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ORCIDJournal 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,