Open source ≈ Open source
View article: The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package<sup>*</sup>
The Astropy Project: Building an Open-science Project and Status of the v2.0 Core Package<sup>*</sup> Open
The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package…
View article
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses Open
PartitionFinder 2 is a program for automatically selecting best-fit partitioning schemes and models of evolution for phylogenetic analyses. PartitionFinder 2 is substantially faster and more efficient than version 1, and incorporates many …
View article
MolProbity: More and better reference data for improved all‐atom structure validation Open
This paper describes the current update on macromolecular model validation services that are provided at the MolProbity website, emphasizing changes and additions since the previous review in 2010. There have been many infrastructure impro…
View article
Juicer Provides a One-Click System for Analyzing Loop-Resolution Hi-C Experiments Open
Hi-C experiments explore the 3D structure of the genome, generating terabases of data to create high-resolution contact maps. Here, we introduce Juicer, an open-source tool for analyzing terabase-scale Hi-C datasets. Juicer allows users wi…
View article
The Astropy Project: Sustaining and Growing a Community-oriented Open-source Project and the Latest Major Release (v5.0) of the Core Package Open
The Astropy Project supports and fosters the development of open-source and openly developed Python packages that provide commonly needed functionality to the astronomical community. A key element of the Astropy Project is the core package…
View article
<span>BORIS</span>: a free, versatile open‐source event‐logging software for video/audio coding and live observations Open
Summary Quantitative aspects of the study of animal and human behaviour are increasingly relevant to test hypotheses and find empirical support for them. At the same time, photo and video cameras can store a large number of video recording…
View article
Opening the black box: an open‐source release of Maxent Open
This software note announces a new open‐source release of the Maxent software for modeling species distributions from occurrence records and environmental data, and describes a new R package for fitting such models. The new release (ver. 3…
View article
oTree—An open-source platform for laboratory, online, and field experiments Open
National audience
View article
OpenFace: An open source facial behavior analysis toolkit Open
Over the past few years, there has been an increased interest in automatic facial behavior analysis and understanding. We present OpenFace - an open source tool intended for computer vision and machine learning researchers, affective compu…
View article
AmberTools Open
AmberTools is a free and open-source collection of programs used to set up, run, and analyze molecular simulations. The newer features contained within AmberTools23 are briefly described in this Application note.
View article
Qiskit: An Open-source Framework for Quantum Computing Open
Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms. https://qiskit.org
View article
SALib: An open-source Python library for Sensitivity Analysis Open
SALib contains Python implementations of commonly used global sensitivity analysis methods, including Sobol (Sobol’ 2001, Andrea Saltelli (2002), Andrea Saltelli et al. (2010)), Morris (Morris 1991 ...
View article
ELATE: an open-source online application for analysis and visualization of elastic tensors Open
We report on the implementation of a tool for the analysis of second-order elastic stiffness tensors, provided with both an open-source Python module and a standalone online application allowing the visualization of anisotropic mechanical …
View article
<span>Psi4</span> 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and Interoperability Open
Psi4 is an ab initio electronic structure program providing methods such as Hartree-Fock, density functional theory, configuration interaction, and coupled-cluster theory. The 1.1 release represents a major update meant to automate complex…
View article
CaImAn an open source tool for scalable calcium imaging data analysis Open
Advances in fluorescence microscopy enable monitoring larger brain areas in-vivo with finer time resolution. The resulting data rates require reproducible analysis pipelines that are reliable, fully automated, and scalable to datasets gene…
View article
RTAB‐Map as an open‐source lidar and visual simultaneous localization and mapping library for large‐scale and long‐term online operation Open
Distributed as an open‐source library since 2013, real‐time appearance‐based mapping (RTAB‐Map) started as an appearance‐based loop closure detection approach with memory management to deal with large‐scale and long‐term online operation. …
View article
ipyrad: Interactive assembly and analysis of RADseq datasets Open
Summary ipyrad is a free and open source tool for assembling and analyzing restriction site-associated DNA sequence datasets using de novo and/or reference-based approaches. It is designed to be massively scalable to hundreds of taxa and t…
View article
D-GENIES: dot plot large genomes in an interactive, efficient and simple way Open
Dot plots are widely used to quickly compare sequence sets. They provide a synthetic similarity overview, highlighting repetitions, breaks and inversions. Different tools have been developed to easily generated genomic alignment dot plots,…
View article
QuPath: Open source software for digital pathology image analysis Open
QuPath is new bioimage analysis software designed to meet the growing need for a user-friendly, extensible, open-source solution for digital pathology and whole slide image analysis. In addition to offering a comprehensive panel of tumor i…
View article
BioContainers: an open-source and community-driven framework for software standardization Open
Motivation BioContainers (biocontainers.pro) is an open-source and community-driven framework which provides platform independent executable environments for bioinformatics software. BioContainers allows labs of all sizes to easily install…
View article
How open science helps researchers succeed Open
Open access, open data, open source and other open scholarship practices are growing in popularity and necessity. However, widespread adoption of these practices has not yet been achieved. One reason is that researchers are uncertain about…
View article
decoupleR: ensemble of computational methods to infer biological activities from omics data Open
Summary Many methods allow us to extract biological activities from omics data using information from prior knowledge resources, reducing the dimensionality for increased statistical power and better interpretability. Here, we present deco…
View article
Integrating Hi-C links with assembly graphs for chromosome-scale assembly Open
Long-read sequencing and novel long-range assays have revolutionized de novo genome assembly by automating the reconstruction of reference-quality genomes. In particular, Hi-C sequencing is becoming an economical method for generating chro…
View article
tidyLPA: An R Package to Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software Open
Rosenberg et al., (2018). tidyLPA: An R Package to Easily Carry Out Latent Profile Analysis (LPA) Using Open-Source or Commercial Software. Journal of Open Source Software, 3(30), 978, https://doi.org/10.21105/joss.00978
View article
A Comparative Analysis of Object Detection Metrics with a Companion Open-Source Toolkit Open
Recent outstanding results of supervised object detection in competitions and challenges are often associated with specific metrics and datasets. The evaluation of such methods applied in different contexts have increased the demand for an…
View article
Open Ephys: an open-source, plugin-based platform for multichannel electrophysiology Open
The Open Ephys GUI is the first widely used application for multichannel electrophysiology that leverages a plugin-based workflow. We hope that it will lower the barrier to entry for electrophysiologists who wish to incorporate real-time f…
View article
Bibliometric Analysis using Bibliometrix an R Package Open
This study aims to explore the usage of Open-source software in bibliometric analysis. Biblio-metrix an R package for bibliometric and co-citation analysis was used to achieve the research activities. R is an ecosystem software meaning all…
View article
<i>ggtranscript</i> : an R package for the visualization and interpretation of transcript isoforms using <i>ggplot2</i> Open
Motivation The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily ident…
View article
COCONUT online: Collection of Open Natural Products database Open
Natural products (NPs) are small molecules produced by living organisms with potential applications in pharmacology and other industries as many of them are bioactive. This potential raised great interest in NP research around the world an…
View article
OpenMDAO: an open-source framework for multidisciplinary design, analysis, and optimization Open
Multidisciplinary design optimization (MDO) is concerned with solving design problems involving coupled numerical models of complex engineering systems. While various MDO software frameworks exist, none of them take full advantage of state…