development, optimisation and deployment of automated trading systems. From sim

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

Sionna: An Open-Source Library for Next-Generation Physical Layer Research Sionna™ is an open-source Python library for link-level simulations of digi

Viewer for MuJoCo in Python Interactive renderer to use with the official Python bindings for MuJoCo. Starting with version 2.1.2, MuJoCo comes with n

Fixing Malfunctional Objects With Learned Physical Simulation and Functional Prediction Figure 1. Teaser. Introduction This paper studies the problem

OpenCOOD OpenCOOD is an Open COOperative Detection framework for autonomous driving. It is also the official implementation of the ICRA 2022 paper OPV

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

ICON: Implicit Clothed humans Obtained from Normals Yuliang Xiu · Jinlong Yang · Dimitrios Tzionas · Michael J. Black CVPR 2022 News 🚩 [2022/04/26] H

XGI CompleX Group Interactions (XGI) is a Python package for the representation, manipulation, and study of the structure, dynamics, and functions of

PWF 2021 Física Sin Fronteras es un proyecto del Centro Internacional de Física Teórica (ICTP) en Trieste Italia. El ICTP es un centro dedicado a fome

Smooth ReLU in PyTorch Unofficial PyTorch reimplementation of the Smooth ReLU (SmeLU) activation function proposed in the paper Real World Large Scale

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

Phoenix-Drone-Simulation An OpenAI Gym environment based on PyBullet for learning to control the CrazyFlie quadrotor: Can be used for Reinforcement Le

This is the official implementation of our paper: Bowen Wen, Wenzhao Lian, Kostas Bekris, and Stefan Schaal. "CaTGrasp: Learning Category-Level Task-R

🦕 👨‍💻 nanosaur_gazebo nanosaur The smallest NVIDIA Jetson dinosaur robot, open-source, fully 3D printable, based on ROS2 & Isaac ROS. Designed & ma

solarSystemOrbitalSimulation graphical orbitational simulation of solar system planets with real values and physics implemented so you get a nice elli

PyMouseBot If you're from GT and annoyed with SGVPN idle timeouts while working on development laptop, You might find this useful. A python cli bot to

autolfads-tf2 A TensorFlow 2.0 implementation of LFADS and AutoLFADS. Installati

Shapeland Simulator Source code to accompany Defunctland's video "FASTPASS: A Complicated Legacy" Download the video at https://www.youtube.com/watch?

Conway's Game of Life The zero player Darwinism simulation game as described by Conway (demonstrates Turing Completeness). I created this script after

Diffrax Numerical differential equation solvers in JAX. Autodifferentiable and GPU-capable. Diffrax is a JAX-based library providing numerical differe

The easiest way to the neuroscience world with the shield for RaspberryPi - PIEEG (website). Open-source. Crowdsupply This project is the result of se

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.

What are the best Systems? New Perspectives on NLP Benchmarking In Machine Learning, a benchmark refers to an ensemble of datasets associated with one

UMPNet: Universal Manipulation Policy Network for Articulated Objects Zhenjia Xu, Zhanpeng He, Shuran Song Columbia University Robotics and Automation

Ontologysim: a Owlready2 library for applied production simulation Ontologysim is an open-source deep production simulation framework, with an emphasi

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

Efficient Deep Learning Systems This repository contains materials for the Efficient Deep Learning Systems course taught at the Faculty of Computer Sc

A mini-scale reproduction code of the AlphaStar program. Note: the original AlphaStar is the AI proposed by DeepMind to play StarCraft II.

Differentiable Simulation of Soft Multi-body Systems Yi-Ling Qiao, Junbang Liang, Vladlen Koltun, Ming C. Lin [Paper] [Code] Updates The C++ backend s

Recommender systems are the systems that are designed to recommend things to the user based on many different factors. The recommender system deals with a large volume of information present by filtering the most important information based on the data provided by a user and other factors that take care of the user’s preference and interest.

Devito-playbox A few of my adventures with Devito. This repository contains a few notebooks and scripts that will lead me in the road of learning this

A stack-based systems language that supports structures, functions, expressions, and user-defined operator behaviour. Currently compiles to URCL with plans to add additional formats in the future.

