Table of contents for issues of Journal of Open Research Software

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Volume 1, Number 1, October 08, 2013
Volume 2, Number 1, July 09, 2014
Volume 3, Number 1, November 23, 2015
Volume 4, Number 1, November 25, 2016
Volume 5, Number 1, January 09, 2017
Volume 6, Number 1, January 08, 2018
Volume 7, Number 1, January 07, 2019
Volume 8, Number 1, January 15, 2020
Volume 9, Number 1, February 02, 2021
Volume 10, Number 1, March 02, 2022
Volume 11, Number 1, 2023


Journal of Open Research Software
Volume 1, Number 1, October 08, 2013

             Muhammad Adnan and   
             Alex Singleton and   
                   Paul Longley   \pkgOACoder: Postcode Coding Tool  . . . e5
              Luis Pedro Coelho   \pkgMahotas: Open source software for
                                  scriptable computer vision . . . . . . . e3
               Sergey Fomel and   
                  Paul Sava and   
                  Ioan Vlad and   
                   Yang Liu and   
            Vladimir Bashkardin   \pkgMadagascar: open-source software
                                  project for multidimensional data
                                  analysis and reproducible computational
                                  experiments  . . . . . . . . . . . . . . e8
           Daniel Graziotin and   
              Pekka Abrahamsson   A Web-based modeling tool for the SEMAT
                                  Essence theory of software engineering   e4
                Derek Groen and   
              Steven Rieder and   
          Simon Portegies Zwart   \pkgMPWide: a light-weight library for
                                  efficient message passing over wide area
                                  networks . . . . . . . . . . . . . . . . e9
               Laura Luyten and   
         Frederik Van Cappellen   \pkgExpTimer: timer software to
                                  facilitate complex, multi-step
                                  procedures . . . . . . . . . . . . . . . e2
          Sarunas Marciuska and   
              Pekka Abrahamsson   \pkgFeature Usage Explorer: Usage
                                  Monitoring and Visualization Tool in
                                  HTML5 Based Applications . . . . . . . . e7
         Konstantin Nikolic and   
                  Joaquim Loizu   \bionameDrosophila Photo-transduction
                                  Simulator  . . . . . . . . . . . . . . . e1
            Thorsten Wagner and   
             Hans-Gerd Lipinski   \pkgIJBlob: An ImageJ Library for
                                  Connected Component Analysis and Shape
                                  Analysis . . . . . . . . . . . . . . . . e6


Journal of Open Research Software
Volume 2, Number 1, July 09, 2014

              Brian Blanton and   
                 Chris Lenhardt   A Scientist's Perspective on Sustainable
                                  Scientific Software  . . . . . . . . . . e17
                    Karl Broman   Fourteen Years of \pkgR/qtl: Just Barely
                                  Sustainable  . . . . . . . . . . . . . . e11
                 Sou-Cheng Choi   \pkgMINRES-QLP Pack and Reliable
                                  Reproducible Research via Supportable
                                  Scientific Software  . . . . . . . . . . e22
               Jeremy Cohen and   
             Chris Cantwell and   
             Neil Chue Hong and   
                David Moxey and   
        Malcolm Illingworth and   
              Andrew Turner and   
            John Darlington and   
                Spencer Sherwin   Simplifying the Development, Use and
                                  Sustainability of HPC Software . . . . . e16
                Anshu Dubey and   
             Brian Van Straalen   Experiences from Software Engineering of
                                  Large Scale AMR Multiphysics Code
                                  Frameworks . . . . . . . . . . . . . . . e7
                Anshu Dubey and   
               Steve Brandt and   
             Richard Brower and   
                Merle Giles and   
               Paul Hovland and   
                Donald Lamb and   
         Frank Löffler and   
              Boyana Norris and   
               Brian O'Shea and   
              Claudio Rebbi and   
                  Marc Snir and   
              Rajeev Thakur and   
              Petros Tzeferacos   Software Abstractions and Methodologies
                                  for HPC Simulation Codes on Future
                                  Architectures  . . . . . . . . . . . . . e14
            Matthew Forster and   
               Lyn Paterson and   
