Related papers: MCNP-GO: A python package for assembling MCNP inpu…
This article introduces CluBear, a Python-based open-source package for interactive massive data analysis. The key feature of CluBear is that it enables users to conduct convenient and interactive statistical analysis of massive data with…
Machine learning applications, especially in the fields of me\-di\-cine and social sciences, are slowly being subjected to increasing scrutiny. Similarly to sample size planning performed in clinical and social studies, lawmakers and…
This paper introduces ROmodel, an open source Python package extending the modeling capabilities of the algebraic modeling language Pyomo to robust optimization problems. ROmodel helps practitioners transition from deterministic to robust…
The AGP format is a tab-separated table format describing how components of a genome assembly fit together. A standard submission format for genome assemblies is a fasta file giving the sequence of contigs along with an AGP file showing how…
Trajectories, sequentially measured quantities that form a path, are an important presence in many different fields, from hadronic beams in physics to electrocardiograms in medicine. Trajectory anal-ysis requires the quantification and…
Open-source scientific software is a major driver of scientific progress, yet its development and reuse remain difficult in collaborative settings. Researchers repeatedly face four recurring challenges: discovering and reproducing existing…
De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex…
Montage is a portable software toolkit for constructing custom, science-grade mosaics by composing multiple astronomical images. The mosaics constructed by Montage preserve the astrometry (position) and photometry (intensity) of the sources…
The objective of this work is to manipulate visual timelines (e.g. a video) through natural language instructions, making complex timeline editing tasks accessible to non-expert or potentially even disabled users. We call this task…
In this work, we present scikit-fingerprints, a Python package for computation of molecular fingerprints for applications in chemoinformatics. Our library offers an industry-standard scikit-learn interface, allowing intuitive usage and easy…
This document serves to complement our website which was developed with the aim of exposing the students to Gaussian Processes (GPs). GPs are non-parametric Bayesian regression models that are largely used by statisticians and geospatial…
Performance assessment is a key issue in the process of proposing new machine learning/statistical estimators. A possible method to complete such task is by using simulation studies, which can be defined as the procedure of estimating and…
We present Ringo, a system for analysis of large graphs. Graphs provide a way to represent and analyze systems of interacting objects (people, proteins, webpages) with edges between the objects denoting interactions (friendships, physical…
Motivated by easy access to complete corepresentation (corep) data of all the 1651 magnetic space groups (MSGs) in three-dimensional space, we have developed a Mathematica package MSGCorep to provide an offline database of coreps and…
The SunPy Project is a community of scientists and software developers creating an ecosystem of Python packages for solar physics. The project includes the sunpy core package as well as a set of affiliated packages. The sunpy core package…
Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is…
The last improvements in programming languages, programming models, and frameworks have focused on abstracting the users from many programming issues. Among others, recent programming frameworks include simpler syntax, automatic memory…
mmid (Multi-Modal Integration and Downstream analyses for healthcare analytics) is a Python package that offers multi-modal fusion and imputation, classification, time-to-event prediction and clustering functionalities under a single…
This paper introduces CONFIGEN, a tool that helps modularizing software. CONFIGEN allows the developer to select a set of elementary components for his software through an interactive interface. Configuration files for use by C/assembly…
Numerical stability is a crucial requirement of reliable scientific computing. However, despite the pervasiveness of Python in data science, analyzing large Python programs remains challenging due to the lack of scalable numerical analysis…