Welcome to AirSim AirSim is a simulator for drones, cars and more, built on Unreal Engine (we now also have an experimental Unity release). It is open

A micro-service that can be extended to help in monitoring systems. Be extensible to be incorporated in any of the systems to facilitate timely interventions.

Algorithm and Structured Programming course project for the first semester of the Internet Systems course at IFPB

LabGraph is a a Python-first framework used to build sophisticated research systems with real-time streaming, graph API, and parallelism.

Generate 3D Locomotion Data This module is intended to create 2D video trajector

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

Liquid Rocket Engine Cooling Simulation NASA CEA The implemented class calls NASA CEA via RocketCEA. INSTALL GUIDE In progress install instructions fo

Evolution Gym A large-scale benchmark for co-optimizing the design and control of soft robots. As seen in Evolution Gym: A Large-Scale Benchmark for E

Openspoor The openspoor package is intended to allow easy transformation between different geographical and topological systems commonly used in Dutch

This project uses the mosaik co-simulation framework, developed by the brilliant developers at the high-ranked Offis institue for computer science, Oldenburg, Germany, to simulate multidimensional LED matrices.

Unicorn can be used for performance analyses of highly configurable systems with causal reasoning. Users or developers can query Unicorn for a performance task.

GAN-based Matrix Factorization for Recommender Systems This repository contains the datasets' splits, the source code of the experiments and their res

On the adaptation of recurrent neural networks for system identification This repository contains the Python code to reproduce the results of the pape

Consumer Fairness in Recommender Systems: Contextualizing Definitions and Mitigations This is the repository for the paper Consumer Fairness in Recomm

Stability Audit This repository contains code used to audit the stability of personality predictions made by two algorithmic hiring systems, Humantic

Rip Raw Rip Raw is a small tool to analyse the memory of compromised Linux systems. It is similar in purpose to Bulk Extractor, but particularly focus

SSA Our implementation of Gillespie's Stochastic Simulation Algorithm (SSA) Requirements python =3.7 numpy pandas matplotlib pyyaml Command line usag

solsim is the Solana complex systems simulator. It simulates behavior of dynamical systems—DeFi protocols, DAO governance, cryptocurrencies, and more—built on the Solana blockchain

E2EDNA2 - An automated pipeline for simulation of DNA aptamers complexed with small molecules and short peptides

pyclimb A library to easily convert climbing route grades between different grading systems. In rock climbing, mountaineering, and other climbing disc

Modeling and Simulation of Satellite Servicing Manipulators Final Project for the course ENPM662: Introduction to Robot Modeling (Fall 2021). This pro

Recommendation-Systems-for-IBM-Watson-Studio-platform Project Overview In this project, I analyze the interactions that users have with articles on th

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

WATTS (Workflow and Template Toolkit for Simulation) provides a set of Python classes that can manage simulation workflows for multiple codes where information is exchanged at a coarse level.

Recommender-Systems Two types of Recommender System : Content-based Recommender System and Colaborating filtering based recommender system So the data

A collection of automation aids to connect various database systems into Lookout for Metrics

Turtlebot-NavigationStack-Fixed-Waypoints fixed waypoint(pose) navigation for turtlebot simulation. Task Details Task Permformed using Navigation Stac

pybullet_sim_panda Pybullet simulation environment for Franka Emika Panda Dependency pybullet, numpy, spatial_math_mini Simple example (please check s

GNES is Generic Neural Elastic Search, a cloud-native semantic search system based on deep neural network.