                 Robert Forster   \pkgLIIS: A web-based system for culture
                                  collections and sample annotation  . . . e2
               Derek Gaston and   
              John Peterson and   
               Cody Permann and   
                David Andrs and   
           Andrew Slaughter and   
                   Jason Miller   Continuous Integration for Concurrent
                                  Computational Framework and Application
                                  Development  . . . . . . . . . . . . . . e10
                 Jeffrey Girard   \pkgCARMA: Software for Continuous
                                  Affect Rating and Media Annotation . . . e5
                  Abhisek Hazra   \pkgImage Enhancer: A Graphic Editor to
                                  Apply Numerous Effects in Digital Image  e31
                    Adam Hughes   \pkgpyparty: Intuitive Particle
                                  Processing in Python . . . . . . . . . . e26
           Sebastian Illing and   
          Christopher Kadow and   
               Kunst Oliver and   
                 Ulrich Cubasch   \pkgMurCSS: A Tool for Standardized
                                  Evaluation of Decadal Hindcast Systems   e24
           Christian Jacobs and   
           Alexandros Avdis and   
              Gerard Gorman and   
                Matthew Piggott   \pkgPyRDM: A Python-based library for
                                  automating the management and online
                                  publication of scientific software and
                                  data . . . . . . . . . . . . . . . . . . e28
                  Martin Jucker   Scientific Visualisation of Atmospheric
                                  Data with \pkgParaView . . . . . . . . . e4
                Daniel Katz and   
                  David Proctor   A Framework for Discussing e-Research
                                  Infrastructure Sustainability  . . . . . e13
                Daniel Katz and   
             Sou-Cheng Choi and   
                Hilmar Lapp and   
           Ketan Maheshwari and   
         Frank Löffler and   
               Matthew Turk and   
             Marcus Hanwell and   
        Nancy Wilkins-Diehr and   
         James Hetherington and   
              James Howison and   
               Shel Swenson and   
            Gabrielle Allen and   
                Anne Elster and   
             Bruce Berriman and   
                  Colin Venters   Summary of the First Workshop on
                                  Sustainable Software for Science:
                                  Practice and Experiences (WSSSPE1) . . . e6
                    Daniel Katz   Transitive Credit as a Means to Address
                                  Social and Technological Concerns
                                  Stemming from Citation and Attribution
                                  of Digital Products  . . . . . . . . . . e20
                 W Lenhardt and   
              Stanley Ahalt and   
              Brian Blanton and   
       Laura Christopherson and   
                    Ray Idaszak   Data Management Lifecycle and Software
                                  Lifecycle Management in the Context of
                                  Conducting Science . . . . . . . . . . . e15
         Frank Löffler and   
              Steven Brandt and   
            Gabrielle Allen and   
                 Erik Schnetter   \pkgCactus: Issues for Sustainable
                                  Simulation Software  . . . . . . . . . . e12
            Saundra Manning and   
                    Lior Shamir   \pkgCHLOE: A Software Tool for Automatic
                                  Novelty Detection in Microscopy Image
                                  Datasets . . . . . . . . . . . . . . . . e25
               Reagan Moore and   
            Arcot Rajasekar and   
                         Hao Xu   Extensible Generic Data Management
                                  Software . . . . . . . . . . . . . . . . e9
              Shane Mueller and   
                 Alena Esposito   Computerized Testing Software for
                                  Assessing Interference Suppression in
                                  Children and Adults: The Bivalent Shape
                                  Task (BST) . . . . . . . . . . . . . . . e3
             Nicola Osborne and   
            George Hamilton and   
               Stuart Macdonald   Historical Post Office Directory Parser
                                  (POD Parser) Software From the
                                  AddressingHistory Project  . . . . . . . e23
            Christian Oxvig and   
           Patrick Pedersen and   
            Thomas Arildsen and   
