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Journal of Open Source Software, Volume 6
Volume 6, Number 57, January 2021
- Andrea Arcuri
, Juan Pablo Galeotti
, Bogdan Marculescu
, Man Zhang
:
EvoMaster: A Search-Based System Test Generation Tool. 2153 - Shubhadeep Sadhukhan
, Shashwat Bhattacharya
, Mahendra K. Verma
:
fastSF: A parallel code for computing the structure functions of turbulence. 2185 - Marine Martin-Lagarde
, Christophe Cossou
, René Gastaud:
Exonoodle: Synthetic time-series spectra generator for transiting exoplanets. 2287 - Benjamin Michaud
, Mickaël Begon
:
biorbd: A C++, Python and MATLAB library to analyze and simulate the human body biomechanics. 2562 - Keith J. Roberts, Rafael dos Santos Gioria, William J. Pringle:
SeismicMesh: Triangular meshing for seismology. 2687 - Sebastian Haan
:
GeoBO: Python package for Multi-Objective Bayesian Optimisation and Joint Inversion in Geosciences. 2690 - Florian Faucher
:
hawen: time-harmonic wave modeling and inversion using hybridizable discontinuous Galerkin discretization. 2699 - Gustave Coste
, Yannick Biard
, Philippe Roux
, Arnaud Hélias
:
ELDAM: A Python software for Life Cycle Inventory data management. 2765 - Sebastian Kokott
, Iker Hurtado
, Christian Vorwerk
, Claudia Draxl
, Volker Blum
, Matthias Scheffler
:
GIMS: Graphical Interface for Materials Simulations. 2767 - Ryo Kobayashi
:
nap: A molecular dynamics package with parameter-optimization programs for classical and machine-learning potentials. 2768 - Luke Zoltan Kelley
:
kalepy: a Python package for kernel density estimation, sampling and plotting. 2784 - Henry Senyondo
, Daniel J. McGlinn
, Pranita Sharma
, David J. Harris
, Hao Ye
, Shawn D. Taylor
, Jeroen Ooms
, Francisco J. Rodríguez-Sanchez
, Karthik Ram
, Apoorva Pandey
, Harshit Bansal
, Max Pohlman, Ethan P. White
:
Rdataretriever: R Interface to the Data Retriever. 2800 - Arianna I. Krinos
, Sarah K. Hu
, Natalie R. Cohen
, Harriet Alexander
:
EUKulele: Taxonomic annotation of the unsung eukaryotic microbes. 2817 - Jens Eriksson
, Daniel Styrström, Mikael E. Sellin
:
Cellocity: A Python package for analysis of confluent cell layer dynamics. 2818 - Vincent A. Landau
, Viral B. Shah
, Ranjan Anantharaman, Kimberly R. Hall
:
Omniscape.jl: Software to compute omnidirectional landscape connectivity. 2829 - Léo Simpson, Patrick L. Combettes, Christian L. Müller
:
c-lasso - a Python package for constrained sparse and robust regression and classification. 2844 - Seb Dalgarno
:
shinyssdtools: A web application for fitting Species Sensitivity Distributions (SSDs). 2848 - Damien Marsic
:
Parent-map: analysis of parental contributions to evolved or engineered protein or DNA sequences. 2864 - Hugo Ledoux
, Filip Biljecki
, Balázs Dukai
, Kavisha Kumar, Ravi Y. Peters, Jantien E. Stoter
, Tom Commandeur:
3dfier: automatic reconstruction of 3D city models. 2866 - Gabriel Dansereau
, Timothée Poisot
:
SimpleSDMLayers.jl and GBIF.jl: A Framework for Species Distribution Modeling in Julia. 2872 - M. Hakan Satman
, Shreesh Adiga
, Guillermo Angeris
, Emre Akadal
:
LinRegOutliers: A Julia package for detecting outliers in linear regression. 2892 - John Huddleston
, James Hadfield
, Thomas R. Sibley
, Jover Lee
, Kairsten Fay
, Misja Ilcisin
, Elias Harkins
, Trevor Bedford
, Richard A. Neher
, Emma B. Hodcroft
:
Augur: a bioinformatics toolkit for phylogenetic analyses of human pathogens. 2906 - William Michael Landau
:
The targets R package: a dynamic Make-like function-oriented pipeline toolkit for reproducibility and high-performance computing. 2959