PL-LOW A high-performance deep learning model lightweight pipeline that gradually lightens deep neural networks in order to utilize high-performance d

ProjetRIPlay v2 Simulation simplifiée du fonctionnement du protocole RIP par Eric Buonocore le 18/01/2022 Sur la base de l'exercice 5 du sujet zéro du

implementation of MM1 and MMC Queue on randomly generated data and evaluate simulation results then compare with analytical results and draw a plot curve for them, simulate some integrals and compare results and run monte carlo algorithm with them

Private Recommender Systems: How Can Users Build Their Own Fair Recommender Systems without Log Data? (SDM 2022) We consider how a user of a web servi

RPi Example Code Example Python code for building RPi-controlled robotic systems These python files have been compiled / developed by the Neurobionics

Table of contents 1 Introduction 1.1 Major features 1.2 Architecture 2 Code and Installation 2.1 Code 2.2 Installation 3 Repository of DNNs in vision

Pytorch Implementation of Learning Mesh-based Simulation With Graph Networks This is the unofficial implementation of the approach described in the pa

PyElastica PyElastica is the python implementation of Elastica: an open-source project for simulating assemblies of slender, one-dimensional structure

The project aims to develop a personal-assistant for Windows & Linux-based systems. Samiksha draws its inspiration from virtual assistants like Cortana for Windows, and Siri for iOS. It has been designed to provide a user-friendly interface for carrying out a variety of tasks by employing certain well-defined commands.

StableSims is an open-source project aimed at simulating MakerDAO's Dai stablecoin system, initially used for researching optimal incentive parameters for Liquidations 2.0.

SSMLearn Data-driven Reduced Order Models for Nonlinear Dynamical Systems This package perform data-driven identification of reduced order model based

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

Aircraft design optimization made fast through modern automatic differentiation. Plug-and-play analysis tools for aerodynamics, propulsion, structures, trajectory design, and much more.

The Autonomous Driving Cookbook (Preview) NOTE: This project is developed and being maintained by Project Road Runner at Microsoft Garage. This is cur

Code For the Paper "Understanding Entropy Coding With Asymmetric Numeral Systems (ANS): a Statistician's Perspective" Author: Robert Bamler Date: 22 D

An Evaluation of Generative Adversarial Networks for Collaborative Filtering. This repository was developed by Fernando B. Pérez Maurera. Fernando is

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

Safe Control for Black-box Dynamical Systems via Neural Barrier Certificates Installation Clone the repository: git clone https://github.com/Zengyi-Qi

{ATAM} Active Transport Analytics Model Active Transport Analytics Model (“ATAM”

Free Unified Rendering in Python A software library for scientific visualization in Python. General Information • Key Features • Installation • How to

Eventify A lightweight python module for building event driven distributed systems. Installation pip install eventify Problem Developers need a easy a

Trade Engine a library for demo trading | backtest and forward test simulation Features Limit/Market orders: you can place a Limit or Market order in

Gordo Building thousands of models with timeseries data to monitor systems. Table of content About Examples Install Uninstall Developer manual How to

DSpaceDL A tool for downloading files from DSpace items. For some reason, DSpace systems have a dogshit UI, and Universities absolutely LOOOVE to use

Operating Systems Lab (ETCS-352) Experiments for Operating Systems Lab (ETCS-352) performed by me in 2021 at uni. All codes are written by me except t

iGibson: A Simulation Environment to train Robots in Large Realistic Interactive Scenes iGibson is a simulation environment providing fast visual rend

Reproducible research and reusable acyclic workflows in Python. Execute code on HPC systems as if you executed them on your machine! Motivation Would

A Python package that unifies the Google Earth Engine ecosystem. EarthEngine.jl | rgee | rgee+ | eemont GitHub: https://github.com/r-earthengine/ee_ex

What is it? Program for scientific research, which allows to simulate the phenomenon of self-focusing of different laser beams (including Gaussian, ri

PIXEL-LEVEL CRACK DETECTION FROM IMAGES OF LEVEE SYSTEMS : A COMPARATIVE STUDY G

PySDM PySDM is a package for simulating the dynamics of population of particles. It is intended to serve as a building block for simulation systems mo

msprime msprime is a population genetics simulator based on tskit. Msprime can simulate random ancestral histories for a sample of individuals (consis

Armer Driver Armer aims to provide an interface layer between the hardware drivers of a robotic arm giving the user control in several ways: Joint vel

Conway's Game of Life My PyGame implementation of Conway's Game of Life. This implementation involves treating all edges of the grid as stitched toget

SysIdentPy is a Python module for System Identification using NARMAX models built on top of numpy and is distributed under the 3-Clause BSD license. N

ehtim (eht-imaging) Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This ve