      Jan Òstergaard and   
                  Torben Larsen   \pkgMagni: A Python Package for
                                  Compressive Sampling and Reconstruction
                                  of Atomic Force Microscopy Images  . . . e29
                    Nial Peters   \pkgAvoPlot: An extensible scientific
                                  plotting tool based on \pkgmatplotlib    e1
                Ikaro Silva and   
                   George Moody   An Open-source Toolbox for Analysing and
                                  Processing \pkgPhysioNet Databases in
                                  MATLAB and Octave  . . . . . . . . . . . e27
           Victoria Stodden and   
                  Sheila Miguez   Best Practices for Computational
                                  Science: Software Infrastructure and
                                  Environments for Reproducible and
                                  Extensible Research  . . . . . . . . . . e21
          William Thielicke and   
                  Eize Stamhuis   \pkgPIVlab --- Towards User-friendly,
                                  Affordable and Accurate Digital Particle
                                  Image Velocimetry in MATLAB  . . . . . . e30
               Erik Trainer and   
     Chalalai Chaihirunkarn and   
                 James Herbsleb   The Big Effects of Short-term Efforts:
                                  Mentorship and Code Integration in Open
                                  Source Scientific Software . . . . . . . e18
              Colin Venters and   
                  Lydia Lau and   
          Michael Griffiths and   
             Violeta Holmes and   
                Rupert Ward and   
               Caroline Jay and   
           Charlie Dibsdale and   
                         Jie Xu   The Blind Men and the Elephant: Towards
                                  an Empirical Evaluation Framework for
                                  Software Sustainability  . . . . . . . . e8
               Lynn Zentner and   
            Michael Zentner and   
        Victoria Farnsworth and   
           Michael McLennan and   
           Krishna Madhavan and   
                Gerhard Klimeck   \tt nanoHUB.org: Experiences and
                                  Challenges in Software Sustainability
                                  for a Large Scientific Community . . . . e19


Journal of Open Research Software
Volume 3, Number 1, November 23, 2015

                Alice Allen and   
                   Judy Schmidt   Looking before Leaping: Creating a
                                  Software Registry  . . . . . . . . . . . e15
                     Megan Argo   The \pkge-MERLIN Data Reduction Pipeline e2
               Iain Bethune and   
                    Yves Gallot   \pkgGenefer: Programs for Finding Large
                                  Probable Generalized Fermat Primes . . . e10
             Carl Boettiger and   
          Scott Chamberlain and   
                Edmund Hart and   
                    Karthik Ram   Building Software, Building Community:
                                  Lessons from the \pkgrOpenSci Project    e8
                 Edem Dovlo and   
                Natalie Baddour   Toolbox for the Computation of $2$D
                                  Fourier Transforms in Polar Coordinates
                                  via Maple  . . . . . . . . . . . . . . . e3
            Robert R. Downs and   
    W. Christopher Lenhardt and   
              Erin Robinson and   
                Ethan Davis and   
                 Nicholas Weber   Community Recommendations for
                                  Sustainable Scientific Software  . . . . e11
              Morteza Haeri and   
                 Mohammad Haeri   ImageJ Plugin for Analysis of Porous
                                  Scaffolds used in Tissue Engineering . . e1
                Adam Hughes and   
                Zhaowen Liu and   
                      M. Reeves   \pkgScikit-spectra: Explorative
                                  Spectroscopy in Python . . . . . . . . . e6
             Daniel S. Katz and   
                 Arfon M. Smith   Transitive Credit and \pkgJSON-LD  . . . e7
           Marlon E. Pierce and   
               Suresh Marru and   
                 Chris Mattmann   Patching It Up, Pulling It Forward . . . e12
        Andrew E. Slaughter and   
           John W. Peterson and   
            Derek R. Gaston and   
            Cody J. Permann and   
                David Andrs and   
                Jason M. Miller   Continuous Integration for Concurrent
                                  MOOSE Framework and Application
                                  Development on GitHub  . . . . . . . . . e14
