J. Open Source Softw.

Publications

volume 9, number 96, 2024

Frank Male
Pywaterflood: Well connectivity analysis through capacitance-resistance modeling. J. Open Source Softw. 9 (96) (2024)
Rohini S. Gupta, Chris R. Vernon, Travis Thurber, David F. Gold, Zachary M. Hirsch, Antonia Hadjimichael, Patrick M. Reed
statemodify: a Python framework to facilitate accessible exploratory modeling for discovering drought vulnerabilities. J. Open Source Softw. 9 (96) (2024)
Martin Kuric, Regina Ebert
plotastic: Bridging Plotting and Statistics in Python. J. Open Source Softw. 9 (96) (2024)
Anselm Hudde
greeks: Sensitivities of Prices of Financial Options and Implied Volatilities. J. Open Source Softw. 9 (96) (2024)
Eric Lindgren, Magnus Rahm, Erik Fransson, Fredrik Eriksson, Nicklas Österbacka, Zheyong Fan, Paul Erhart
calorine: A Python package for constructing and sampling neuroevolution potential models. J. Open Source Softw. 9 (96) (2024)
Andrew Gard, Alexia Myers, Irene Luwabelwa
The fqar package: R tools for analyzing floristic quality assessment data. J. Open Source Softw. 9 (96) (2024)
Sadegh Mohammadi
Pyheartlib: A Python package for processing electrocardiogram signals. J. Open Source Softw. 9 (96) (2024)
Pierre J. Walker, Andrés Riedemann, Zhen-Gang Wang
GCIdentifier.jl: A Julia package for identifying molecular fragments from SMILES. J. Open Source Softw. 9 (96) (2024)
Josu C. Aurrekoetxea, Jamie Bamber, Sam E. Brady, Katy Clough, Thomas Helfer, James Marsden, Miren Radia, Dina Traykova, Zipeng Wang
GRDzhadzha: A code for evolving relativistic matter on analytic metric backgrounds. J. Open Source Softw. 9 (96) (2024)
Giulia Crocioni, Dani L. Bodor, Coos Baakman, Farzaneh M. Parizi, Daniel-T. Rademaker, Gayatri Ramakrishnan, Sven van der Burg, Dario F. Marzella, João M. C. Teixeira, Li C. Xue
DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning. J. Open Source Softw. 9 (96) (2024)
Moritz L. Obenauer, Kai N. Spauszus, Pol Besenius, Friederike Schmid
Project RACCOON: Automated construction of PDB files for polymers and polymer peptide conjugates. J. Open Source Softw. 9 (96) (2024)
Indrajeet Haldar
The plebeian Graph Library: A WebGL based network visualisation and diagnostics package. J. Open Source Softw. 9 (96) (2024)
Seán R. Kavanagh, Alexander G. Squires, Adair Nicolson, Irea Mosquera-Lois, Alex M. Ganose, Bonan Zhu, Katarina Brlec, Aron Walsh, David O. Scanlon
doped: Python toolkit for robust and repeatable charged defect supercell calculations. J. Open Source Softw. 9 (96) (2024)
Xinye Chen, Stefan Güttel
fABBA: A Python library for the fast symbolic approximation of time series. J. Open Source Softw. 9 (96) (2024)
Guillaume Dalle
HiddenMarkovModels.jl: generic, fast and reliable state space modeling. J. Open Source Softw. 9 (96) (2024)
Étienne Lac, Guy Spiegeleer, Adrien Delsalle, Frédéric Collonval, Duc-Trung Lê, Mathias Malandain
CoSApp: a Python library to create, simulate and design complex systems. J. Open Source Softw. 9 (96) (2024)
Nicolas Frerebeau
aion: An R Package to Represent Archaeological Time Series. J. Open Source Softw. 9 (96) (2024)
