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ORCIDJournal of Open Source Software, Volume 8
Volume 8, Number 81, January 2023
- Tristan Konolige
:
City2BA: Tools for creating synthetic bundle adjustment problems. 3125 - Grégoire Hugues Cattan, César Mendoza:
Tagging Latency Estimator: A Standalone Software for Estimating Latency of Event-Related Potentials in P300-based Brain-Computer Interfaces. 4114 - Henrik Nicolay Topnes Finsberg, Ilsbeth Gerarda Maria van Herck, Cécile Daversin-Catty, Hermenegild Arevalo, Samuel T. Wall:
simcardems: A FEniCS-based cardiac electro-mechanics solver. 4753 - Valentin Christiaens, Carlos Alberto Gomez Gonzalez, Ralf Farkas, Carl-Henrik Dahlqvist, Evert Nasedkin, Julien Milli, Olivier Absil, Henry Ngo, Carles Cantero, Alan Rainot, Iain Hammond, Markus J. Bonse, Faustine Cantalloube, Arthur Vigan, Vijay Phanindra Srikanth Kompella, Paul J. Hancock:
VIP: A Python package for high-contrast imaging. 4774 - Lorenzo Pizzuti, Ippocratis D. Saltas, Andrea Biviano, Gary Mamon, Luca Amendola:
MG-MAMPOSSt, a Fortran code to test gravity at galaxy-cluster scales. 4800 - Szabolcs Horvát, Jakub Podkalicki, Gábor Csárdi, Tamás Nepusz, Vincent A. Traag, Fabio Zanini, Daniel Noom:
IGraph/M: graph theory and network analysis for Mathematica. 4899 - Kadeem Dennis, Michael Marxen, Kamran Siddiqui:
PIVC: A C/C++ Program for Particle Image Velocimetry Vector Computation. 3736 - James W. Nightingale, Aristeidis Amvrosiadis, Richard G. Hayes, Qiuhan He, Amy Etherington, XiaoYue Cao, Shaun Cole, Jonathan Frawley, Carlos S. Frenk, Sam Lange, Ran Li, Richard J. Massey, Mattia Negrello, Andrew Robertson:
PyAutoGalaxy: Open-Source Multiwavelength Galaxy Structure & Morphology. 4475 - Rich Townsend, Aaron Lopez:
MSG: A software package for interpolating stellar spectra in pre-calculated grids. 4602 - Joseph H. P. Jackson, Ian Harry, Coleman Krawczyk:
PyFPT: A Python package for first-passage times. 4607 - Lluís Jofre, Ahmed Abdellatif, Guillermo Oyarzun:
RHEA: an open-source Reproducible Hybrid-architecture flow solver Engineered for Academia. 4637 - Erik Poppleton, Michael Matthies, Debesh Mandal, Flavio Romano, Petr Sulc, Lorenzo Rovigatti:
oxDNA: coarse-grained simulations of nucleic acids made simple. 4693 - Ayoub Malek:
Spafe: Simplified python audio features extraction. 4739 - Ian Frederick Vigogne Goodbody Hunter:
GNOLL: Efficient Multi-Lingual Software for Real-World Dice Notation and Extensions. 4816 - Anna Jenul, Stefan Schrunner:
UBayFS: An R Package for User Guided Feature Selection. 4848 - Ryan J. MacDonald:
POSEIDON: A Multidimensional Atmospheric Retrieval Code for Exoplanet Spectra. 4873 - Martin Lackner, Peter Regner, Benjamin Krenn:
abcvoting: A Python package for approval-based multi-winner voting rules. 4880 - Stephen J. Beckett, Freyja A. Brandel-Tanis, Quan Nguyen, Aroon T. Chande, Lavanya Rishishwar, Clio Andris, Joshua S. Weitz:
localcovid19now: processing and mapping COVID-19 case data at subnational scales. 4898 - Edward Antonian, Gareth W. Peters, Michael J. Chantler:
PyKronecker: A Python Library for the Efficient Manipulation of Kronecker Products and Related Structures. 4900 - Dennis Gläser, Timo Koch, Sören Peters, Sven Marcus, Bernd Flemisch:
fieldcompare: A Python package for regression testing simulation results. 4905 - Gabriel Mariano Marcelino:
PyNGHam: A Python library of the NGHam protocol. 4915 - Christopher Popp:
BellDiagonalQudits: A package for entanglement analyses of mixed maximally entangled qudits. 4924 - Alex Golts, Moshe Raboh, Yoel Shoshan, Sagi Polaczek, Simona Rabinovici-Cohen, Efrat Hexter:
FuseMedML: a framework for accelerated discovery in machine learning based biomedicine. 4943 - Romain Fernandez, Cédric Moisy:
FijiRelax: Fast and noise-corrected estimation of MRI relaxation maps in 3D + t. 4981 - David E. Shean, J. P. Swinski, Ben Smith, Tyler Clark Sutterley, Scott Henderson, Carlos Ugarte, Eric Lidwa, Thomas Neumann:
SlideRule: Enabling rapid, scalable, open science for the NASA ICESat-2 mission and beyond. 4982 - David Schoch:
signnet: An R package for analyzing signed networks. 4987 - Niels A. Wouda, Leon Lan:
ALNS: a Python implementation of the adaptive large neighbourhood search metaheuristic. 5028 - Simon Nolte:
spiro: An R package for analyzing data from cardiopulmonary exercise testing. 5089
Volume 8, Number 82, February 2023
- Niek Beckers, Olger Siebinga, Joris Giltay, André van der Kraan:
JOAN: a framework for human-automated vehicle interaction experiments in a virtual reality driving simulator. 4250 - Tyler H. Chang, Stefan M. Wild:
ParMOO: A Python library for parallel multiobjective simulation optimization. 4468 - Beatrice Marti, Tobias Siegfried:
riversCentralAsia: An R package to support data pre- and postprocessing for hydrological modelling with RS MINERVE. 4805 - Tomasz Tarkowski:
Quilë: C++ genetic algorithms scientific library. 4902 - Hilaire Drouineau, Benjamin Planque, Christian Mullon:
RCaNmodel: An R package for Chance and Necessity modelling. 4955 - Alexander G. Squires, David O. Scanlon, Benjamin J. Morgan:
py-sc-fermi: self-consistent Fermi energies and defect concentrations from electronic structure calculations. 4962 - Ryan R. Curtin, Marcus Edel, Omar Shrit, Shubham Agrawal, Suryoday Basak, James Joseph Balamuta, Ryan Birmingham, Kartik Dutt, Dirk Eddelbuettel, Rishabh Garg, Shikhar Jaiswal, Aakash Kaushik, Sangyeon Kim, Anjishnu Mukherjee, Nanubala Gnana Sai, Nippun Sharma, Yashwant Singh Parihar, Roshan Swain, Conrad Sanderson:
mlpack 4: a fast, header-only C++ machine learning library. 5026 - Jakob Dürrwächter, Thomas Kuhn, Fabian Meyer, Andrea Beck, Claus-Dieter Munz:
PoUnce: A framework for automatized uncertainty quantification simulations on high-performance clusters. 4683 - Fatma Sevinç Kurnaz, Peter Filzmoser:
enetLTS: Robust and Sparse Methods for High Dimensional Linear, Binary, and Multinomial Regression. 4773 - Philip Sandwell, Benedict Winchester, Hamish Beath, Jenny Nelson:
CLOVER: A modelling framework for sustainable community-scale energy systems. 4799 - Olivier Chabot, Louis Brillon:
guitarsounds: A Python package to visualize harmonic sounds for musical instrument design. 4878 - Sermad Abbas, Barbara Brune, Roland Fried:
robnptests - An R package for robust two-sample location and dispersion tests. 4947 - Arne Küderle, Robert Richer, Raul C. Sîmpetru, Bjoern M. Eskofier:
tpcp: Tiny Pipelines for Complex Problems - A set of framework independent helpers for algorithms development and evaluation. 4953 - Thomas E. Riley, Devarshi Choudhury, Tuomo E. Salmi, Serena Vinciguerra, Yves Kini, Bas Dorsman, Anna L. Watts, Daniela Huppenkothen, Sebastien Guillot:
X-PSI: A Python package for neutron star X-ray pulse simulation and inference. 4977 - Thomas M. Bury:
ewstools: A Python package for early warning signals of bifurcations in time series data. 5038 - Tony M. Abou Zeidan, Mark Rempel:
GeoHexViz: A Python package for the visualizing hexagonally binned geospatial data. 5073 - Mark Heckmann, Viv Burr, Nigel King:
OpenRepGrid.ic: A software for Interpretive Clustering. 3292 - Benjamin Edward Bolling:
Computer-Aided Generation of N-shift RWS. 3431 - David McCoy, Alan E. Hubbard, Mark J. van der Laan:
CVtreeMLE: Efficient Estimation of Mixed Exposures using Data Adaptive Decision Trees and Cross-Validated Targeted Maximum Likelihood Estimation in R. 4181
Volume 8, Number 83, March 2023
- Dazhong Wu, Jian Hua, Feng Xu:
pydynpd: A Python package for dynamic panel model. 4416 - Daniel Schalk, Verena S. Hoffmann, Bernd Bischl, Ulrich Mansmann:
dsBinVal: Conducting distributed ROC analysis using DataSHIELD. 4545 - George Dan Miron, Allan M. M. Leal, S. V. Dmytrieva, Dmitrii A. Kulik:
ThermoFun: A C++/Python library for computing standard thermodynamic properties of substances and reactions across wide ranges of temperatures and pressures. 4624 - Shreyas Sunil Gaikwad, Laurent Hascoët, Sri Hari Krishna Narayanan, Liz Curry-Logan, Ralf Greve, Patrick Heimbach:
SICOPOLIS-AD v2: tangent linear and adjoint modeling framework for ice sheet modeling enabled by automatic differentiation tool Tapenade. 4679 - Skipton N. C. Woolley, Scott D. Foster:
The ppmData R-package for setting up spatial point process models. 4771 - Zequn Jia, Yantao Sun, Qiang Liu:
OPSDN: an enhanced SDN simulation framework for OPNET Modeler. 4815 - Babak Shaban, Maria Mar del Quiroga, Robert Turnbull, Edoardo Tescari, Kim-Anh Lê Cao, Heroen Verbruggen:
MetaGenePipe: An Automated, Portable Pipeline for Contig-based Functional and Taxonomic Analysis. 4851 - José Dias Neto, Guilherme P. Castelão:
lidarwind: A Python package for retrieving wind profiles from Doppler lidar observations. 4852 - Thomas Hilder, Daniele Fasano, Francesco Bollati, Jacob Vandenberg:
Wakeflow: A Python package for semi-analytic models of planetary wakes. 4863 - Félix Olart, Thibault Oudart, Olivier Bertrand, Mehdi Pierre Daou:
NIMPHS: Numerous Instruments to Manipulate and Post-process Hydraulic Simulations. 4868 - Bruno Lebon:
directChillFoam: an OpenFOAM application for direct-chill casting. 4871 - Jérémy Lerond, Aowabin Rahman, Jian Zhang, Michael Rosenberg:
Copper: a performance curve generator for building energy simulation. 4876 - Margaret Eminizer, Sam Tabrisky, Amir Sharif-Zadeh, Christopher DiMarco, Jacob M. Diamond, K. T. Ramesh, Todd C. Hufnagel, Tyrel M. McQueen, David Elbert:
OpenMSIStream: A Python package for facilitating integration of streaming data in diverse laboratory environments. 4896 - Dirk Eilander, Hélène Boisgontier, Laurène J. E. Bouaziz, Joost Buitink, Anaïs Couasnon, Brendan Dalmijn, Mark Hegnauer, Tjalling de Jong, Sibren Loos, Indra Marth, Willem van Verseveld:
HydroMT: Automated and reproducible model building and analysis. 4897 - Maximilian Denninger, Dominik Winkelbauer, Martin Sundermeyer, Wout Boerdijk, Markus Knauer, Klaus H. Strobl, Matthias Humt, Rudolph Triebel:
BlenderProc2: A Procedural Pipeline for Photorealistic Rendering. 4901 - Ajayrama Kumaraswamy, Georg Raiser, C. Giovanni Galizia:
PyView: A general purpose tool for analyzing calcium imaging data. 4936 - Hao Yin, Gianluca Cusatis:
RingsPy: A Python package for Voronoi mesh generation of cellular solids with radial growth pattern. 4945 - Emily Bourne, Yaman Güçlü, Said Hadjout, Ahmed Ratnani:
Pyccel: a Python-to-X transpiler for scientific high-performance computing. 4991 - Barnaby Dobson, Leyang Liu, Ana Mijic:
Water Systems Integrated Modelling framework, WSIMOD: A Python package for integrated modelling of water quality and quantity across the water cycle. 4996 - Maximilian Bittens, Robert L. Gates:
DistributedSparseGrids.jl: A Julia library implementing an Adaptive Sparse Grid collocation method. 5003 - Kaze W. K. Wong, Marylou Gabrié, Daniel Foreman-Mackey:
flowMC: Normalizing flow enhanced sampling package for probabilistic inference in JAX. 5021 - Luis Scoccola, Alexander Rolle:
Persistable: persistent and stable clustering. 5022 - Koen Van Daele, Tinne Cahy, Wim De Clercq, Jonas Geuens, Bram Goessens, Jonathan Piraux, Bart Saelen, Maarten Taeymans, Cedrik Vanderhaegen:
Atramhasis: An online SKOS vocabulary editor. 5040 - Iker Rivas-González, Lars Nørvang Andersen, Asger Hobolth:
PhaseTypeR: an R package for phase-type distributions in population genetics. 5054 - Mitchell Pound, Spencer Clemens, Tyler Brough, Pedram Jahangiry, Janette Goodridge:
Bruno: A Julia package for simulation, financial asset pricing and delta hedging. 5056 - Ayush Pandey, William Poole, Anandh Swaminathan, Victoria Hsiao, Richard M. Murray:
Fast and flexible simulation and parameter estimation for synthetic biology using bioscrape. 5057 - E. Theodore L. Omtzigt, James Quinlan:
Universal Numbers Library: Multi-format Variable Precision Arithmetic Library. 5072 - Jindra Lacko:
RCzechia: Spatial Objects of the Czech Republic. 5082 - Karl Otness, Donsub Rim:
adrt: approximate discrete Radon transform for Python. 5083 - Amedeo Ceglia, Felipe Verdugo, Mickaël Begon:
Biosiglive: an Open-Source Python Package for Real-time Biosignal Processing. 5091 - Claudio Moroni, Pietro Monticone:
MultilayerGraphs.jl: Multilayer Network Science in Julia. 5116 - Benjamin A. Storer, Hussein Aluie:
FlowSieve: A Coarse-Graining Utility for Geophysical Flows on the Sphere. 4277 - Nicolas Raillard, Simon Chabot, Christophe Maisondieu, David Darbynian, Gregory F. Payne, Louis Papillon:
RESOURCECODE: A Python package for statistical analysis of sea-state hindcast data. 4366 - Scott Sievert, Robert D. Nowak, Timothy T. Rogers:
Efficiently Learning Relative Similarity Embeddings with Crowdsourcing. 4517 - Linus Seelinger, Vivian Cheng-Seelinger, Andrew D. Davis, Matthew D. Parno, Anne Reinarz:
UM-Bridge: Uncertainty quantification and modeling bridge. 4748 - Connor Barnes, Luke Henke, Lorena Henke, Ivan Krukov, Owen Hildreth:
SwiftVISA: Controlling Instrumentation with a Swift-based Implementation of the VISA Communication Protocol. 4752 - Christof Obertscheider, Ewald Fauster:
RTMsim - A Julia module for filling simulations in Resin Transfer Moulding with the Finite Area Method. 4763 - Jesse D. Smith, Marcus L. Young:
APAV: An Open-Source Python Package for Mass Spectrum Analysis in Atom Probe Tomography. 4862 - Hongyang Zhou:
Vlasiator.jl: A Julia package for processing Vlasiator data. 4906 - Jessica Scheick, Wei Ji Leong, Kelsey Bisson, Anthony Arendt, Shashank Bhushan, Zachary Fair, Norland Raphael Hagen, Scott Henderson, Friedrich Knuth, Tian Li, Zheng Liu, Romina Piunno, Nitin Ravinder, Landung Setiawan, Tyler Clark Sutterley, J. P. Swinski, Anubhav:
icepyx: querying, obtaining, analyzing, and manipulating ICESat-2 datasets. 4912 - Gianluca Iori, Gianluigi Crimi, Enrico Schileo, Fulvia Taddei, Giulia Fraterrigo, Martino Pani:
Ciclope: micro Computed Tomography to Finite Elements. 4952 - Felix Nitsch, Christoph Schimeczek, Ulrich J. Frey, Benjamin Fuchs:
FAME-Io: Configuration tools for complex agent-based simulations. 4958 - J. Michael Burgess:
ronswanson: Building Table Models for 3ML. 4969 - Aashish N. Patel, Andrew R. Sedler, Jingya Huang, Chethan Pandarinath, Vikash Gilja:
High-performance neural population dynamics modeling enabled by scalable computational infrastructure. 5023 - Panagiotis Anagnostou, Sotiris K. Tasoulis, Vassilis P. Plagianakos, Dimitris K. Tasoulis:
HiPart: Hierarchical Divisive Clustering Toolbox. 5024 - Christoph Schimeczek, Kristina Nienhaus, Ulrich J. Frey, Evelyn Sperber, Seyedfarzad Sarfarazi, Felix Nitsch, Johannes Kochems, Aboubakr Achraf El Ghazi:
AMIRIS: Agent-based Market model for the Investigation of Renewable and Integrated energy Systems. 5041 - Utkarsh Sharma, Qingyuan Zhang, Jordan Dennis, Benjamin J. S. Pope:
ticktack: A Python package for carbon box modelling. 5084 - Christoph Schimeczek, Marc Deissenroth-Uhrig, Ulrich J. Frey, Benjamin Fuchs, Aboubakr Achraf El Ghazi, Manuel Wetzel, Kristina Nienhaus:
FAME-Core: An open Framework for distributed Agent-based Modelling of Energy systems. 5087 - Mohamed Masoud, Farfalla Hu, Sergey M. Plis:
Brainchop: In-browser MRI volumetric segmentation and rendering. 5098 - Song-min Yu, Zhanyi Hou:
Melodie: Agent-based Modeling in Python. 5100 - Andrew Rohskopf, C. Sievers, Nicholas Lubbers, Mary Alice Cusentnio, James Goff, Jan Janssen, Megan McCarthy, David Montes Oca de Zapiain, Svetoslav Nikolov, Khachik Sargsyan, Dionysios Sema, Ember Sikorski, Logan Williams, Aidan P. Thompson, Mitchell A. Wood:
FitSNAP: Atomistic machine learning with LAMMPS. 5118 - Yingjie Li, Veronica F. Frans, Yongze Song, Meng Cai, Yuqian Zhang, Jianguo Liu:
SDGdetector: an R-based text mining tool for quantifying efforts toward Sustainable Development Goals. 5124 - Matthew Caudill:
Openseize: A digital signal processing package for large EEG datasets in Python. 5126 - Eva Maxfield Brown, To Huynh, Nicholas Weber:
Speakerbox: Few-Shot Learning for Speaker Identification with Transformers. 5132 - Meghna Thomas, Tyler Trimble, Lina Sela:
VisWaterNet: A Python package for visualization of water distribution networks. 5139 - Trygve Magnus Ræder:
Dark-field X-ray microscopy visualization. 5177 - Orion Archer Cohen, Hugo MacDermott-Opeskin, Lauren Lee, Tingzheng Hou, Kara D. Fong, Ryan Kingsbury, Jingyang Wang, Kristin A. Persson:
SolvationAnalysis: A Python toolkit for understanding liquid solvation structure in classical molecular dynamics simulations. 5183 - Martin Bernstorff, Kenneth C. Enevoldsen, Jakob Damgaard, Andreas Danielsen, Lasse Hansen:
timeseriesflattener: A Python package for summarizing features from (medical) time series. 5197 - Romain Sacchi:
unfold: removing the barriers to sharing and reproducing prospective life-cycle assessment databases. 5198 - Fritz Lekschas:
Regl-Scatterplot: A Scalable Interactive JavaScript-based Scatter Plot Library. 5275 - Semidán Robaina-Estévez, José M. González:
Pynteny: a Python package to perform synteny-aware, profile HMM-based searches in sequence databases. 5289 - Rex Parsons, Robin D. Blythe, Adrian G. Barnett, Susanna M. Cramb, Steven M. McPhail:
predictNMB: An R package to estimate if or when a clinical prediction model is worthwhile. 5328 - Eryk J. Walczak:
PostcodesioR: An R package for UK geocoding. 5334 - David Nicholson:
Crowsetta: A Python tool to work with any format for annotating animal vocalizations and bioacoustics data. 5338
Volume 8, Number 84, April 2023
- Morten Ledum, Manuel Carrer, Samiran Sen, Xinmeng Li, Michele Cascella, Sigbjørn Løland Bore:
HylleraasMD: Massively parallel hybrid particle-field molecular dynamics in Python. 4149 - Daniel Williams, John Veitch, Maria Luisa Chiofalo, Patricia Schmidt, Rhiannon P. Udall, Avi Vajpeji, Charlie Hoy:
Asimov: A framework for coordinating parameter estimation workflows. 4170 - Jeremiah Corrado, Jake J. Harmon, Milan M. Ilic, Branislav M. Notaros:
FEM_2D: A Rust Package for 2D Finite Element Method Computations with Extensive Support for hp-refinement. 4172
Volume 8, Number 85, May 2023
- Vlad Stefan Barbu, Florian Lecocq, Corentin Lothodé, Nicolas Vergne:
smmR: A Semi-Markov R package. 4365