              J. S. Spencer and   
                N. S. Blunt and   
                W. A. Vigor and   
            Fionn D. Malone and   
           W. M. C. Foulkes and   
          James J. Shepherd and   
                  A. J. W. Thom   Open-Source Development Experiences in
                                  Scientific Software: The HANDE Quantum
                                  Monte Carlo Project  . . . . . . . . . . e9
                James Stone and   
                     John Towse   A Working Memory Test Battery:
                                  Java-Based Collection of Seven Working
                                  Memory Tasks . . . . . . . . . . . . . . e5
         Isuru Suriarachchi and   
                  Quan Zhou and   
                     Beth Plale   \pkgKomadu: A Capture and Visualization
                                  System for Scientific Data Provenance    e4
             John G. Wright and   
              B. Sriram Shastry   \pkgDiracQ: A Package for Algebraic
                                  Manipulation of Non-Commuting Quantum
                                  Variables  . . . . . . . . . . . . . . . e13


Journal of Open Research Software
Volume 4, Number 1, November 25, 2016

                Ayala Allon and   
                      Roy Luria   \pkgprepdat --- An R Package for
                                  Preparing Experimental Data for
                                  Statistical Analysis . . . . . . . . . . e43
        Christopher Beckham and   
                  Mark Hall and   
                     Eibe Frank   \pkgWekaPyScript: Classification,
                                  Regression, and Filter Schemes for WEKA
                                  Implemented in Python  . . . . . . . . . e33
              Nathan Bryant and   
                Jeremy Wildfire   \pkgWebcharts --- A Web-based Charting
                                  Library for Custom Interactive Data
                                  Visualization  . . . . . . . . . . . . . e29
             Michael Crusoe and   
                       C. Brown   Channeling Community Contributions to
                                  Scientific Software: A Sprint Experience e27
             Michael Crusoe and   
                       C. Brown   Walking the Talk: Adopting and Adapting
                                  Sustainable Scientific Software
                                  Development processes in a Small Biology
                                  Lab  . . . . . . . . . . . . . . . . . . e44
               Adrian Daerr and   
                   Adrien Mogne   \pkgPendent\_Drop: An ImageJ Plugin to
                                  Measure the Surface Tension from an
                                  Image of a Pendent Drop  . . . . . . . . e3
                  Andrew Dawson   \pkgeofs: A Library for EOF Analysis of
                                  Meteorological, Oceanographic, and
                                  Climate Data . . . . . . . . . . . . . . e14
                  Andrew Dawson   \pkgWindspharm: A High-Level Library for
                                  Global Wind Field Computations Using
                                  Spherical Harmonics  . . . . . . . . . . e31
          Josselin Defrance and   
       Caroline Lema\^\itre and   
                 Rabih Ajib and   
          Jessica Benedicto and   
             Emilien Mallet and   
       Rémi Poll\`es and   
         Jean-Pierre Plumey and   
         Martine Mihailovic and   
           Emmanuel Centeno and   
         Cristian Cirac\`\i and   
                David Smith and   
                 Antoine Moreau   \pkgMoosh: A Numerical Swiss Army Knife
                                  for the Optics of Multilayers in
                                  Octave/Matlab  . . . . . . . . . . . . . e13
       Andrés Demski and   
          Mariano Llamedo Soria   \pkgecg-kit: a Matlab Toolbox for
                                  Cardiovascular Signal Processing . . . . e8
               Nuno Fachada and   
                Vitor Lopes and   
                Rui Martins and   
                 Agostinho Rosa   PerfAndPubTools --- Tools for Software
                                  Performance Analysis and Publishing of
                                  Results  . . . . . . . . . . . . . . . . e18
               Nuno Fachada and   
                Vitor Lopes and   
                Rui Martins and   
                 Agostinho Rosa   SimOutUtils --- Utilities for Analyzing
                                  Time Series Simulation Output  . . . . . e38
                 Damien Farrell   \pkgDataExplore: An Application for
                                  General Data Analysis in Research and
