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ORCIDJournal of Open Source Software, Volume 7
Volume 7, Number 69, January 2022
- Eike Steinig
, Lachlan J. M. Coin:
Nanoq: ultra-fast quality control for nanopore reads. 2991 - Jack L. B. Line:
'WODEN': A CUDA-enabled package to simulate low-frequency radio interferometric data. 3676 - Stephanie Frank Singer, Eric M. Tsai:
electiondata: a Python package for consolidating, checking, analyzing, visualizing and exporting election results. 3739 - Thejasvi Beleyur:
"beamshapes": a Python package to generate directivity patterns for various sound source models. 3740 - Benoît Pasquier, François W. Primeau, Seth G. John:
AIBECS.jl: A tool for exploring global marine biogeochemical cycles. 3814 - Nicolas Legrand, Micah Allen:
Systole: A python package for cardiac signal synchrony and analysis. 3832 - Sebastian M. Stammler, Tilman Birnstiel:
Simframe: A Python Framework for Scientific Simulations. 3882 - Nima S. Hejazi, Kara E. Rudolph, Iván Díaz:
'medoutcon': Nonparametric efficient causal mediation analysis with machine learning in 'R'. 3979 - Pascal T. Merz, Wei-Tse Hsu, Matt W. Thompson, Simon Boothroyd, Chris C. Walker, Michael R. Shirts:
physical_validation: A Python package to assess the physical validity of molecular simulation results. 3981 - Thomas Weiß, Tonio Fincke:
SenSARP: A pipeline to pre-process Sentinel-1 SLC data by using ESA SNAP Sentinel-1 Toolbox. 3337 - Tomaz Bregar, Ahmed Mahmoudi, Miha Kodric, Domen Ocepek, Francesco Trainotti, Miha Pogacar, Mert Göldeli, Gregor Cepon, Miha Boltezar, Daniel Rixen:
pyFBS: A Python package for Frequency Based Substructuring. 3399 - William Savran, Maximilian Werner, Danijel Schorlemmer, Philip Maechling:
pyCSEP: A Python Toolkit For Earthquake Forecast Developers. 3658 - Ajay Khanna, David E. Larson, Srivatsan Sridhar, Matthew Mosior, Travis E. Abbott, Susanna Kiwala, Timothy J. Ley, Eric J. Duncavage, Matthew J. Walter, Jason R. Walker, Obi L. Griffith, Malachi Griffith, Christopher A. Miller:
Bam-readcount - rapid generation of basepair-resolution sequence metrics. 3722 - Thibault Roch, Fabian Barras, Philippe H. Geubelle, Jean-François Molinari:
cRacklet: a spectral boundary integral method library for interfacial rupture simulation. 3724 - B. Lungsi Sharma:
diman: A Clojure Package for Dimensional Analysis. 3735 - Jason J. Gellis, Camila Rangel Smith, Robert A. Foley:
PyLithics: A Python package for stone tool analysis. 3738 - Jon Sampedro, Zarrar Khan, Chris R. Vernon, Steven J. Smith, Stephanie Waldhoff, Rita Van Dingenen:
rfasst: An R tool to estimate air pollution impacts on health and agriculture. 3820 - Team Compas, Jeff Riley, Poojan Agrawal, Jim W. Barrett, Kristian Boyett, Floor Broekgaarden, Debatri Chattopadhyay, Sebastian M. Gaebel, Fabian Gittins, Ryosuke Hirai, George Howitt, Stephen Justham, Lokesh Khandelwal, Floris Kummer, Mike Lau, Ilya Mandel, Selma de Mink, Coenraad J. Neijssel, Tim Riley, Lieke van Son, Simon Stevenson, Alejandro Vigna-Gómez, Serena Vinciguerra, Tom Wagg, Reinhold Willcox:
COMPAS: A rapid binary population synthesis suite. 3838 - Perry de Valpine, Sally Paganin, Daniel Turek:
compareMCMCs: An R package for studying MCMC efficiency. 3844 - James Duncan, Rush Kapoor, Abhineet Agarwal, Chandan Singh, Bin Yu:
VeridicalFlow: a Python package for building trustworthy data science pipelines with PCS. 3895 - Arundale Ramanathan:
Unishox: A hybrid encoder for Short Unicode Strings. 3919 - Zeng Liew, Shozen Dan, Naoki Saito:
WaveletsExt.jl: Extending the boundaries of wavelets in Julia. 3937 - Michael Hall:
Rasusa: Randomly subsample sequencing reads to a specified coverage. 3941 - Justin Shenk, Mats L. Richter, Wolf Byttner:
Delve: Neural Network Feature Variance Analysis. 3992 - Alan A. Kaptanoglu, Brian de Silva, Urban Fasel, Kadierdan Kaheman, Andy Goldschmidt, Jared Callaham, Charles B. Delahunt, Zachary Nicolaou, Kathleen P. Champion, Jean-Christophe Loiseau, J. Nathan Kutz, Steven L. Brunton:
PySINDy: A comprehensive Python package for robust sparse system identification. 3994 - Youjiao Yu:
mixR: An R package for Finite Mixture Modeling for Both Raw and Binned Data. 4031 - Michael J. Mahoney, Colin M. Beier, Aidan Ackerman:
terrainr: An R package for creating immersive virtual environments. 4060 - Aaron Bray, Rachel B. Clipp, M. Umar Qureshi, Sorin Mitran, Andinet Enquobahrie:
gLBM: A GPU enabled Lattice Boltzmann Method Library. 2555 - Szymon Molinski:
Pyinterpolate: Spatial interpolation in Python for point measurements and aggregated datasets. 2869 - Eric Winter, Robert Weigel:
'nnde': A Python package for solving differential equations using neural networks. 3465 - Nicholas Gorman, Anna Bruce, Iain MacGill:
Nempy: A Python package for modelling the Australian National Electricity Market dispatch procedure. 3596 - Samuel Duffield:
bmm: Bayesian Map-matching. 3651 - John Brennan, Lee J. O'Riordan, Kenneth Hanley, Myles Doyle, Momme Allalen, David Brayford, Luigi Iapichino, Niall Moran:
QXTools: A Julia framework for distributed quantum circuit simulation. 3711 - Marten Koopmans, Vincent M. Le Corre, L. Jan Anton Koster:
'SIMsalabim': An open-source drift-diffusion simulator for semiconductor devices. 3727 - Vishwas Rao, Charlotte A. L. Haley, Mihai Anitescu:
LaplaceInterpolation.jl: A Julia package for fast interpolation on a grid. 3766 - Larkin Liu, Jun Tao Luo:
mctreesearch4j: A Monte Carlo Tree Search Implementation for the JVM. 3804 - Christopher Cave-Ayland, Michael J. Bearpark, Charles Romain, Henry S. Rzepa:
CHAMP is a HPC Access and Metadata Portal. 3824 - Ronny Bergmann:
Manopt.jl: Optimization on Manifolds in Julia. 3866 - Alexander Rockhill, Eric Larson, Brittany Stedelin, Alessandra Mantovani, Ahmed M. Raslan, Alexandre Gramfort, Nicole C. Swann:
Intracranial Electrode Location and Analysis in MNE-Python. 3897 - Juan E. Sanchez:
DEVSIM: A TCAD Semiconductor Device Simulator. 3898 - Alexander Pastukhov:
bistablehistory: an R package for history-dependent analysis of perceptual time series. 3901 - Christopher J. Woods, Lester O. Hedges, Christopher Edsall, Ellen Brooks-Pollock, Christopher Parton-Fenton, Trevelyan J. McKinley, Matt J. Keeling, Leon Danon:
MetaWards: A flexible metapopulation framework for modelling disease spread. 3914 - Guillaume Sagnol, Maximilian Stahlberg:
PICOS: A Python interface to conic optimization solvers. 3915 - Nora Loose, Ryan Abernathey, Ian G. Grooms, Julius Busecke, Arthur Guillaumin, Elizabeth Yankovsky, Gustavo Marques, Jacob Steinberg, Andrew Slavin Ross, Hemant Khatri, Scott Bachman, Laure Zanna, Paige Martin:
GCM-Filters: A Python Package for Diffusion-based Spatial Filtering of Gridded Data. 3947 - Bram van Dijk:
Cacatoo: building, exploring, and sharing spatially structured models of biological systems. 3948 - Dominique Sydow, Jaime Rodríguez-Guerra, Andrea Volkamer:
OpenCADD-KLIFS: A Python package to fetch kinase data from the KLIFS database. 3951 - Tangi Migot, Dominique Orban, Abel Soares Siqueira:
DCISolver.jl: A Julia Solver for Nonlinear Optimization using Dynamic Control of Infeasibility. 3991 - Anthony Villano, Kitty Harris, Staci Brown:
'nrCascadeSim' - A simulation tool for nuclear recoil cascades resulting from neutron capture. 3993 - Tom Wagg, Katelyn Breivik, Selma de Mink:
LEGWORK: A python package for computing the evolution and detectability of stellar-origin gravitational-wave sources with space-based detectors. 3998 - Thomas G. Tranter, Robert Timms, Valentin Sulzer, Ferran Brosa Planella, Gavin M. Wiggins, Suryanarayana Vikrant Karra, Priyanshu Agarwal, Saransh Chopra, Srikanth Allu, Paul R. Shearing, Dan J. L. Brett:
liionpack: A Python package for simulating packs of batteries with PyBaMM. 4051 - Rafael Henkin, Michael R. Barnes:
visxhclust: An R Shiny package for visual exploration of hierarchical clustering. 4074 - Nicki Skafte Detlefsen, Jirí Borovec, Justus Schock, Ananya Harsh Jha, Teddy Koker, Luca Di Liello, Daniel Stancl, Changsheng Quan, Maxim Grechkin, William Falcon:
TorchMetrics - Measuring Reproducibility in PyTorch. 4101
Volume 7, Number 71, March 2022
- Alex Malins, Thom Lemoine:
radioactivedecay: A Python package for radioactive decay calculations. 3318 - Eric W. H. Hutton, Mark D. Piper, Gregory E. Tucker:
The Babelizer: language interoperability for model coupling in the geosciences. 3344 - Richard A. Erickson, Daniel S. Stich, Jillian L. Hebert:
fishStan: Hierarchical Bayesian models for fisheries. 3444 - Noah Pflugradt, Peter Stenzel, Leander Kotzur, Detlef Stolten:
LoadProfileGenerator: An Agent-Based Behavior Simulation for Generating Residential Load Profiles. 3574 - Dan E. Kelley, Clark Richards, Chantelle Layton:
oce: an R package for Oceanographic Analysis. 3594 - Milan S. Roberson, Christoffer Fremling, Mansi M. Kasliwal:
DBSP_DRP: A Python package for automated spectroscopic data reduction of DBSP data. 3612 - Arkajyoti Saha, Sumanta Basu, Abhirup Datta:
RandomForestsGLS: An R package for Random Forests for dependent data. 3780 - Maria Politi, Abdul Moeez, David Beck, Stuart Adler, Lilo Pozzo:
HARDy: Handling Arbitrary Recognition of Data in Python. 3829 - Boris Shminke:
gym-saturation: an OpenAI Gym environment for saturation provers. 3849 - Margaret C. Siple, André E. Punt, Tessa B. Francis, Philip S. Hammond, Dennis Heinemann, Kristy J. Long, Jeffrey Moore, Maritza Sepúlveda, Randall R. Reeves, Guðjón Már Sigurðsson, Gísli Víkingsson, Paul R. Wade, Rob Williams, Alexandre N. Zerbini:
mmrefpoints: Projecting long-term marine mammal abundance with bycatch. 3888 - Frederik De Ceuster, Thomas Ceulemans, Atulit Srivastava, Ward Homan, Jan Bolte, Jeremy Yates, Leen Decin, Peter Boyle, James Hetherington:
3D Line Radiative Transfer & Synthetic Observations with Magritte. 3905 - David E. Graff, Connor W. Coley:
pyscreener: A Python Wrapper for Computational Docking Software. 3950 - Thomas A. r. Purcell, Matthias Scheffler, Christian Carbogno, Luca M. Ghiringhelli:
SISSO++: A C++ Implementation of the Sure-Independence Screening and Sparsifying Operator Approach. 3960 - Matthieu Aussal, Marc Bakry, Laurent Séries:
Castor: A C++ library to code "à la Matlab". 3965 - Jan Baumgärtner, Torben Miller:
TriP: A Python package for the kinematic modeling of serial-parallel hybrid robots. 3967 - Sindre Nordmark Olufsen, Rene Kaufmann, Egil Fagerholt, Vegard Aune:
RECOLO: A Python package for the reconstruction of surface pressure loads from kinematic fields using the virtual fields method. 3980 - Joe Wandy, Vinny Davies, Ross McBride, Stefan Weidt, Simon Rogers, Rónán Daly:
ViMMS 2.0: A framework to develop, test and optimise fragmentation strategies in LC-MS metabolomics. 3990 - Joshua Tse, Marco Molinari, Stephen C. Parker, Adam Symington:
SurfinPy 2.0: A Phase Diagram Generator for Surfaces and Bulk Phases. 4014 - Björn Biltzinger, J. Michael Burgess, Thomas Siegert:
PySPI: A python analysis framework for INTEGRAL/SPI. 4017 - Qing Yu, Jian Yuan:
TransBigData: A Python package for transportation spatio-temporal big data processing, analysis and visualization. 4021 - Charles Li:
helayo: Reconstructing Sanskrit texts from manuscript witnesses. 4022 - Houman Mirzaalian-Dastjerdi, Reza Gholami Mahmoodabadi, Matthias Bär, Vahid Sandoghdar, Harald Köstler:
PiSCAT: A Python Package for Interferometric Scattering Microscopy. 4024 - Rick Helmus, Bas van de Velde, Andrea M. Brunner, Thomas L. ter Laak, Annemarie P. van Wezel, Emma Schymanski:
patRoon 2.0: Improved non-target analysis workflows including automated transformation product screening. 4029 - Jeffrey W. Hollister, Dorothy Q. Kellogg, Qian Lei-Parent, Emily Wilson, Cary Chadwick, David Dickson, Arthur Gold, Chester Arnold:
nsink: An R package for flow path nitrogen removal estimation. 4039 - Nastaran Saffaryazdi, Aidin Gharibnavaz, Mark Billinghurst:
Octopus Sensing: A Python library for human behavior studies. 4045 - Frederik Kratzert, Martin Gauch, Grey Nearing, Daniel Klotz:
NeuralHydrology - A Python library for Deep Learning research in hydrology. 4050 - Daniel Dee, Dean Corriveau, Jeffrey R. Ladd, Lakshmi Nannapaneni, John Arkins, Jeffrey Brown:
PopMedNet: A scalable and extensible open-source informatics platform designed to facilitate the implementation and operation of distributed health data networks. 4062 - Victor Sacek, Jamison Assunção, Agustina Pesce, Rafael Monteiro da Silva:
Mandyoc: A finite element code to simulate thermochemical convection in parallel. 4070 - Jiahe Cui, Karen M. Hampson, Matthew Wincott, Martin J. Booth:
SenAOReFoc: A Closed-Loop Sensorbased Adaptive Optics and Remote Focusing Control Software. 4075 - Floris van Breugel, Yuying Liu, Bingni W. Brunton, J. Nathan Kutz:
PyNumDiff: A Python package for numerical differentiation of noisy time-series data. 4078 - Aliaksei Pilko, Zachary Tait:
SEEDPOD Ground Risk: A Python application and library for Uncrewed Aerial Systems ground risk analysis and risk-aware path finding. 4079 - Alphons Gwatimba, Joseph Ho, Thomas Iosifidis, Yuliya V. Karpievitch:
Rainbow: Automated Air-Liquid Interface Cell Culture Analysis Using Deep Optical Flow. 4080 - Brandon Silva, Paul Lunis, Marios Theristis, Hubert Seigneur:
PyPVRPM: Photovoltaic Reliability and Performance Model in Python. 4093 - Leonid P. Pryadko, Vadim A. Shabashov, Valerii K. Kozin:
QDistRnd: A GAP package for computing the distance of quantum error-correcting codes. 4120 - Paul Stocker:
'NGSTrefftz': Add-on to NGSolve for Trefftz methods. 4135 - Benjamin M. Gyori, Charles Tapley Hoyt:
PyBioPAX: biological pathway exchange in Python. 4136 - Aaron R. Caldwell:
SimplyAgree: An R package and jamovi Module for Simplifying Agreement and Reliability Analyses. 4148 - Coleman R. Harris, Julia Wrobel, Simon N. Vandekar:
mxnorm: An R Package to Normalize Multiplexed Imaging Data. 4180
Volume 7, Number 72, April 2022
- Grant Giesbrecht, Ariel Amsellem, Timo Bauer, Brian Mak, Brian Wynne, Zhihao Qin, Arun Persaud:
Hardware-Control: Instrument control and automation package. 2688 - Jorge Dávila-Chacón, Max Pumperla:
Logodetect: One-shot detection of logos in image and video data. 3124 - Piotr Bartman, Oleksii Bulenok, Kamil Górski, Anna Jaruga, Grzegorz Lazarski, Michael A. Olesik, Bartosz Piasecki, Clare E. Singer, Aleksandra Talar, Sylwester Arabas:
PySDM v1: particle-based cloud modeling package for warm-rain microphysics and aqueous chemistry. 3219 - Juniper Simonis, Glenda Yenni, Ellen Bledsoe, Erica Christensen, Henry Senyondo, Shawn D. Taylor, Hao Ye, Ethan P. White, S. K. Morgan Ernest:
portalcasting: Supporting automated forecasting of rodent populations. 3220 - Dustin S. Stoltz, Marshall A. Taylor:
text2map: R Tools for Text Matrices. 3741 - Simon Dobson:
epyc: Computational experiment management in Python. 3764 - Joshua D. Larsen, Ayman H. Alzraiee, Richard G. Niswonger:
Integrated hydrologic model development and postprocessing for GSFLOW using pyGSFLOW. 3852 - Fabian Wüllhorst, Thomas Storek, Philipp Mehrfeld, Dirk Müller:
AixCaliBuHA: Automated calibration of building and HVAC systems. 3861 - Mithun Bairagi:
GiNaCDE: the high-performance F-expansion and First Integral Methods with C++ library for solving Nonlinear Differential Equations. 3885 - Nicholas M. Anthony, Vadim Backman:
PWSpy: A Python library dedicated to the analysis of Partial Wave Spectroscopic Microscopy data. 3957 - Fredrik Strömberg:
hilbertmodgroup: Reduction algorithms and framework for Hilbert Modular Groups. 3996 - Francesco Nattino, Ou Ku, Meiert W. Grootes, Emma Izquierdo-Verdiguier, Serkan Girgin, Raúl Zurita-Milla:
CGC: a Scalable Python Package for Co- and Tri-Clustering of Geodata Cubes. 4032 - Chung-hong Chan:
sweater: Speedy Word Embedding Association Test and Extras Using R. 4036 - Andrea M. Whittaker:
ADaPT-ML: A Data Programming Template for Machine Learning. 4038 - Sigurd M. Albrektsen, Kasper Gade Bøtker Rasmussen, Anders E. Liverud, Steffen Dalgard, Jakob Høgenes, Silje Ekroll Jahren, Jan Kocbach, Trine M. Seeberg:
The AutoActive Research Environment. 4061 - Jeremie Coullon, Christopher Nemeth:
SGMCMCJax: a lightweight JAX library for stochastic gradient Markov chain Monte Carlo algorithms. 4113 - Stuart R. Slattery, Samuel Temple Reeve, Christoph Junghans, Damien Lebrun-Grandié, Robert F. Bird, Guangye Chen, Shane Fogerty, Yuxing Qiu, Stephan Schulz, Aaron Scheinberg, Austin Isner, Kwitae Chong, Stan G. Moore, Timothy C. Germann, James F. Belak, Susan M. Mniszewski:
Cabana: A Performance Portable Library for Particle-Based Simulations. 4115 - Gereon A. Kaiping, Melvin S. Steiger, Natalia Chousou-Polydouri:
Lexedata: A toolbox to edit CLDF lexical datasets. 4140 - Nathan Bell, Luke N. Olson, Jacob B. Schroder:
PyAMG: Algebraic Multigrid Solvers in Python. 4142 - Tsung-Lin Wu, Amr Alhossary, Todd C. Pataky, Wei Tech Ang, Cyril J. Donnelly:
pyemgpipeline: A Python package for electromyography processing. 4156 - Bardhyl Miftari, Mathias Berger, Hatim Djelassi, Damien Ernst:
GBOML: Graph-Based Optimization Modeling Language. 4158 - Michal M. Wieclaw:
tesliper: a theoretical spectroscopist's little helper. 4164 - Peter Kraus, Nicolas Vetsch, Corsin Battaglia:
yadg: yet another datagram. 4166 - Elizabeth Newman, Lars Ruthotto:
'hessQuik': Fast Hessian computation of composite functions. 4171 - Roi Kugel, Josh Borrow:
swift-emulator: A Python package for emulation of simulated scaling relations. 4240 - Martin Larralde:
Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. 4296 - Stefan Jaud, Helge Hecht