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Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
Language models (LMs) have become ubiquitous in both NLP research and in commercial product offerings. As their commercial importance has surged, the most powerful models have become closed off, gated behind proprietary interfaces, with…
Molecular structures are always depicted as 2D printed form in scientific documents like journal papers and patents. However, these 2D depictions are not machine-readable. Due to a backlog of decades and an increasing amount of these…
Motivation: SBML is the most widespread language for the definition of biochemical models. Although dozens of SBML simulators are available, there is a general lack of support to the integration of SBML models within open-standard…
Image-guided robotic interventions involve the use of medical imaging in tandem with robotics. SlicerROS2 is a software module that combines 3D Slicer and robot operating system (ROS) in pursuit of a standard integration approach for…
Keeping track of all relevant recent publications and experimental results for a research area is a challenging task. Prior work has demonstrated the efficacy of information extraction models in various scientific areas. Recently, several…
The conformation space of a 20-residue antiparallel $\beta$-sheet peptide, sampled by molecular dynamics simulations, is mapped to a network. Conformations are nodes of the network, and the transitions between them are links. The…
The applications of large language models (LLMs) are promising for biomedical and healthcare research. Despite the availability of open-source LLMs trained using a wide range of biomedical data, current research on the applications of LLMs…
Just like the scientific data they generate, simulation workflows for research should be findable, accessible, interoperable, and reusable (FAIR). However, while significant progress has been made towards FAIR data, the majority of science…
This document contains the mathematical introduction to RORPack - a Python software library for robust output tracking and disturbance rejection for linear PDE systems. The RORPack library is open-source and freely available at…
Simflowny is an open platform which automatically generates parallel code of scientific dynamical models for different simulation frameworks. Here we present major upgrades on this software to support an extended set of families of models,…
We introduce PyPulse, a Python package for imputation of biosignals in both clinical and wearable sensor settings. Missingness is commonplace in these settings and can arise from multiple causes, such as insecure sensor attachment or data…
PCMSolver is an open-source library for continuum electrostatic solvation. It can be combined with any quantum chemistry code and requires a minimal interface with the host program, greatly reducing programming effort. As input, PCMSolver…
Scientific research relies on well-structured, standardized data; however, much of it is stored in formats such as free-text lab notebooks, non-standardized spreadsheets, or data repositories. This lack of structure challenges…
Combinatorial algorithms such as those that arise in graph analysis, modeling of discrete systems, bioinformatics, and chemistry, are often hard to parallelize. The Combinatorial BLAS library implements key computational primitives for…
We present OpenML and mldata, open science platforms that provides easy access to machine learning data, software and results to encourage further study and application. They go beyond the more traditional repositories for data sets and…
ESPResSo 4.0 is an extensible simulation package for research on soft matter. This versatile molecular dynamics program was originally developed for coarse-grained simulations of charged systems Limbach et al., Comput. Phys. Commun. 174,…
The Robot Operating System (ROS) has become the de facto standard middleware in robotics, widely adopted across domains ranging from education to industrial applications. The RoboStack distribution, a conda-based packaging system for ROS,…
\texttt{Mixture-Models} is an open-source Python library for fitting Gaussian Mixture Models (GMM) and their variants, such as Parsimonious GMMs, Mixture of Factor Analyzers, MClust models, Mixture of Student's t distributions, etc. It…
The use of several open source scientific packages in the Schr\"odinger Materials Science Suite will be discussed. A typical workflow for materials discovery will be described, discussing how open source packages have been incorporated at…