                                  Education  . . . . . . . . . . . . . . . e9
            Daniel P. Foose and   
           Ioana E. P. Sizemore   \pkgVespucci: A Free, Cross-Platform
                                  Tool for Spectroscopic Data Analysis and
                                  Imaging  . . . . . . . . . . . . . . . . e4
         James Gebbie-Rayet and   
             Gareth Shannon and   
         Hannes H. Loeffler and   
            Charles A. Laughton   \pkgLongbow: A Lightweight Remote Job
                                  Submission Tool  . . . . . . . . . . . . e1
       Henrich Glaser-Opitz and   
Kristína Budajová   \pkgMATH: A Scientific Tool for
                                  Numerical Methods Calculation and
                                  Visualization  . . . . . . . . . . . . . e6
                     Paul Govan   \pkgeAnalytics: Dynamic Web-based
                                  Analytics for the Energy Industry  . . . e45
                    Mads Hansen   \pkgPyVDT: A PsychoPy-Based Visual
                                  Sequence Detection Task  . . . . . . . . e22
            Jonathan Helmus and   
                   Scott Collis   The Python ARM Radar Toolkit
                                  (\pkgPy-ART), a Library for Working with
                                  Weather Radar Data in the Python
                                  Programming Language . . . . . . . . . . e25
               Brett Hewitt and   
               Moi Hoon Yap and   
                    Robyn Grant   Manual Whisker Annotator (MWA): A
                                  Modular Open-Source Tool . . . . . . . . e16
                Shuai Huang and   
               Yaqiang Wang and   
                 Yuanli Xie and   
                  Peng Zhao and   
            Johannes Lüers   \pkgOutlierFlag: A Tool for Scientific
                                  Data Quality Control by Outlier Data
                                  Flagging . . . . . . . . . . . . . . . . e20
           Sebastian Illing and   
          Christopher Kadow and   
               Oliver Kunst and   
                 Ulrich Cubasch   Correction: \pkgMurCSS: A Tool for
                                  Standardized Evaluation of Decadal
                                  Hindcast Systems . . . . . . . . . . . . e24
             Daniel S. Katz and   
          Sou-Cheng T. Choi and   
        Nancy Wilkins-Diehr and   
             Neil Chue Hong and   
           Colin C. Venters and   
              James Howison and   
             Frank Seinstra and   
              Matthew Jones and   
          Karen A. Cranston and   
            Thomas L. Clune and   
        Miguel de Val-Borro and   
               Richard Littauer   Report on the Second Workshop on
                                  Sustainable Software for Science:
                                  Practice and Experiences (WSSSPE2) . . . e7
                Daniel Katz and   
             Sou-Cheng Choi and   
              Kyle Niemeyer and   
         James Hetherington and   
         Frank Löffler and   
                 Dan Gunter and   
                Ray Idaszak and   
              Steven Brandt and   
                Mark Miller and   
             Sandra Gessing and   
                 Nick Jones and   
                  Nic Weber and   
               Suresh Marru and   
            Gabrielle Allen and   
       Birgit Penzenstadler and   
              Colin Venters and   
                Ethan Davis and   
             Lorraine Hwang and   
              Ilian Todorov and   
                Abani Patra and   
            Miguel de Val-Borro   Report on the Third Workshop on
                                  Sustainable Software for Science:
                                  Practice and Experiences (WSSSPE3) . . . e37
                   Jared Kibele   Benthic Photo Survey: Software for
                                  Geotagging, Depth-tagging, and
                                  Classifying Photos from Survey Data and
                                  Producing Shapefiles for Habitat Mapping
                                  in GIS . . . . . . . . . . . . . . . . . e10
             Vincent Knight and   
              Owen Campbell and   
                Marc Harper and   
              Karol Langner and   
             James Campbell and   
            Thomas Campbell and   
                Alex Carney and   
             Martin Chorley and   
     Cameron Davidson-Pilon and   
             Kristian Glass and   
          Nikoleta Glynatsi and   
       Tomás Ehrlich and   
               Martin Jones and   
      Georgios Koutsovoulos and   
               Holly Tibble and   
         Jochen Müller and   