Kevin D. Murray, Justin O. Borevitz, Detlef Weigel, Norman Warthmann
Acanthophis: a comprehensive plant hologenomics pipeline. J. Open Source Softw. 9 (96) (2024)
Bhavin S. Patel, Peter Hill, Liam Pattinson, Maurizio Giacomin, Arkaprava Bokshi, Daniel Kennedy, Harry G. Dudding, Jason. F. Parisi, Tom F. Neiser, Ajay C. Jayalekshmi, David Dickinson, Juan Ruiz Ruiz
Pyrokinetics - A Python library to standardise gyrokinetic analysis. J. Open Source Softw. 9 (96) (2024)
Alexander Jüstel, Frank Strozyk
PyHeatDemand - Processing Tool for Heat Demand Data. J. Open Source Softw. 9 (96) (2024)
David J. McKenna, Evan F. Keane, Peter T. Gallagher, Joe McCauley
udpPacketManager: An International LOFAR Station Data (Pre-)Processor. J. Open Source Softw. 9 (96) (2024)
Arianna I. Renzini, Alba Romero-Rodriguez, Colm Talbot, Max Lalleman, Shivaraj Kandhasamy, Kevin Turbang, Sylvia Biscoveanu, Katarina Martinovic, Patrick M. Meyers, Leo Tsukada, Kamiel Janssens, Derek Davis, Andrew Matas, Philip Charlton, Guo-chin Liu, Irina Dvorkin
pygwb: a Python-based library for gravitational-wave background searches. J. Open Source Softw. 9 (96) (2024)
J. Michael Johnson, Shahab Afshari, Arash Modaresi Rad
AHGestimation: An R package for computing robust, mass preserving hydraulic geometries and rating curves. J. Open Source Softw. 9 (96) (2024)
Simon Dirmeier
Surjectors: surjection layers for density estimation with normalizing flows. J. Open Source Softw. 9 (96) (2024)
Brenda Praggastis, Sinan Aksoy, Dustin Arendt, Mark Bonicillo, Cliff A. Joslyn, Emilie Purvine, Madelyn Shapiro, Ji Young Yun
HyperNetX: A Python package for modeling complex network data as hypergraphs. J. Open Source Softw. 9 (96) (2024)
Gabriele Ottino, Daniele Panico, Daniele Tomatis, Pierre-Alexandre Pantel
lbh15: a Python package for standard use and implementation of physical data of heavy liquid metals used in nuclear reactors. J. Open Source Softw. 9 (96) (2024)
Hendrik Mann
dropout: an R Package for Addressing Dropouts, Missing Values, and Sectional Challenges in Survey Data Analysis. J. Open Source Softw. 9 (96) (2024)
Bartholomew Andrews
HofstadterTools: A Python package for analyzing the Hofstadter model. J. Open Source Softw. 9 (96) (2024)
Shuang Song, Shuai Wang, Chentai Jiao, Elías José Mantilla Ibarra
ABSESpy: An agent-based modeling framework for social-ecological systems. J. Open Source Softw. 9 (96) (2024)
Caleb Weinreb, Mohammed Abdal Monium Osman, Maya Jay, Sandeep R. Datta
Systems Neuro Browser (SNUB). J. Open Source Softw. 9 (96) (2024)
Nathan Musoke
UltraDark.jl: A Julia package for simulation of cosmological scalar fields. J. Open Source Softw. 9 (96) (2024)
Dmitry Ustalov, Nikita Pavlichenko, Boris Tseitlin
Learning from Crowds with Crowd-Kit. J. Open Source Softw. 9 (96) (2024)
Benjamin Lansdell, Abbas Shirinifard
Ethome: tools for machine learning of animal behavior. J. Open Source Softw. 9 (96) (2024)
Thomas Berlok, Léna Jlassi, Ewald Puchwein, Troels Haugbølle
Paicos: A Python package for analysis of (cosmological) simulations performed with Arepo. J. Open Source Softw. 9 (96) (2024)
Oskar Laverny, Santiago Jiménez