Volume 6, Number 58, February 2021
- Florian Rhiem
:
SampleDB: A sample and measurement metadata database. 2107 - Jordan Perr-Sauer
, Mike Optis
, Jason M. Fields
, Nicola Bodini
, Joseph C. y. Lee
, Austin Todd
, Eric Simley
, Robert Hammond
, Caleb Phillips, Monte Lunacek
, Travis W. Kemper, Lindy Williams, Anna Craig, Nathan Agarwal
, Shawn Sheng
, John Meissner:
OpenOA: An Open-Source Codebase For Operational Analysis of Wind Farms. 2171 - Alex Mikes, Katherine Edmonds, Robert B. Stone, Bryony DuPont:
AutoFunc: A Python package for automating and verifying functional modeling. 2362 - Praneeth Balakrishna, Gerrit Book, Wilhelm Kirchgässner
, Maximilian Schenke
, Arne Traue, Oliver Wallscheid
:
gym-electric-motor (GEM): A Python toolbox for the simulation of electric drive systems. 2498 - James W. Nightingale
, Richard G. Hayes, Matthew Griffiths
:
PyAutoFit: A Classy Probabilistic Programming Language for Model Composition and Fitting. 2550 - Eugene Huang, Adam Skoufis, Terence Denning, Jianzhong Qi
, Raymond R. Dagastine
, Rico F. Tabor
, Joseph D. Berry
:
OpenDrop: Open-source software for pendant drop tensiometry & contact angle measurements. 2604 - Michael T. Fitzgerald
, Edward Gomez
, Saeed Salimpour
, Joe Singleton
, Ridlo W. Wibowo:
"astrosource": automating optical astronomy measurement, calibration and analysis for variable stellar sources from provided photometry. 2641 - Jeffrey S. Hazboun
, Brent Shapiro-Albert
, Paul T. Baker
, Amelia M. Henkel
, Cassidy M. Wagner
, Jacob Hesse, Paul R. Brook
, Michael T. Lam
, Maura Mclaughlin
, Nathaniel Garver-Daniels
:
The Pulsar Signal Simulator: A Python package for simulating radio signal data from pulsars. 2757 - Tobias Olsson
, Morgan Ericsson
, Anna Wingkvist
:
s4rdm3x: A Tool Suite to Explore Code to Architecture Mapping Techniques. 2791 - The Pencil Code Collaboration, Axel Brandenburg
, Anders Johansen
, Philippe A. Bourdin
, Wolfgang Dobler, Wladimir Lyra
, Matthias Rheinhardt, Sven Bingert
, Nils Erland L. Haugen
, Antony Mee, Frederick Gent
, Natalia Babkovskaia, Chao-Chin Yang
, Tobias Heinemann
, Boris Dintrans, Dhrubaditya Mitra
, Simon Candelaresi
, Jörn Warnecke
, Petri J. Käpylä
, Andreas Schreiber, Piyali Chatterjee
, Maarit J. Käpylä
, Xiang-Yu Li
, Jonas Krüger
, Jørgen R. Aarnes
, Graeme R. Sarson
, Jeffrey S. Oishi
, Jennifer Schober
, Raphaël Plasson
, Christer Sandin
, Ewa Karchniwy
, Luiz Felippe S. Rodrigues
, Alexander Hubbard, Gustavo Guerrero
, Andrew Snodin, Illa R. Losada
, Johannes Pekkilä
, Chengeng Qian
:
The Pencil Code, a modular MPI code for partial differential equations and particles: multipurpose and multiuser-maintained. 2807 - Claudio Zandonella Callegher
, Giulia Bertoldo
, Enrico Toffalini
, Anna Vesely
, Angela Andreella
, Massimiliano Pastore
, Gianmarco Altoé
:
PRDA: An R package for Prospective and Retrospective Design Analysis. 2810 - Lukas Heinrich
, Matthew Feickert
, Giordon Stark
, Kyle Cranmer
:
pyhf: pure-Python implementation of HistFactory statistical models. 2823 - James W. Nightingale
, Richard G. Hayes, Ashley Kelly
, Aristeidis Amvrosiadis, Amy Etherington, Qiuhan He, Nan Li, XiaoYue Cao, Jonathan Frawley
, Shaun Cole
, Andrea Enia, Carlos S. Frenk
, David R. Harvey, Ran Li, Richard J. Massey, Mattia Negrello, Andrew Robertson
:
PyAutoLens: Open-Source Strong Gravitational Lensing. 2825 - Vahid S. Bokharaie
:
MiTfAT: A Python-based Analysis Tool for Molecular fMRI Experiments. 2827 - Brian M. de Silva
, Krithika Manohar
, Emily Clark, Bingni W. Brunton
, J. Nathan Kutz