             Geraint Palmer and   
              Piotr Petunov and   
                Paul Slavin and   
            Timothy Standen and   
             Luis Visintini and   
                    Karl Molden   An Open Framework for the Reproducible
                                  Study of the Iterated Prisoner's Dilemma e35
              Anton Korosov and   
              Morten Hansen and   
        Knut-Frode Dagestad and   
             Asuka Yamakawa and   
           Aleksander Vines and   
                  Maik Riechert   \pkgNansat: a Scientist-Orientated
                                  Python Package for Geospatial Data
                                  Processing . . . . . . . . . . . . . . . e39
                   Nir Krakauer   \pkgSeFo: A Package for Generating
                                  Probabilistic Forecasts from NMME
                                  Predictive Ensembles . . . . . . . . . . e19
           Alastair Lansley and   
              Peter Vamplew and   
               Philip Smith and   
                  Cameron Foale   \pkgCaliko: An Inverse Kinematics
                                  Software Library Implementation of the
                                  FABRIK Algorithm . . . . . . . . . . . . e36
             Bryan Lougheed and   
               Stephen Obrochta   \pkgMatCal: Open Source Bayesian
                                  $^{14}$C Age Calibration in Matlab . . . e42
                 Thor Markussen   \pkgParchar --- Characterization of
                                  Suspended Particles Through Image
                                  Processing in Matlab . . . . . . . . . . e26
               Yosef Meller and   
                  Alex Liberzon   Particle Data Management Software for
                                  $3$D Particle Tracking Velocimetry and
                                  Related Applications --- The
                                  \pkgFlowtracks Package . . . . . . . . . e23
                    Joris Meurs   Flow Rates in Liquid Chromatography, Gas
                                  Chromatography and Supercritical Fluid
                                  Chromatography: A Tool for Optimization  e32
         Birgit Möller and   
          Markus Glaß and   
               Danny Misiak and   
                   Stefan Posch   MiToBo --- A Toolbox for Image
                                  Processing and Analysis  . . . . . . . . e17
                 Akio Onogi and   
                Hiroyoshi Iwata   \pkgVIGoR: Variational Bayesian
                                  Inference for Genome-Wide Regression . . e11
                  Matti Pastell   CowLog --- Cross-Platform Application
                                  for Coding Behaviours from Video . . . . e15
               Fabio Pavesi and   
                Anna Basoni and   
          Cristiano Fugazza and   
            Stefano Menegon and   
         Alessandro Oggioni and   
                Monica Pepe and   
           Paolo Tagliolato and   
                  Paola Carrara   EDI --- A Template-Driven Metadata
                                  Editor for Research Data . . . . . . . . e40
                Philip Rinn and   
                 Pedro Lind and   
      Matthias Wächter and   
                 Joachim Peinke   The Langevin Approach: An R Package for
                                  Modeling Markov Processes  . . . . . . . e34
       Abel Soares Siqueira and   
     Raniere Costa da Silva and   
             Luiz-Rafael Santos   \pkgPerprof-py: A Python Package for
                                  Performance Profile of Mathematical
                                  Optimization Software  . . . . . . . . . e12
                     Andy Stock   Open Source Software for Mapping Human
                                  Impacts on Marine Ecosystems with an
                                  Additive Model . . . . . . . . . . . . . e21
         Maarten van Gompel and   
            Antal van den Bosch   Efficient $n$-gram, Skipgram and
                                  Flexgram Modelling with \pkgColibri Core e30
               Mark Vousden and   
       Marc-Antonio Bisotti and   
          Maximilian Albert and   
                   Hans Fangohr   Virtual Micromagnetics: A Framework for
                                  Accessible and Reproducible
                                  Micromagnetic Simulation . . . . . . . . e41
                 Bas Wijnen and   
         Gerald C. Anzalone and   
      Amberlee S. Haselhuhn and   
              P. G. Sanders and   
               Joshua M. Pearce   Free and Open-source Control Software
                                  for $3$-D Motion and Processing  . . . . e2
                 Hang Xiong and   
