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ORCIDJournal of Open Source Software, Volume 10
Volume 10, Number 105, January 2025
- Geert Raaijmakers
, Nathan Rutherford, Patrick Timmerman, Tuomo E. Salmi, Anna L. Watts, Chanda Prescod-Weinstein, Isak Svensson, Melissa Mendes:
NEoST: A Python package for nested sampling of the neutron star equation of state. 6003 - Hajime Senuma:
mmh3: A Python extension for MurmurHash3. 6124 - Flaminia Catalli, Matteo Spada:
ProMCDA: A Python package for Probabilistic Multi-Criteria Decision Analysis. 6190 - Theresa Klütz, Kevin Knosala, Johannes Behrens, Rachel Maier, Maximilian Hoffmann, Noah Pflugradt, Detlef Stolten:
ETHOS.FINE: A Framework for Integrated Energy System Assessment. 6274 - Stijn Wittouck, Tim Van Rillaer, Wenke Smets, Sarah Lebeer:
Tidytacos: An R package for analyses on taxonomic composition of microbial communities. 6313 - Anna Tartaglia, Kazunori Akiyama, Paul Tiede:
ScatteringOptics.jl: An Interstellar Scattering Framework in the Julia Programming Language. 6354 - David Tschumperlé, Sébastien Fourey, Garry Osgood:
G'MIC: An Open-Source Self-Extending Framework for Image Processing. 6618 - Sara Ha, Simona Onori:
COBRAPRO: A MATLAB toolbox for Physics-based Battery Modeling and Co-simulation Parameter Optimization. 6803 - Daniel J. Asay, Timothy M. O'Keefe, Randy L. Buckner, Ross W. Mair:
DWIQC: A Python package for preprocessing and quality assurance of diffusion weighted images. 6974 - Wesley H. Holliday, Eric Pacuit:
pref_voting: The Preferential Voting Tools package for Python. 7020 - Sinan Ozaydin, Lu Li, Utpal Singh, Patrice Rey, Maria Constanza Manassero:
pide: Petrophysical Interpretation tools for geoDynamic Exploration. 7021 - Niklas S. Neher, Erik Faulhaber, Sven Berger, Gregor J. Gassner, Michael Schlottke-Lakemper:
TrixiParticles.jl: Particle-based multiphysics simulation in Julia. 7044 - Raoul Schram, Samuel Spithorst, Erik-Jan van Kesteren:
Metasyn: Transparent Generation of Synthetic Tabular Data with Privacy Guarantees. 7099 - Robert M. Cook, Md. Asaduzzaman, Sarahjane Jones:
Deident: An R package for data anonymization. 7157 - Daniel Otto de Mentock, Sharan Roongta, Franz Roters, Philip Eisenlohr, Martin Diehl:
A Python Library for Pre- and Post-Processing of DAMASK Simulations. 7164 - John M. Volk, Christian Dunkerly, Christopher Pearson, Charles G. Morton, Justin L. Huntington:
gridwxcomp: A Python package to evaluate and interpolate biases between station and gridded weather data. 7178 - Hause Lin, Tawab Safi:
ollamar: An R package for running large language models. 7211 - Jacob Tiegs, Julia Raykin, Ilia Rochlin:
BART-Survival: A Bayesian machine learning approach to survival analyses in Python. 7213 - Cedric Kulbach, Lucas Cazzonelli, Hoang-Anh Ngo, Max Halford, Saulo Martiello Mastelini:
DeepRiver: A Deep Learning Library for Data Streams. 7226 - Sajjad Khan, Sandeep Pallikkuth, David J. Schodt, Marjolein B. m. Meddens, Hanieh Mazloom-Farsibaf, Michael J. Wester, Sheng Liu, Ellyse Taylor, Mohamadreza Fazel, Farzin Farzam, Keith A. Lidke:
A MATLAB-based Instrument Control (MIC) package for fluorescence imaging. 7275 - Gareth Cross:
wrenfold: Symbolic code generation for robotics. 7303 - Felix Böhm, Moritz Makowski, Patrick Aigner, Jia Chen:
Tenta: Remote and Real-Time Sensor Network Management. 7311 - Sevgi Akten Karakaya, Mehmet Hakan Satman:
pycellga: A Python package for improved cellular genetic algorithms. 7322 - David Landa-Marbán, Tor Harald Sandve:
pyopmspe11: A Python framework using OPM Flow for the SPE11 benchmark project. 7357 - Brice Letcher:
delfies: a Python package for the detection of DNA breakpoints with neo-telomere addition. 7385 - Tom Wagg, Katelyn Breivik, Mathieu Renzo, Adrian M. Price-Whelan:
cogsworth: A Gala of COSMIC proportions combining binary stellar evolution and galactic dynamics. 7400 - Logan Mondal Bhamidipaty, Mykel J. Kochenderfer, Trevor Hastie:
ExpFamilyPCA.jl: A Julia Package for Exponential Family Principal Component Analysis. 7403 - Yuefan Ji, Matthew Murbach, Daniel T. Schwartz:
nleis.py: A Nonlinear Electrochemical Impedance Analysis Toolbox. 7424 - Elmongi Elbellili, Daan Huybrechs, Ben Lauwens:
QuantizedSystemSolver: A discontinuous ODE system solver in Julia. 7434 - Mark Zolotas, Philip Long, Taskin Padir:
robot_collision_checking: A Lightweight ROS 2 Interface to FCL (Flexible Collision Library). 7473 - Daniel S. Stich, Julie L. Nieland, Timothy F. Sheehan:
dia: An R package for the National Oceanic and Atmospheric Administration dam impact analysis. 7475 - Joe Thorley, Rebecca Fisher, David Fox, Carl Schwarz:
ssdtools v2: An R package to fit Species Sensitivity Distributions. 7492 - Lionel Constantin, Brunner Dominik, Joel Thanwerdas, Corina Keller, Michael Steiner, Erik Koene:
Emiproc: A Python package for emission inventory processing. 7509 - Rohan Babbar, Matteo Ravasi, Yuxi Hong:
PyLops-MPI - MPI Powered PyLops with mpi4py. 7512 - Peter Gadomski, Preston J. Hartzell:
antimeridian: A Python package for correcting geometries that cross the 180th meridian. 7530 - Vladimir Mikheev, Benedikt V. Ehinger:
UnfoldMakie.jl: EEG/ERP visualization package. 7560 - Clemens Eppner, Adithyavairavan Murali, Caelan Reed Garrett, Rowland O'Flaherty, Tucker Hermans, Wei Yang, Dieter Fox:
scene_synthesizer: A Python Library for Procedural Scene Generation in Robot Manipulation. 7561 - Dylan Bouchard, Mohit Singh Chauhan, David Skarbrevik, Viren Bajaj, Zeya Ahmad:
LangFair: A Python Package for Assessing Bias and Fairness in Large Language Model Use Cases. 7570 - Jed Homer, Oliver Friedrich:
SBIAX: Density-estimation simulation-based inference in JAX. 7606
Volume 10, Number 106, February 2025
- Tim Furlan, Jonathan Stollberg, Andreas Menzel:
Paraqus: Exporting Finite Element Simulation Results from Abaqus to VTK. 5729 - Maggie Voetberg, Ashia Livaudais, Becky Nevin, Omari Paul, Brian Nord:
DeepBench: A simulation package for physical benchmarking data. 6774 - Johannes Holke, Johannes Markert, David Knapp, Lukas Dreyer, Sandro Elsweijer, Niklas Böing, Ioannis Lilikakis, Jakob Fussbroich, Tabea Leistikow, Florian Becker, Veli Uenlue, Ole Albers, Carsten Burstedde, Achim Basermann, Chiara Hergl, Weber Julia, Kathrin Schoenlein, Jonas Ackerschott, Andreev Evgenii, Zoltan Csati, Alexandra Dutka, Benedict Geihe, Pierre Kestener, Andrew Kirby, Hendrik Ranocha, Michael Schlottke-Lakemper:
t8code - modular adaptive mesh refinement in the exascale era. 6887 - Manuel Rausch, Sascha Meyen, Sebastian Hellmann:
statConfR: An R Package for Static Models of Decision Confidence and Metacognition. 6966 - Theresa Pollinger, Marcel Hurler, Alexander Van Craen, Michael Obersteiner, Dirk Pflüger:
DisCoTec: Distributed higher-dimensional HPC simulations with the sparse grid combination technique. 7018 - John M. Aiken, Gareth Jones, Xueqing Yin, Anrijs Abele, Christopher J. Woods, Richard M. Westaway, Jonathan L. Bamber:
4DModeller: a spatio-temporal modelling package. 7047 - Robin Chartrand, Robert Fajber, Georgy E. Manucharyan:
NcCut: A NetCDF Viewer and Transecting Tool. 7185 - Maximilian Wolf, Selina Götz, Georg K. H. Madsen, Theodoros Dimopoulos:
COHESIVM: Combinatorial h+/e- Sample Investigation using Voltaic Measurements. 7291 - Joseph Emile Honour Percival, Benjamin Palsa Leamon:
PyForestScan: A Python library for calculating forest structural metrics from lidar point cloud data. 7314 - Jennifer A. Clark, Nathan Duff, Andrew Abi Mansour, Erik E. Santiso:
DESPASITO: A Python Package for SAFT EOS Parametrization and Thermodynamic Calculations. 7365 - Jan F. Wiegner, Julia L. Tiggeloven, Luca Bertoni, Inge M. Ossentjuk, Matteo Gazzani:
AdOpT-NET0: A technology-focused Python package for the optimization of multi-energy systems. 7402 - Jonathan M. Waldrop, Ryan M. Richard:
Sigma: Uncertainty Propagation for C++. 7404 - Thomas Holland, Daniel Cummins, Monica Marinescu:
PyProBE: Python Processing for Battery Experiments. 7474 - Raphaël Prat, Thierry Carrard, Lhassan Amarsid, Vincent Richefeu, Carlo-Elia Doncecchi, Paul Lafourcade, Guillaume Latu, Jean-Mathieu Vanson:
ExaDEM: a HPC application based on exaNBody targeting scalable DEM simulations with complex particle shapes. 7484 - Ankush Aggarwal, Ross Williams, Claire Rosnel, Silvia Renon, Jude M. Hussain, André F. Schmidt, Shiting Huang, Sean McGinty, Andrew McBride:
pyMechT: A Python package for mechanics of soft tissues. 7490 - Darren J. Wilkinson:
jax-smfsb: A Python library for stochastic systems biology modelling and inference. 7491 - Dingshan Deng, Ilaria Pascucci, Rachel B. Fernandes:
ysoisochrone: A Python package to estimate masses and ages for YSOs. 7493 - David O'Gara, Mickaël Binois, Roman Garnett, Ross A. Hammond:
hetGPy: Heteroskedastic Gaussian Process Modeling in Python. 7518 - David Woodburn:
r3f: Rotation of 3-dimensional Reference Frames. 7534 - Gabriel Couture, Yannick Lemaréchal, Philippe Després:
PyOrthanc: A Python Interface for Orthanc DICOM Servers. 7562 - Mistral Contrastin, Raoul Hidalgo Charman, Matthew Danish, Benjamin Orchard, Dominic Orchard, Andrew Rice, Jason Xu:
fortran-src: Fortran static analysis infrastructure. 7571 - Salvador V. Balkus, Nima S. Hejazi:
CausalTables.jl: Simulating and storing data for statistical causal inference in Julia. 7580 - Fábio Madeira, Nandana Madhusoodanan, Joonheung Lee, Alberto Eusebi, Ania Niewielska, Sarah Butcher:
Taxonomy Resolver: A Python package for building and filtering taxonomy trees. 7604 - Markus Pichler:
idf-analysis: Heavy rainfall intensity as a function of duration and return period. 7607 - Toru Seo:
UXsim: lightweight mesoscopic traffic flow simulator in pure Python. 7617 - Simon R. Parker, Linda Vesel, Eric O. Ohuma:
gigs: A package for standardising fetal, neonatal, and child growth assessment. 7655
Volume 10, Number 107, March 2025
- Joshua Benjamin Schramm, Marcel Lichters:
validateHOT - an R package for the analysis of holdout/validation tasks and other choice modeling tools. 6708 - Evaristo Rojas-Mayoral, Braulio Rojas-Mayoral, Federico A. Méndez-Sánchez:
NERD: Numerical Estimation of Rodenticide Density. 6736 - Martin Rätz, Fabian Wüllhorst, Rita Streblow, Dirk Müller:
AixWeather: A Weather Data Generation Tool for Building Energy System Simulations. Pull, Transform, Export. 7344 - Simon Sekavcnik, Kareem H. El-Safty, Janis Nötzel:
PhotonWeave. 7468 - Steven Golovkine:
FDApy: a Python package for functional data. 7526 - Truls Flatberg, Julian Straus, Lars Hellemo:
TimeStruct.jl - flexible multi-horizon time modelling in optimization models. 7578
Volume 10, Number 108, April 2025
- David L. Birtwell, Heather Williams, Tom Hutchinson, Louis Lee, Hayden Freedman, Christian J. Stoeckert Jr.:
Carnival: JVM Property graph data unification toolkit. 5117 - Christopher G. Stahl, Kristan J. Markey, Brian C. Jewell, Dahnish Shams, Michele M. Taylor, A. Amina Wilkins, Sean Watford, Andy Shapiro, Michelle Angrish:
PDF Entity Annotation Tool (PEAT). 5336 - Anthony Lim:
quickBayes: An analytical approach to Bayesian marginal likelihoods. 6230 - Judith Schepers, Luis Lips, Maanik Marathe, Benedikt V. Ehinger:
UnfoldSim.jl: Simulating continuous event-based time series data for EEG and beyond. 6641 - Philip Gouverneur, Frédéric Li, Luisa Luebke, Tibor M. Szikszay, Sonja-Dana Roelen, Jarek Krajewski, Kerstin Luedtke, Marcin Grzegorzek:
eVAS: A user-friendly electronic Visual Analogue Scale. 6876 - Fabia Miorelli, Niklas Wulff, Benjamin Fuchs, Hans Christian Gils, Patrick Jochem:
venco.py: A Python model to represent the charging flexibility and vehicle-to-grid potential of electric vehicles in energy system models. 6896 - Keisuke Adachi, Minoru Kanega:
TopologicalNumbers.jl: A Julia package for topological number computation. 6944 - Scott W. Linderman, Peter G. Chang, Giles Harper-Donnelly, Aleyna Kara, Xinglong Li, Gerardo Duran-Martin, Kevin Murphy:
Dynamax: A Python package for probabilistic state space modeling with JAX. 7069 - Scott E. Field, Vijay Varma, Jonathan Blackman, Bhooshan Gadre, Chad R. Galley, Tousif Islam, Keefe Mitman, Michael Pürrer, Adhrit Ravichandran, Mark A. Scheel, Leo C. Stein, Jooheon Yoo:
GWSurrogate: A Python package for gravitational wave surrogate models. 7073 - Julius Gervelmeyer, Sarah Müller, Ziwei Huang, Philipp Berens:
Fundus Image Toolbox: A Python package for fundus image processing. 7101 - Aravind Sundararajan, Varun Joshi, Brian R. Umberger, Matthew C. O'Neill:
MocoExtendProblem: Interface Between OpenSim and MATLAB for Rapidly Developing Direct Collocation Goals in Moco. 7110 - Silke Maes, Frederik De Ceuster, Marie Van de Sande, Leen Decin:
MACE: a Machine-learning Approach to Chemistry Emulation. 7148 - Lucas Korol, Robert J. Green, Jesus P. Curbelo, Raymond J. Spiteri:
GO-RXR: Global Optimization of Resonant X-ray Reflectometry. 7165 - Jim Hester, Florent Angly, Michael Chirico, Russ Hyde, Ren Kun, Indrajeet Patil, Alexander Rosenstock:
Static Code Analysis for R. 7240 - Matias D. Cattaneo, Rajita Chandak, Michael Jansson, Xinwei Ma:
lpcde: Estimation and Inference for Local Polynomial Conditional Density Estimators. 7241 - Firas A. Khasawneh, Elizabeth Munch, Danielle Barnes, Max M. Chumley, Ismail Güzel, Audun D. Myers, Sunia Tanweer, Sarah Tymochko, Melih C. Yesilli:
Teaspoon: A Python Package for Topological Signal Processing. 7243
Volume 10, Number 109, May 2025
- Yongji Wang, Ching-Yao Lai:
DIFFICE-jax: Differentiable neural-network solver for data assimilation of ice shelves in JAX. 7254 - Lorena Acuña, Laura Kreidberg, Meng Zhai, Paul Mollière, Morgan Fouesneau:
GASTLI: A Python package for coupled interior-atmosphere modelling of volatile-rich planets. 7288 - Tobias Bode:
AutoPDEx: An Automized Partial Differential Equation solver based on JAX. 7300 - Michael S. Petersen, Martin D. Weinberg:
EXP: a Python/C++ package for basis function expansion methods in galactic dynamics. 7302 - Miguel Castillón:
PhaseFieldX: An Open-Source Framework for Advanced Phase-Field Simulations. 7307 - Juan Pablo P. de Aquino, José Fernando M. de Firmino, Diogo D. Moreira, Ricardo S. de Job:
DemeterWatch: A Java tool to detect Law of Demeter violations in Java collections. 7308 - James C. Ross, Tingting Zhao:
bayes_traj: A Python package for Bayesian trajectory analysis. 7323 - Asim Shrestha, Adam Watkins, Fereshteh Yousefirizi, Arman Rahmim, Carlos F. Uribe:
RT-utils: A Minimal Python Library for RT-struct Manipulation. 7361 - Danilo Couto de Souza, Pedro Leite da Silva Dias, Carolina B. Gramcianinov, Ricardo Saraiva de Camargo:
CycloPhaser: A Python Package for Detecting Extratropical Cyclone Life Cycles. 7363 - George Simmons, David Stern, Georg Osang, Luigi Ponti, Andrew Paul Gutierrez, Chiara Facciolà, Timothy Hosgood:
Psymple: A Python package for complex systems modelling. 7364 - Jaren N. Ashcraft, Ewan S. Douglas, William Melby, Manxuan Zhang, Kenji Mulhall, Ramya M. Anche, Emory Jenkins, Maxwell A. Millar-Blanchaer:
Katsu: A Python package for Mueller and Stokes simulation and polarimetry. 7375 - Yicheng Qiang, David Zwicker:
flory: A Python package for finding coexisting phases in multicomponent mixtures. 7388 - Newell H. Moser, Alexander K. Landauer, Orion L. Kafka:
IMPPY3D: Image Processing in Python for 3D Image Stacks. 7405 - Philip Cardiff, Ivan Batistic, Zeljko Tukovic:
solids4foam: A toolbox for performing solid mechanics and fluid-solid interaction simulations in OpenFOAM. 7407 - Matilde Gargiani, Philip Pawlowsky, Robin Sieber, Václav Hapla, John Lygeros:
madupite: A High-Performance Distributed Solver for Large-Scale Markov Decision Processes. 7411 - Nicholas Van Alfen, Duncan Campbell, Andrew Hearin, Jonathan Blazek:
Halotools: A New Release Adding Intrinsic Alignments to Halo-Based Methods. 7421 - Humberto Medina, Christopher D. Ellis, Tom Mazin, Oscar Osborn, Timothy Ward, Stephen Ambrose, Svetlana Aleksandrova, Benjamin Rothwell, Carol Eastwick:
XCALibre.jl: A Julia XPU unstructured finite volume Computational Fluid Dynamics library. 7441 - Isaac Kinley:
tempodisco: an R package for temporal discounting. 7472 - Lukas Burgholzer, Yannick Stade, Tom Peham, Robert Wille:
MQT Core: The Backbone of the Munich Quantum Toolkit (MQT). 7478 - Mark Zolotas, Philip Long, Keerthi Sagar, Taskin Padir:
constrained_manipulability: A ROS 2 library to Compute and Visualize Constrained Capacities for Robotic Manipulators. 7481 - Sayak Chakrabarty, Souradip Pal:
ReadmeReady: Free and Customizable Code Documentation with LLMs - A Fine-Tuning Approach. 7489 - Martin Wendt, Marvin Henschel, Oskar Fjonn Soth:
FELINE: A Tool to Detect Emission Line Galaxies in 3D Data. 7528 - Austin M. Weber:
Algorithms for SEM-EDS Mineral Dust Classification. 7533 - Henrik Melin:
h3ppy: An open-source Python package for modelling and fitting H$_3^+$ spectra. 7536 - Leonie Sara Plaga, Valentin Bertsch:
cd2es: Converting climate data to energy system input data. 7541 - Jacques Dainat:
AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment. 7545 - Selvakumar Kamatchinathan, Suresh Hewapathirana, Chakradhar Bandla, Santiago Insua, Juan Antonio Vizcaíno, Yasset Pérez-Riverol:
pridepy: A Python package to download and search data from PRIDE database. 7563 - Alaa Reguei, Samuel Murail:
Af-analysis: a Python package for Alphafold analysis. 7577 - Ioannis G. Tsoulos, Vasileios Charilogis, Glykeria Kyrou, Vasileios N. Stavrou, Alexandros T. Tzallas:
OPTIMUS: A Multidimensional Global Optimization Package. 7584 - Johannes Zauner, Steffen Hartmeyer, Manuel Spitschan:
LightLogR: Reproducible analysis of personal light exposure data. 7601 - Jack Atkinson, Athena Elafrou, Elliott Kasoar, Joseph G. Wallwork, Thomas Meltzer, Simon Clifford, Dominic Orchard, Chris Edsall:
FTorch: a library for coupling PyTorch models to Fortran. 7602 - Trung Ha, Joonas Nättilä, Jordy Davelaar:
aweSOM: a CPU/GPU-accelerated Self-organizing Map and Statistically Combined Ensemble Framework for Machine-learning Clustering Analysis. 7613 - Riccardo Boero:
An Introduction to prismAId: Open-Source and Open Science AI for Advancing Information Extraction in Systematic Reviews. 7616 - Martin A. Stoffel, Bryan M. Li, Kalle Westerling, Sophie Arana, Maximilian Balmus, Eric G. Daub, Steven A. Niederer:
AutoEmulate: A Python package for semi-automated emulation. 7626 - Ewout ter Hoeven, Jan Kwakkel, Vincent Hess, Thomas Pike, Boyu Wang, Rht, Jackie Kazil:
Mesa 3: Agent-based modeling with Python in 2025. 7668 - Robrecht Cannoodt, Louise Deconinck, Artuur Couckuyt, Nikolay S. Markov, Luke Zappia, Malte D. Lücken, Marta Interlandi, Yvan Saeys, Wouter Saelens:
funkyheatmap: Visualising data frames with mixed data types. 7698 - Damar Wicaksono, Uwe Hernandez Acosta, Sachin Krishnan Thekke Veettil, Jannik Kissinger, Michael Hecht:
Minterpy: multivariate polynomial interpolation in Python. 7702 - Younes Strittmatter, Sebastian Musslick:
SweetBean: A declarative language for behavioral experiments with human and artificial participants. 7703 - Evan T. Hockings:
QuantumACES.jl: design noise characterisation experiments for quantum computers. 7707 - J. Eduardo Vera-Valdés:
LongMemory.jl: Generating, Estimating, and Forecasting Long Memory Models in Julia. 7708 - Thomas Helfer, Guillaume Latu, Raphaël Prat, Maxence Wangermez, Francesca Cuteri:
MFEM/MGIS, a HPC mini-application targeting nonlinear thermo-mechanical simulations of nuclear fuels at mesoscale. 7719 - Emily Tour, Kabir Manandhar Shrestha, Robert Turnbull:
Potnia: A Python library for the conversion of transliterated ancient texts to Unicode. 7725 - Adam Wysokinski:
NeuroAnalyzer: Julia toolbox for analyzing neurophysiological data. 7734 - Michael Foster, Andrew G. Clark, Christopher Wild, Farhad Allian, Robert D. Turner, Richard J. Somers, Nicholas Latimer, Neil Walkinshaw, Robert M. Hierons:
The Causal Testing Framework. 7739 - Pierre-Antoine Comby, Guillaume Daval-Frerot, Caini Pan, Asma Tanabene, Léna Oudjman, Matteo Cencini, Philippe Ciuciu, Chaithya G. R.:
MRI-NUFFT: Doing non-Cartesian MRI has never been easier. 7743 - Jan Boelts, Michael Deistler, Manuel Glöckler, Álvaro Tejero-Cantero, Jan-Matthis Lueckmann, Guy Moss, Peter Steinbach, Thomas Moreau, Fabio Muratore, Julia Linhart, Conor Durkan, Julius Vetter, Benjamin Kurt Miller, Maternus Herold, Abolfazl Ziaeemehr, Matthijs Pals, Theo Gruner, Sebastian Bischoff, Nastya Krouglova, Richard Gao, Janne K. Lappalainen, Bálint Mucsányi, Felix Pei, Auguste Schulz, Zinovia Stefanidi, Pedro Rodrigues, Cornelius Schröder, Faried Abu Zaid, Jonas Beck, Jaivardhan Kapoor, David S. Greenberg, Pedro J. Gonçalves, Jakob H. Macke:
sbi reloaded: a toolkit for simulation-based inference workflows. 7754 - Matthew N. Crowe:
QGDipoles.jl: A Julia package for calculating dipolar vortex solutions to the Quasi-Geostrophic equations. 7767 - Nathaniel Starkman, Adrian M. Price-Whelan, Jake Nibauer:
unxt: A Python package for unit-aware computing with JAX. 7771 - Jan Janssen, Michael Gilbert Taylor, Ping Yang, Jörg Neugebauer, Danny Perez:
Executorlib - Up-scaling Python workflows for hierarchical heterogenous high-performance computing. 7782 - Sayak Chakrabarty, Souradip Pal:
MM-PoE: Multiple Choice Reasoning via. Process of Elimination using Multi-Modal Models. 7783 - Odd A. Andersen:
Topography-based surface water modeling in Julia, with support for infiltration and temporal developments. 7785 - Daniel Schuch:
eva3dm: A R-package for model evaluation of 3D weather and air quality models. 7797 - Ruoyan Meng, Gabriella d'Albenzio, Ole Vegard Solberg, Geir Arne Tangen, Rafael Palomar:
Slicer-Liver: A 3D Slicer Extension for Liver Surgery Planning. 7798 - Spyros Rigas, Michalis Papachristou:
jaxKAN: A unified JAX framework for Kolmogorov-Arnold Networks. 7830 - Wenbo Wu, Xinyi Zhang, Jann Spiess, Rahul Ladhania:
rjaf: Regularized Joint Assignment Forest with Treatment Arm Clustering. 7843 - Kurt Irvin M. Rojas, Yoshitada Morikawa, Ikutaro Hamada:
VibIR-Parallel-Compute: Enhancing Vibration and Infrared Analysis in High-Performance Computing Environments. 7855 - Rahil Makadia, Davide Farnocchia, Steven R. Chesley, Siegfried Eggl:
Gauss-Radau Small-body Simulator (GRSS): An Open-Source Library for Planetary Defense. 7861 - Thomas Kerwin:
Pydre: A Python package for driving simulation data reduction. 7870 - Rhyd Lewis, Geraint Palmer:
GCol: A High-Performance Python Library for Graph Colouring. 7871 - James W. Trayford, Samantha Youles, Chris M. Harrison, Rose Shepherd, Nicolas Bonne:
strauss: Sonification Tools and Resources for Analysis Using Sound Synthesis. 7875 - Apostolos Chalkis, Vissarion Fisikopoulos, Marios Papachristou, Elias P. Tsigaridas:
volesti: A C++ library for sampling and volume computation on convex bodies. 7886 - Patrick J. Taylor, Benjamin J. Morgan:
pengWann: Descriptors of chemical bonding from Wannier functions. 7890 - Dan Bonachea, Katherine Rasmussen, Brad Richardson, Damian W. I. Rouson:
Caffeine: A parallel runtime library for supporting modern Fortran compilers. 7895 - Adam B. Rohrlach, Jonathan Tuke, Divya Ratan Popli, Wolfgang Haak:
BREADR: An R Package for the Bayesian Estimation of Genetic Relatedness from Low-coverage Genotype Data. 7916 - Alexander Coulter, Rebecca Lee, Irina Gaynanova:
fastfrechet: An R package for fast implementation of Fréchet regression with distributional responses. 7925 - Daniel Peláez-Zapata, Frédéric Dias:
EWDM: A wavelet-based method for estimating directional spectra of ocean waves. 7942 - Micah D. Gale, Travis J. Labossiere-Hickman, Brenna A. Carbno, Andrew J. Bascom:
MontePy: a Python library for reading, editing, and writing MCNP input files. 7951 - Adrian Niemann, Dmitry Puzyrev, Ralf Stannarius:
ParticleTracking: A GUI and library for particle tracking on stereo camera images. 5986 - Mohammad Amin Sadeghi, Runze Zhang, Jason Hattrick-Simpers:
AutoEIS: Automated equivalent circuit modeling from electrochemical impedance spectroscopy data using statistical machine learning. 6256 - Nathan Decaux, Pierre-Henri Conze, Juliette Ropars, Xinyan He, Frances T. Sheehan, Christelle Pons, Douraied Ben Salem, Sylvain Brochard, François Rousseau:
LabelProp: A semi-automatic segmentation tool for 3D medical images. 6284 - Trevor Gokey:
BESMARTS: A toolkit for data-driven force field design using binary-encoded SMARTS. 6653
Volume 10, Number 110, June 2025
- Nathan Martindale, Scott Stewart:
ICAT: The Interactive Corpus Analysis Tool. 6873 - Utpal Singh, Sinan Ozaydin, Vasileios Chatzaras, Patrice Rey:
SAnTex: A Python-based Library for Seismic Anisotropy Calculation. 6886 - Subhadeep Sarkar, Michael S. Petersen:
commensurability: a Python package for classifying astronomical orbits based on their toroid volume. 7009 - Hao-Ting Wang, Rémi Gau, Natasha Clarke, Quentin Dessain, Lune Bellec:
Giga Connectome: a BIDS-app for time series and functional connectome extraction. 7061 - Dena J. Clink, Abdul Hamid Ahmad:
gibbonNetR: an R Package for the Use of Convolutional Neural Networks for Automated Detection of Acoustic Data. 7250 - Igor Dornelles Schoeller Siciliani, Paulo Henrique dos Santos:
corrp: An R package for multiple correlation-like analysis and clustering in mixed data. 7319 - Andy Wilkins, Nicholas J. Beeton, Maud El-Hachem, Keith R. Hayes, Geoffrey R. Hosack:
Mozzie: a computationally efficient simulator for the spatio-temporal modelling of mosquitoes. 7324 - Nikita Kavokine, Hao Lu, Thomas Ayral, Michel Ferrero, Nils Wentzell, Olivier Parcollet:
CTSEG: A segment picture quantum impurity solver based on TRIQS. 7425 - Matthew T. Warkentin, John M. Hutchinson, Yibing Ruan, Darren R. Brenner:
openmpp: An R package for dynamic microsimulation modeling using OpenM++. 7435 - Christopher Donnay, Moon Duchin, Jack Gibson, Zach Glaser, Andrew Hong, Malavika Mukundan, Jennifer Wang:
VoteKit: A Python package for computational social choice research. 7477 - Garrett K. Keating, Bryna J. Hazelton, Matthew Kolopanis, Steven G. Murray, Adam P. Beardsley, Daniel C. Jacobs, Nicholas S. Kern, Adam Lanman, Paul La Plante, Jonathan C. Pober, Pyxie Star:
pyuvdata v3: an interface for astronomical interferometric data sets in Python. 7482 - Anders Reenberg Andersen, Jesper Fink Andersen:
MDPSolver: An Efficient Solver for Markov Decision Processes. 7544 - Arkavo Hait, Santanu Mahapatra:
CUDA-METRO: Parallel Metropolis Monte Carlo for 2D Atomistic Spin Texture Simulation. 7589 - Karthik Menon, Jakob Richter, Martin R. Pfaller, Jonathan Pham, Emilin M. Mathew, Kaitlin E. Harold, Nicholas C. Dorn, Aekaansh Verma, Alison L. Marsden:
svZeroDSolver: A modular package for lumped-parameter cardiovascular simulations. 7595 - Abhinav Sharma, Talya Conradie, David Martino, Stephen Stick, Patricia Agudelo-Romero:
target-methylseq-qc: a lightweight pipeline for collecting metrics from targeted sequence mapping files. 7608 - Sebastián José Herrera Monterrosa, Carlos Andrés Masmela Pinilla:
Phitter: A library designed to streamline the process of fitting and analyzing probability distributions. 7625 - Gabriel S. Gerlero, Pablo A. Kler:
foamlib: A modern Python package for working with OpenFOAM. 7633 - Vijini Mallawaarachchi, Anuradha Wickramarachchi, Robert McArthur, Yapeng Lang, Katherine Caley, Gavin A. Huttley:
GraphBin-Tk: assembly graph-based metagenomic binning toolkit. 7713 - Jonas Pleyer, Christian Fleck:
cellular_raza: Cellular Agent-based Modeling from a Clean Slate. 7723 - Harrison Nicholls, Raymond Pierrehumbert, Tim Lichtenberg:
AGNI: A radiative-convective model for lava planet atmospheres. 7726 - Barnaby Dobson, Diego Alonso-Álvarez, Taher Chegini:
SWMManywhere: Synthesise Urban Drainage Network Models Anywhere in the World. 7729 - Kjetil Olsen Lye, Tobias Meyer Andersen, Atgeirr Flø Rasmussen, Jakob Torben:
gpu-ISTL - Extending OPM Flow with GPU Linear Solvers. 7740 - Thomas Helfer, Maxence Wangermez, Eric Simo, Thomas Nagel, Christian B. Silbermann, Lorenzo Riparbelli:
The MFrontGallery project. 7742 - Aristarchos Mavridis, Carmine D'Agostino:
NMRInversions.jl, a Julia package for time-domain Nuclear Magnetic Resonance. 7745 - Tian Tian, Lucas R. Timmerman, Shashikant Kumar, Benjamin M. Comer, Andrew J. Medford, Phanish Suryanarayana:
SPARC-X-API: Versatile Python Interface for Real-space Density Functional Theory Calculations. 7747 - Snir Meiri, Efi Efrati:
LCOI: Local crystalline orientation identifier using mask fitting implemented in MATLAB. 7748 - Colm Talbot, Amanda Farah, Shanika Galaudage, Jacob Golomb, Hui Tong:
GWPopulation: Hardware agnostic population inference for compact binaries and beyond. 7753 - Gavin Huttley, Katherine Caley, Robert McArthur:
diverse-seq: an application for alignment-free selecting and clustering biological sequences. 7765 - Greg Sallaberry, Zofia Kaczmarek, Peter McGill, Scott E. Perkins, William A. Dawson, Caitlin G. Begbie:
popclass: A Python Package for Classifying Microlensing Events. 7769 - John Coleman, Kellis Kincaid, Gerry L. Knapp, Benjamin Stump, Samuel Temple Reeve, Matthew Rolchigo, Alex Plotkowski:
AdditiveFOAM: A Continuum Multiphysics Code for Additive Manufacturing. 7770 - Gerd Specht, Clemens Schmid, Denise Kühnert, Arthur Kocher:
ggret: An R package for visualising and manipulating tree‑based phylogenetic networks. 7773 - Robbi Bishop-Taylor, Claire Phillips, Stephen Sagar, Vanessa Newey, Tyler Clark Sutterley:
eo-tides: Tide modelling tools for large-scale satellite Earth observation analysis. 7786 - Saransh Chopra, Henry Schreiner, Eduardo Rodrigues, Jonas Eschle, Jim Pivarski:
Vector: JIT-compilable mathematical manipulations of ragged Lorentz vectors. 7791 - Jacob Hartzer, Srikanth Saripalli:
EKF_CAL: Extended Kalman Filter-based Calibration and Localization. 7793 - Alexander V. Mantzaris:
BenchmarkDataNLP.jl: Synthetic Data Generation for NLP Benchmarking. 7844 - Fabian Schmidt, Nathan Weisz, Thomas Hartmann:
PyRASA - Spectral parametrization in python based on IRASA. 7852 - Kathleen M. Kuesters, Jessica M. Blanton, Jeffrey D. Kovach, Walter A. Blank, Lúcio M. Barbosa, Luciano K. Silva, Mitermayer G. Reis, Ronald E. Blanton:
pooledpeaks: Open-Source Fragment Scoring and Analysis Workflow for Population Genetic Analyses of Microsatellite Markers in Pooled Samples. 7853 - Moritz Leucke, Ramón L. Panadés-Barrueta, Ekin E. Bas, Dorothea Golze:
Analytic continuation component of the GreenX library: robust Padé approximants with symmetry constraints. 7859 - Silvia Barbiero, Charlotte Soneson, Prisca Liberali, Michael B. Stadler:
ez-zarr: A Python package for easy access and visualisation of OME-Zarr filesets. 7882 - Maximilian Weigert, Alexander Bauer, Jana Gauß, Asmik Nalmpatian:
fuzzyclara: Efficient Medoid-based Clustering Algorithms for Large and Fuzzy Data. 7887 - Logan Lang, Eduardo Hernández, Kamal Choudhary, Aldo H. Romero:
ParquetDB: A Lightweight Python Parquet-Based Database. 7932 - Clay J. Morrow, Anthony R. Ives:
remotePARTS: Spatiotemporal autoregression analyses for large data sets. 7937 - Gabriel Díaz Iturry, Marco C. Matthies, Guy Peer, Daniel Vedder:
AquaCrop.jl: A Process-Based Model of Crop Growth. 7944 - Zhaiyu Chen:
abspy: A Python package for 3D adaptive binary space partitioning and modeling. 7946 - Paula Rulff:
elfe3D v1.0.1: Modelling with the total electric field approach using finite elements in 3D. 7949 - Hannah Klion, Robert Hetland, Jean M. Sexton, Ann S. Almgren, Iulian R. Grindeanu, Kyle Hinson, Vijay Mahadevan:
REMORA: Regional Modeling of Oceans Refined Adaptively (built on AMReX). 7958 - Dominique Makowski, Mattan S. Ben-Shachar, Brenton M. Wiernik, Indrajeet Patil, Rémi Thériault, Daniel Lüdecke:
modelbased: An R package to make the most out of your statistical models through marginal means, marginal effects, and model predictions. 7969 - Romain Egele, Prasanna Balaprakash, Gavin M. Wiggins, Brett Eiffert:
DeepHyper: A Python Package for Massively Parallel Hyperparameter Optimization in Machine Learning. 7975 - Ola Tangen Kulseng, Stanley Miao, Franz G. Fuchs, Alexander J. Stasik:
QuantumReservoirPy: A Software Package for Time Series Prediction. 7994 - Agathe Senellart, Clément Chadebec, Stéphanie Allassonnière:
MultiVae: A Python package for Multimodal Variational Autoencoders on Partial Datasets. 7996 - Seb Dalgarno, John Boulanger, Ayla Pearson, Joe Thorley, Troy Hegel, Barry Nobert, Dave Hervieux:
bbousuite: A set of R packages to facilitate analysis of boreal caribou survival and recruitment data. 7997 - Michal Charemza:
OpenTTDLab: A Python framework for reproducible experiments using OpenTTD. 8014 - Dennis Klinkhammer:
AI-ANNE: (A) (N)eural (N)et for (E)xploration. 8039 - Sam Harrison, Cansu Uluseker, Patrizia Pfohl, Katherine Santizo, Joana Sipe, Brandon Lopez, Antonia Praetorius, Richard K. Cross, Gbotemi A. Adediran, Claus Svendsen, Wendel Wohlleben, Mark Wiesner:
FRAGMENT-MNP: A model of micro- and nanoplastic fragmentation in the environment. 8061 - Robert L. Baker, Colin Smith, Sarah E. Wright, Issac Quevedo, Kristin Vanderbilt, Carl Boettiger, Judd M. Patterson, Joe DeVivo:
NPSdataverse: a suite of R packages for data processing, authoring Ecological Metadata Language metadata, checking data-metadata congruence, and accessing data. 8066 - Marilyn De Graeve, Wout Bittremieux, Thomas Naake, Carolin Huber, Matthias Anagho-Mattanovich, Nils Hoffmann, Pierre Marchal, Victor Chrone, Philippine Louail, Helge Hecht, Michael Witting, Johannes Rainer:
SpectriPy: Enhancing Cross-Language Mass Spectrometry Data Analysis with R and Python. 8070 - Aslan Noorghasemi, Christopher McComb:
KeepDelta: A Python Library for Human-Readable Data Differencing. 8075 - Maxim Van de Wynckel, Beat Signer:
OpenHPS: A Modular Framework to Facilitate the Development of FAIR Positioning Systems. 8113 - Stefan Kopecz, Joshua Lampert, Hendrik Ranocha:
PositiveIntegrators.jl: A Julia library of positivity-preserving time integration methods. 8130 - Milan Rother:
PathSim - A System Simulation Framework. 8158 - Lars Ivar Hatledal:
Ecos: An accessible and intuitive co-simulation framework. 8182 - Alexander V. Mantzaris:
LMDiskANN.jl: An Implementation of the Low Memory Disk Approximate Nearest Neighbors Search Algorithm. 8199 - Alasdair Warwick, Benjamin Zuckerman, Chuin Ying Ung, Robert Luben, Abraham Olvera Barrios:
gtexr: A convenient R interface to the Genotype-Tissue Expression (GTEx) Portal API. 8249 - Alexander Kolpakov, Igor Rivin:
DiRe - JAX: A JAX based Dimensionality Reduction Algorithm for Large-scale Data. 8264
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