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Similarity search is one of the most fundamental computations that are regularly performed on ever-increasing protein datasets. Scalability is of paramount importance for uncovering novel phenomena that occur at very large scales. We…
We present the ALPS (Algorithms and Libraries for Physics Simulations) project, an international open source software project to develop libraries and application programs for the simulation of strongly correlated quantum lattice models…
The ESP32-CAM is one of the most widely adopted open-source modules for prototyping embedded vision applications. Since its release in 2019, it has gained popularity among both hobbyists and professional developers due to its affordability,…
Expectation maximisation (EM) is an unsupervised learning method for estimating the parameters of a finite mixture distribution. It works by introducing "hidden" or "latent" variables via Baum's auxiliary function $Q$ that allow the joint…
The search for symbolic regression models with genetic programming (GP) has a tendency of revisiting expressions in their original or equivalent forms. Repeatedly evaluating equivalent expressions is inefficient, as it does not immediately…
Even though numerous researchers require stable datasets along with source code and basic metrics calculated on them, neither GitHub nor any other code hosting platform provides such a resource. Consequently, each researcher must download…
Low-temperature plasmas are essential to both fundamental scientific research and critical industrial applications. As in many areas of science, numerical simulations have become a vital tool for uncovering new physical phenomena and…
We present SpM, a sparse modeling tool for the analytic continuation of imaginary-time Green's function, licensed under GNU General Public License version 3. In quantum Monte Carlo simulation, dynamic physical quantities such as…
LibRPA is a software package designed for efficient calculations of random phase approximation (RPA) electron correlation energies from first principles using numerical atomic orbital (NAOs). Leveraging a localized resolution of identity…
Low-temperature X-ray photoemission electron microscopy (X-PEEM) is used to measure the electric potential at domain walls in improper ferroelectric Er0.99Ca0.01MnO3. By combining X-PEEM with scanning probe microscopy and theory, we develop…
JBotSim is a java library that offers basic primitives for prototyping, running, and visualizing distributed algorithms in dynamic networks. With JBotSim, one can implement an idea in minutes and interact with it ({\it e.g. }, add, move, or…
SOFTSUSY is a program which accurately calculates the spectrum of superparticles in the CP-conserving Minimal Supersymmetric Standard Model (MSSM), with a full flavour mixing structure. The program solves the renormalisation group equations…
Molecular surface representations have been advertised as a great tool to study protein structure and functions, including protein-ligand binding affinity modeling. However, the conventional surface-area-based methods fail to deliver a…
Solving the electronic structure from a generalized or standard eigenproblem is often the bottleneck in large scale calculations based on Kohn-Sham density-functional theory. This problem must be addressed by essentially all current…
MuSim is a new user-friendly program designed to interface to many different particle simulation codes, regardless of their data formats or geometry descriptions. It presents the user with a compelling graphical user interface that includes…
Identifying similar protein sequences is a core step in many computational biology pipelines such as detection of homologous protein sequences, generation of similarity protein graphs for downstream analysis, functional annotation and gene…
Far-UV circular dichroism (CD) spectroscopy provides a rapid, sensitive, nondestructive tool to analyze protein conformation by monitoring secondary structure composition. Originally intended for educational purposes, a spreadsheet-based…
Enhancing cryogenic electron microscopy (cryo-EM) 3D density maps at intermediate resolution (4-8 {\AA}) is crucial in protein structure determination. Recent advances in deep learning have led to the development of automated approaches for…
ZV-Sim is an open-source, modular Python framework for probabilistic simulation and analysis of pre-emergent novel zoonotic diseases using pervasive sensing data. It incorporates customizable Human and Animal Presence agents that leverage…
Background and Objective: Data from electro-anatomical mapping (EAM) systems are playing an increasingly important role in computational modeling studies for the patient-specific calibration of digital twin models. However, data exported…