                  Pin Xiong and   
                      Hui Xiong   \pkgKAMG: A Tool for Converting Blood
                                  Ties and Affinity Ties into Adjacency
                                  Matrices . . . . . . . . . . . . . . . . e28
           Fabian Zeitvogel and   
                    Martin Obst   \pkgScatterJn: An ImageJ Plugin for
                                  Scatterplot-Matrix Analysis and
                                  Classification of Spatially Resolved
                                  Analytical Microscopy Data . . . . . . . e5


Journal of Open Research Software
Volume 5, Number 1, January 09, 2017

               Richard Otis and   
                     Zi-Kui Liu   \pkgpycalphad: CALPHAD-based
                                  Computational Thermodynamics in Python   1
              Mark Heckmann and   
                     Lukas Burk   \pkgGridsampler --- A Simulation Tool to
                                  Determine the Required Sample Size for
                                  Repertory Grid Studies . . . . . . . . . 2
             Pierre de Buyl and   
               Mu-Jie Huang and   
                 Laurens Deprez   \pkgRMPCDMD: Simulations of Colloids
                                  with Coarse-grained Hydrodynamics,
                                  Chemical Reactions and External Fields   3
            Natalie Baddour and   
                  Ugo Chouinard   Matlab Code for the Discrete Hankel
                                  Transform  . . . . . . . . . . . . . . . 4
             Willem Eerland and   
                  Simon Box and   
  András Sóbester   Cambridge Rocketry Simulator --- A
                                  Stochastic Six-Degrees-of-Freedom Rocket
                                  Flight Simulator . . . . . . . . . . . . 5
                   Yves Bas and   
                 Didier Bas and   
    Jean-François Julien   \pkgTadarida: A Toolbox for Animal
                                  Detection on Acoustic Recordings . . . . 6
               Stefan Posch and   
                 Birgit Moeller   \pkgAlida --- Advanced Library for
                                  Integrated Development of Data Analysis
                                  Applications . . . . . . . . . . . . . . 7
                 Scott A. Sarra   The Matlab Radial Basis Function Toolbox 8
        François Nedelec   \pkgpreconfig: A Versatile Configuration
                                  File Generator for Varying Parameters    9
              Stephan Hoyer and   
                     Joe Hamman   \pkgxarray: $N$-$D$ labeled Arrays and
                                  Datasets in Python . . . . . . . . . . . 10
                Qingzhao Yu and   
                         Bin Li   \pkgmma: An R Package for Mediation
                                  Analysis with Multiple Mediators . . . . 11
       Robert Dahl Jacobsen and   
             Morten Nielsen and   
          Morten Grud Rasmussen   Generalized Sampling in Julia  . . . . . 12
            Michail Alvanos and   
         Theodoros Christoudias   \pkgMEDINA: MECCA Development in
                                  Accelerators --- KPP Fortran to CUDA
                                  source-to-source Pre-processor . . . . . 13
             Willem Eerland and   
                  Simon Box and   
               Hans Fangohr and   
  András Sóbester   \pkgTeetool --- a probabilistic
                                  trajectory analysis tool . . . . . . . . 14
     Christopher Rackauckas and   
                       Qing Nie   \pkgDifferentialEquations.jl --- A
                                  Performant and Feature-Rich Ecosystem
                                  for Solving Differential Equations in
                                  Julia  . . . . . . . . . . . . . . . . . 15
       Micha\l Ptaszy\'nski and   
              Pawe\l Dybala and   
              Rafa\l Rzepka and   
                Kenji Araki and   
                   Fumito Masui   \pkgML-Ask: Open Source Affect Analysis
                                  Software for Textual Input in Japanese   16
          Alexandra K. Diem and   
              Neil W. Bressloff   \pkgVaMpy: A Python Package to Solve
                                  $1$D Blood Flow Problems . . . . . . . . 17
          Martin C. Roberge and   
         Michael P. McGuire and   
                       Jie Lian   \pkgHydroCloud: A Web Application for
                                  Exploring Stream Gage Data . . . . . . . 18
         Mohammad N. Elnesr and   
                   A. A. Alazba   \pkgNeuroCharter: A Neural Networks
                                  Software to Visually Discover the
                                  Effects and Contributions between