Copulas.jl: A fully Distributions.jl-compliant copula package. J. Open Source Softw. 9 (96) (2024)
Meng Cai, Yingjie Li, Dirk Colbry, Veronica F. Frans, Yuqian Zhang
seesus: a social, environmental, and economic sustainability classifier for Python. J. Open Source Softw. 9 (96) (2024)
Patrick Quéméré
Fitspy: A Python package for spectral decomposition. J. Open Source Softw. 9 (96) (2024)
Akkarapakam Suneesh Jacob, Rituparna Datta
Automatic Computation for Robot Design (ACRoD): A Python package for numerical calculation of Jacobian of a robot at a given configuration around a specified end-effector point. J. Open Source Softw. 9 (96) (2024)
Gurjeet Sangra Singh, Luigi Acerbi
PyBADS: Fast and robust black-box optimization in Python. J. Open Source Softw. 9 (96) (2024)
Andrea Spinelli, Timoleon Kipouros
PDOPT: A Python library for Probabilistic Design space exploration and OPTimisation. J. Open Source Softw. 9 (96) (2024)
Joanna Piper Morgan, Ilham Variansyah, Samuel L. Pasmann, Kayla B. Clements, Braxton Cuneo, Alexander Mote, Charles Goodman, Caleb Shaw, Jordan Northrop, Rohan Pankaj, Ethan Lame, Benjamin Whewell, Ryan G. McClarren, Todd S. Palmer, Lizhong Chen, Dmitriy Y. Anistratov, C. T. Kelley, Camille J. Palmer, Kyle E. Niemeyer
Monte Carlo / Dynamic Code (MC/DC): An accelerated Python package for fully transient neutron transport and rapid methods development. J. Open Source Softw. 9 (96) (2024)
Aakash Ashok Naik, Katharina Ueltzen, Christina Ertural, Adam J. Jackson, Janine George
LobsterPy: A package to automatically analyze LOBSTER runs. J. Open Source Softw. 9 (96) (2024)
Fred Shone, Theodore Chatziioannou, Bryn Pickering, Kasia Kozlowska, Michael Fitzmaurice
PAM: Population Activity Modeller. J. Open Source Softw. 9 (96) (2024)
Yu Wang, Emma R. Cobian, Jubilee Lee, Fang Liu, Jonathan D. Hauenstein, Daniele E. Schiavazzi
LINFA: a Python library for variational inference with normalizing flow and annealing. J. Open Source Softw. 9 (96) (2024)
Carson Farmer, Héctor Medina
Hyperelastics.jl: A Julia package for hyperelastic material modelling with a large collection of models. J. Open Source Softw. 9 (96) (2024)
Andres R. Tejedor, Ignacio Sanchez-Burgos, Eduardo Sanz, Carlos Vega, Felipe J. Blas, Ruslan L. Davidchack, Nicodemo Di Pasquale, Jorge Ramirez, Jorge R. Espinosa
Mold: a LAMMPS package to compute interfacial free energies and nucleation rates. J. Open Source Softw. 9 (96) (2024)
Alexander D. Fuchs, Johannes A. F. Lehmeyer, Heinz Junkes, Heiko B. Weber, Michael Krieger
NOMAD CAMELS: Configurable Application for Measurements, Experiments and Laboratory Systems. J. Open Source Softw. 9 (96) (2024)
Metin San
ZodiPy: A Python package for zodiacal light simulations. J. Open Source Softw. 9 (96) (2024)
Tyler K. Chafin, Steven M. Mussmann, Marlis R. Douglas, Michael E. Douglas
autoStreamTree: Genomic variant data fitted to geospatial networks. J. Open Source Softw. 9 (96) (2024)
Matthew Peres Tino, Abbas Yusuf Abdulaziz, Robert Suderman, Thomas Akdeniz, Nasser Mohieddin Abukhdeir
Shapelets: A Python package implementing shapelet functions and their applications. J. Open Source Softw. 9 (96) (2024)