, Steven L. Brunton
:
PySensors: A Python package for sparse sensor placement. 2828 - Robert Morgan
, Brian Nord
, Simon Birrer
, Joshua Yao-Yu Lin
, Jason Poh
:
deeplenstronomy: A dataset simulation package for strong gravitational lensing. 2854 - Jannis M. Hoch
, Sophie de Bruin
, Niko Wanders
:
CoPro: a data-driven modelling framework for conflict risk projections. 2855 - Charley Gros
, Andréanne Lemay
, Olivier Vincent
, Lucas Rouhier, Marie-Helene Bourget
, Anthime Bucquet, Joseph Paul Cohen, Julien Cohen-Adad
:
ivadomed: A Medical Imaging Deep Learning Toolbox. 2868 - Markus Jonsson
, Stefano Ghirlanda
, Johan Lind
, Vera Vinken
, Magnus Enquist:
Learning Simulator: A simulation software for animal and human learning. 2891 - Benjamin Michaud
, Mickaël Begon
:
ezc3d: An easy C3D file I/O cross-platform solution for C++, Python and MATLAB. 2911 - Adam C. Richie-Halford
, Manjari Narayan
, Noah Simon
, Jason D. Yeatman
, Ariel Rokem
:
Groupyr: Sparse Group Lasso in Python. 3024
Volume 6, Number 59, March 2021
- Lydia R. Lucchesi, Petra M. Kuhnert
, Christopher K. Wikle:
Vizumap: an R package for visualising uncertainty in spatial data. 2409 - Marina Manso Jimeno
, John Thomas Vaughan
, Sairam Geethanath
:
Off-resonance CorrecTion OPen soUrce Software (OCTOPUS). 2578 - John T. Gregg
, Trang T. Le
, Jason H. Moore
:
REGENS: an open source Python package for simulating realistic autosomal genotypes. 2743 - Kenneth Higa
, Vincent S. Battaglia
, Venkat Srinivasan
:
PyGDH: Python Grid Discretization Helper. 2744 - Pedro Rafael Diniz Marinho
:
ropenblas: Download, Compile and Link OpenBLAS Library with R. 2769 - Riley X. Brady
, Aaron Spring
:
climpred: Verification of weather and climate forecasts. 2781 - Robert Falck
, Justin S. Gray
, Kaushik Ponnapalli, Ted Wright:
dymos: A Python package for optimal control of multidisciplinary systems. 2809 - Jérôme Buisine
, Samuel Delepoulle, Christophe Renaud
:
Minimalist And Customisable Optimisation Package. 2812 - Adam Symington
:
polypy - Analysis Tools for Solid State Molecular Dynamics and Monte Carlo Trajectories. 2824 - Florian Gacon
, Christophe Godin
, Olivier Ali
:
BVPy: A FEniCS-based Python package to ease the expression and study of boundary value problems in Biology. 2831 - Timo Betcke
, Matthew W. Scroggs
:
Bempp-cl: A fast Python based just-in-time compiling boundary element library. 2879 - Kanishka Narayan
, Chris R. Vernon
, Stephanie Waldhoff
, James A. Edmonds
, Ryna Cui
:
ambrosia: An R package for calculating and analyzing food demand that is responsive to changing incomes and prices. 2890 - Balaje Kalyanaraman
, Michael H. Meylan, Bishnu P. Lamichhane, Luke G. Bennetts
:
iceFEM: A FreeFem package for wave induced ice-shelf vibrations. 2939 - Samay Garg
, Julie C. Fornaciari
, Adam Z. Weber
, Nemanja Danilovic:
fuelcell: A Python package and graphical user interface for electrochemical data analysis. 2940 - Krzysztof Dyba
, Jakub Nowosad
:
rgugik: Search and Retrieve Spatial Data from the Polish Head Office of Geodesy and Cartography in R. 2948 - Jon Schwenk
, Jayaram Hariharan
:
RivGraph: Automatic extraction and analysis of river and delta channel network topology. 2952 - Zeyuan Song, Anastasia Gurinovich, Anthony Federico, Stefano Monti, Paola Sebastiani:
nf-gwas-pipeline: A Nextflow Genome-Wide Association Study Pipeline. 2957 - Qiusheng Wu
:
lidar: A Python package for delineating nested surface depressions from digital elevation data. 2965 - Wouter G. j. van Zeist
, Héloïse F. Stevance, J. J. Eldridge:
Riroriro: Simulating gravitational waves and evaluating their detectability in Python. 2968 - Ghislain Vieilledent
:
forestatrisk: a Python package for modelling and forecasting deforestation in the tropics. 2975 - Andrew J. Quinn
, Vitor Lopes-dos-Santos, David Dupret
, Anna Christina Nobre, Mark W. Woolrich:
EMD: Empirical Mode Decomposition and Hilbert-Huang Spectral Analyses in Python. 2977 - Jacques Serizay
, Julie Ahringer:
Generating fragment density plots in R/Bioconductor with VplotR. 3009 - Andrea Bommert
, Michel Lang
:
stabm: Stability Measures for Feature Selection. 3010 - Wilmer Uruchi
, Miguel Castrillo
, Daniel Beltrán:
Autosubmit GUI: A Javascript-based Graphical User Interface to Monitor Experiments Workflow Execution. 3049 - Alessandro Cheli
:
Metatheory.jl: Fast and Elegant Algebraic Computation in Julia with Extensible Equality Saturation. 3078 - Alex M. Ganose
, Amy Searle
, Anubhav Jain
, Sinéad M. Griffin
:
IFermi: A python library for Fermi surface generation and analysis. 3089
Volume 6, Number 60, April 2021
- Paul Westermann
, Theodor Victor Christiaanse
, Will Beckett, Paul Kovacs, Ralph Evins
:
besos: Building and Energy Simulation, Optimization and Surrogate Modelling. 2677 - Derrick J. A. Chambers
, M. Shawn Boltz, Calum J. Chamberlain
:
ObsPlus: A Pandas-centric ObsPy expansion pack. 2696 - Robert J. Moss
:
POMDPStressTesting.jl: Adaptive Stress Testing for Black-Box Systems. 2749 - Gianmarco Mengaldo
, Romit Maulik:
PySPOD: A Python package for Spectral Proper Orthogonal Decomposition (SPOD). 2862 - Jost Migenda
, Susan Cartwright, Liz Kneale
, Matthew Malek, Yan-Jie Schnellbach
, Owen Stone:
sntools: An event generator for supernova burst neutrinos. 2877 - Narayanarao Bhogapurapu
, Subhadip Dey
, Dipankar Mandal
, Avik Bhattacharya
, Y. S. Rao
:
PolSAR tools: A QGIS plugin for generating SAR descriptors. 2970 - Jackson Borchardt
, Raymond Dunn
, Saul Kato
:
minimo: a linked data and metadata storage system for small labs. 2979 - Alejandra M. Martínez, Matías Salibián Barrera:
RBF: An R package to compute a robust backfitting estimator for additive models. 2992 - Marcelo Ponce
, Amit Sandhel:
covid19.analytics: An R Package to Obtain, Analyze and Visualize Data from the 2019 Coronavirus Disease Pandemic. 2995 - David Keitel
, Rodrigo Tenorio
, Gregory Ashton
, Reinhard Prix
:
PyFstat: a Python package for continuous gravitational-wave data analysis. 3000 - Johannes Buchner
:
UltraNest - a robust, general purpose Bayesian inference engine. 3001 - Oluwasegun Ayokunle Somefun
, Kayode Akingbade, Folasade Mojisola Dahunsi:
NLSIG-COVID19Lab: A modern logistic-growth tool (nlogistic-sigmoid) for descriptively modelling the dynamics of the COVID-19 pandemic process. 3002 - Michael L. Waskom:
seaborn: statistical data visualization. 3021 - Giulio Fabbian
, Julien Peloton
:
Simulating instrumental systematics of Cosmic Microwave Background experiments with s4cmb. 3022 - Robert A. Shaw
, J. Grant Hill
:
libecpint: A C++ library for the efficient evaluation of integrals over effective core potentials. 3039 - Yaron Gvili:
LibSWIFFT - A fast C/C++ Library for the SWIFFT Secure Homomorphic Hash Function. 3040 - Eike Caldeweyher
:
kallisto: A command-line interface to simplify computational modelling and the generation of atomic features. 3050 - Vikram Baliga
:
gaussplotR: Fit, Predict and Plot 2D-Gaussians in R. 3074 - Farshid Tavakolizadeh, Shreekantha Devasya:
Thing Directory: Simple and lightweight registry of IoT device metadata. 3075 - Nils Kroell
:
imea: A Python package for extracting 2D and 3D shape measurements from images. 3091 - Clemens Schmid
