相关论文: MOLS 2.0: Software Package for Peptide Modelling a…
The field of structural bioinformatics has seen significant advances with the use of Molecular Dynamics (MD) simulations of biological systems. The MD methodology has allowed to explain and discover molecular mechanisms in a wide range of…
We introduce Repro, an open-source library which aims at improving the reproducibility and usability of research code. The library provides a lightweight Python API for running software released by researchers within Docker containers which…
Testing and debugging have become major obstacles for robot software development, because of high system complexity and dynamic environments. Standard, middleware-based data recording does not provide sufficient information on internal…
Low-code platforms (latest reincarnation of the long tradition of model-driven engineering approaches) have the potential of saving us countless hours of repetitive boilerplate coding tasks. However, as software systems grow in complexity,…
A reliable and user-friendly characterisation of nano-objects in a target material is presented here in the form of a software data analysis package for interpreting small-angle X-ray scattering (SAXS) patterns. When provided with data on…
We present "DistML.js", a library designed for training and inference of machine learning models within web browsers. Not only does DistML.js facilitate model training on local devices, but it also supports distributed learning through…
Model merging allows combining the capabilities of existing models into a new one - post hoc, without additional training. This has made it increasingly popular thanks to its low cost and the availability of libraries that support merging…
Protein-peptide interactions play a key role in cell functions. Their structural characterization, though challenging, is important for the discovery of new drugs. The CABS-dock web server provides an interface for modeling protein-peptide…
In this chapter we first outline some of the popular computing environments used for analysing neural data, followed by a brief discussion of 'software carpentry', basic tools and skills from software engineering that can be of great use to…
The Minimal Supersymmetric Standard Model is presented as a model for the CompHEP software package as a set of files containing the complete Lagrangian of the MSSM, particle contents and parameters. All resources of CompHEP with a…
TBPLaS is an open-source software package for the accurate simulation of physical systems with arbitrary geometry and dimensionality utilizing the tight-binding (TB) theory. It has an intuitive object-oriented Python application interface…
The Rosetta molecular modeling software package provides experimentally tested and rapidly evolving tools for the 3D structure prediction and high-resolution design of proteins, nucleic acids, and a growing number of non-natural polymers.…
Optunity is a free software package dedicated to hyperparameter optimization. It contains various types of solvers, ranging from undirected methods to direct search, particle swarm and evolutionary optimization. The design focuses on ease…
Mixed Integer Linear Programming (MILP) is a fundamental tool for modeling combinatorial optimization problems. Recently, a growing body of research has used machine learning to accelerate MILP solving. Despite the increasing popularity of…
Rules offer an invaluable combination of predictive and descriptive capabilities. Our package for rule-based data analysis, RuleKit, has proven its effectiveness in classification, regression, and survival problems. Here we present its…
This paper proposes a software repository model together with associated tooling and consists of several complex, open-source GUI driven applications ready to be used in empirical software research. We start by providing the rationale for…
MALDIquant and associated R packages provide a versatile and completely free open-source platform for analyzing 2D mass spectrometry data as generated for instance by MALDI and SELDI instruments. We first describe the various methods and…
Summary: In anticipation of the individualized proteomics era and the need to integrate knowledge from disease studies, we have augmented our peptide identification software RAId DbS to take into account annotated single amino acid…
"PyTorch, Explain!" is a Python module integrating a variety of state-of-the-art approaches to provide logic explanations from neural networks. This package focuses on bringing these methods to non-specialists. It has minimal dependencies…
Background and Objective: Computational ultrasound imaging has become a well-established methodology in the ultrasound community. Simulations of ultrasound sequences and images allow the study of innovative techniques in terms of emission…