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RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement
RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.
ProgPorts is an administrative and easy user interface to hundreds of proteomics, molecular dynamics, and protein crystallography programs. It is a hybrid of the prog/setup system, developed at Johns Hopkins University, and GNU-Darwin ports system.
Using the CUDA API this project modifies the AutoDock software to run in parallel on NVIDIA GPUs. Users will be able to download and compile the code and use AutoDock on CUDA capable Graphics Cards. Autodock is located at http://autodock.scripps.edu/
Command line molar mass calculator that provides typo checking and options for printing elemental analysis and saving a record of previously calculated molar masses.
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StochFit utilizes stochastic fitting methods to model specular x-ray reflectivity or neutron reflectivity data. It provides an easy to use graphical user interface for both model dependent and model independent methods.
Oscilib (Open Science Library) aims to be a comprehensive suite of programs that provide a simple useful way to solve common scientific and mathematical problems.
GParticles is a tool to simulate the growth behaviour of two- and three-dimensional nano particles based on a simple grid model, with adjustable (time-dependent) concentrations of the particle's different components.
4-Dimensional Cell Simulator (4DiCeS) is a framework on hybrid (stochastic and deterministic) modeling and simulation of (whole) cell environments in 4D. The framework may incorporate any reaction and diffusion algorithms applicable in a 4D grid layout.
KrakenD is a stateless, distributed, high-performance API Gateway that helps you effortlessly adopt microservices
KrakenD is a high-performance API Gateway optimized for resource efficiency, capable of managing 70,000 requests per second on a single instance. The stateless architecture allows for straightforward, linear scalability, eliminating the need for complex coordination or database maintenance.
Structlab is a machine learning C++ framework for structured domains, which provides a toolbox of learning methods and tools for preprocessing and visualization. It also provides a GUI to setup elaborate experiments in a visual and intuitive way.
This project was inspired existing cheminformatics APIs such as the CDK, Marvin, and Frowns. The goal of the project is to produce a full featured cheminfo api for the .Net framework. Early stage dev will focus on data structures and classes for file io.
LSG is a Windows application framework designed for visual data integration and based on Microsoft .NET 2.0 and CAB. An admin utility manages LSG apps, modules, events, and services, and a client integrates the modules and provides functionality hooks.
Drchem is a set of various tools useful in my scientific work (I'm a chemist) e.g. GPC calculations, bibliography managment, some of perl scripts helpful in plots/graphs processing.
The aim of the project is to provide open source collection of algorithms in the field of spectroscopy: data handling and processing, modeling and artificial intelligence tools.
TARIS (Tree Analysis and Representation of Isopotential Surfaces) is a software package designed for molecular similarity purposes in the field of Computational Chemistry. Users are allowed to compare molecules through their MEP loading .cube files.
Noemol is a graphical program for calculation of multi-spin nuclear Overhauser effects (nOes) in nuclear magnetic resonance (NMR) spectroscopy, it is a valuable tool for scientists involved in structural biology and chemistry.
ChemCpp is a C++ toolbox for chemoinformatics focusing on the computation of kernel functions between chemical compounds. Together with Support Vector Machines, these kernel functions find natural applications for virtual screening of molecules.
QMcBeaver is an object-oriented program to perform Quantum Monte Carlo calculations on atoms and molecules. It is designed to be easy to modify, allowing new ideas to be quickly implemented.
Open-source Cube Files Manipulator Program (OpenCubMan)is a tool for computational chemists interested in performing operations on files with volumetric data representing wavefunctions or electron densities (often called cube files).
PIMC++ is a code designed to perform fully-correlated simulations of quantum systems in continuous space at finite temperature using Path Integral Monte Carlo.
It is designed in a modular way to facilitate easy addition of new algorithms.
SonicData is a data collection and analysis program used in connection with a sound card voltage-to-frequency interface. Its intended use is for laboratory instrumentation.
GVIB is a user friendly package for vibrational analysis. Given a molecular geometry, it will calculate vibrational frequencies and intensities using anharmonic internuclear potential.
Mito-MAS-m is a simulator of the mitochondrial inner membrane and the enzymatic complexes embedded in it, implementing a coarse-grained (CG) model of the molecules using rigid structures and Dissipative Particules Dynamics (DPD) as motion equation.