, Stephan Schiffels
:
bleiglas: An R package for interpolation and visualisation of spatiotemporal data with 3D tessellation. 3092 - Benjamin F. Maier
:
epipack: An infectious disease modeling package for Python. 3097 - Gabriele Bozzola
:
kuibit: Analyzing Einstein Toolkit simulations with Python. 3099 - Alan Haynes
, Armando Lenz
, Odile Stalder
, Andreas Limacher
:
presize: An R-package for precision-based sample size calculation in clinical research. 3118 - Taylor Griswold, Curtis Kapsak
, Jessica C. Chen, Henk C. den Bakker
, Grant Williams, Alyssa Kelley, Eshaw Vidyaprakash, Lee S. Katz
:
SneakerNet: A modular quality assurance and quality check workflow for primary genomic and metagenomic read data. 2334 - Gael Forget:
IndividualDisplacements.jl: a Julia package to simulate and study particle displacements within the climate system. 2813 - Antonello Lobianco
:
BetaML: The Beta Machine Learning Toolkit, a self-contained repository of Machine Learning algorithms in Julia. 2849 - Saleh Rezaeiravesh
, Ricardo Vinuesa, Philipp Schlatter:
UQit: A Python package for uncertainty quantification (UQ) in computational fluid dynamics (CFD). 2871 - Kevin Kramer
, Johan Chang
:
Visualization of Multi-Dimensional Data - The data-slicer Package. 2969 - Sam Parsons:
splithalf: robust estimates of split half reliability. 3041 - Navid C. Constantinou
, Gregory LeClaire Wagner
, Lia Siegelman
, Brodie C. Pearson
, André Palóczy
:
GeophysicalFlows.jl: Solvers for geophysical fluid dynamics problems in periodic domains on CPUs & GPUs. 3053 - Daniel Lüdecke
, Mattan S. Ben-Shachar
, Indrajeet Patil
, Philip D. Waggoner
, Dominique Makowski
:
performance: An R Package for Assessment, Comparison and Testing of Statistical Models. 3139 - Diego A. Palma
, Christian Soto, Mónica Veliz, Bruno Karelovic, Bernardo Riffo:
TRUNAJOD: A text complexity library to enhance natural language processing. 3153 - William Michael Landau
:
The stantargets R package: a workflow framework for efficient reproducible Stan-powered Bayesian data analysis pipelines. 3193
Volume 6, Number 61, May 2021
- Shannon Axelrod, Matthew Cai
, Ambrose J. Carr
, Jeremy Freeman
, Deep Ganguli, Justin T. Kiggins
, Brian Long
, Tony Tung, Kevin A. Yamauchi
:
starfish: scalable pipelines for image-based transcriptomics. 2440 - Francis Banville
, Steve Vissault
, Timothée Poisot
:
Mangal.jl and EcologicalNetworks.jl: Two complementary packages for analyzing ecological networks in Julia. 2721 - Amir Shahmoradi
, Fatemeh Bagheri:
ParaMonte: A high-performance serial/parallel Monte Carlo simulation library for C, C++, Fortran. 2741 - Steve Macenski
, Ivona Jambrecic:
SLAM Toolbox: SLAM for the dynamic world. 2783 - Nelly Barret
, Fabien Duchateau
, Franck Favetta
:
Predihood: an open-source tool for predicting neighbourhoods' information. 2805 - Vasilis N. Nikolaidis
:
The nnlib2 library and nnlib2Rcpp R package for implementing neural networks. 2876 - Sebastian Kopf
, Brett Davidheiser-Kroll
, Ilja Kocken
:
Isoreader: An R package to read stable isotope data files for reproducible research. 2878 - Andrew C. Teucher
, Sam J. Albers
, Stephanie L. Hazlitt
:
bcdata: An R package for searching & retrieving data from the B.C. Data Catalogue. 2927 - Luka Pecnik
, Iztok Fister Jr.
:
NiaAML: AutoML framework based on stochastic population-based nature-inspired algorithms. 2949 - Julia Wrobel
, Alexander Bauer
:
registr 2.0: Incomplete Curve Registration for Exponential Family Functional Data. 2964 - Banjo Obayomi, Christopher H. Todd, Lucas Cadalzo,