                                  Interrelated Features  . . . . . . . . . 19
                 Foo Cheung and   
           Giovanna Fantoni and   
               Maria Conner and   
           Brian A. Sellers and   
             Yuri Kotliarov and   
       Julián Candia and   
        Katherine Stagliano and   
     Angélique Biancotto   Web Tool for Navigating and Plotting
                                  SomaLogic ADAT Files . . . . . . . . . . 20
                   Xinya Li and   
            Chris R. Vernon and   
          Mohamad I. Hejazi and   
             Robert P. Link and   
                Leyang Feng and   
                 Yaling Liu and   
           Lynn T. Rauchenstein   \pkgXanthos --- A Global Hydrologic
                                  Model  . . . . . . . . . . . . . . . . . 21
             Ryan Henderson and   
                   Rasmus Rothe   \pkgPicasso: A Modular Framework for
                                  Visualizing the Learning Process of
                                  Neural Network Image Classifiers . . . . 22
             Daniel A. Wagenaar   \pkgVScope --- Data Acquisition and
                                  Analysis for Voltage-sensitive Dye
                                  Imaging Using Multiple Cameras and
                                  Electrophysiology  . . . . . . . . . . . 23
             Matthew S. Gillman   \pkgGENESIS --- The GENEric SImulation
                                  System for Modelling State Transitions   24
                 Gray Kimbrough   \pkgATUS-Commuting: Stata Code to
                                  Calculate Commuting Time in the American
                                  Time Use Survey  . . . . . . . . . . . . 25
              Julia Damerow and   
        B. R. Erick Peirson and   
          Manfred D. Laubichler   The Giles Ecosystem --- Storage, Text
                                  Extraction, and OCR of Documents . . . . 26
    Dzhoshkun Ismail Shakir and   
Luis Carlos García-Peraza-Herrera and   
                Pankaj Daga and   
                   Tom Doel and   
        Matthew J. Clarkson and   
  Sébastien Ourselin and   
                Tom Vercauteren   \pkgGIFT-Grab: Real-time C++ and Python
                                  multi-channel video capture, processing
                                  and encoding API . . . . . . . . . . . . 27
                     Tom Lawton   DSCImageCalc --- Software for
                                  Determining Similarity Coefficients for
                                  the Analysis of Image Segmentations  . . 28
                    Tianshu Liu   \pkgOpenOpticalFlow: An Open Source
                                  Program for Extraction of Velocity
                                  Fields from Flow Visualization Images    29
              Luis Pedro Coelho   \pkgJug: Software for Parallel
                                  Reproducible Computation in Python . . . 30
               Aidan O'Mara and   
               Anna E. King and   
           James C. Vickers and   
       Matthew T. K. Kirkcaldie   \pkgImageSURF: An ImageJ Plugin for
                                  Batch Pixel-Based Image Segmentation
                                  Using Random Forests . . . . . . . . . . 31
                  Tom Crick and   
              Benjamin Hall and   
                  Samin Ishtiaq   Reproducibility in Research: Systems,
                                  Infrastructure, Culture  . . . . . . . . 32
                   Inga Schwabe   \pkgBayesTwin: An R Package for Bayesian
                                  Inference of Item-Level Twin Data  . . . 33


Journal of Open Research Software
Volume 6, Number 1, January 08, 2018

             Xavier Barbeau and   
          Antony T. Vincent and   
             Patrick Lagüe   \pkgConfBuster: Open-Source Tools for
                                  Macrocycle Conformational Search and
                                  Analysis . . . . . . . . . . . . . . . . 1
             Pablo Saavedra and   
                 Clemens Simmer   An Octave/MATLAB\reg Interface for Rapid
                                  Processing of SMOS L1C Full Polarization
                                  Brightness Temperature . . . . . . . . . 2
                 Roger Fenn and   
                  Ansgar Wenzel   Quandle and Biquandle Homology
                                  Calculation in R . . . . . . . . . . . . 3
               Thomas Brown and   
          Jonas Hörsch and   
           David Schlachtberger   \pkgPyPSA: Python for Power System
                                  Analysis . . . . . . . . . . . . . . . . 4
                William Griffin   \pkgpyObs: Open-Source Software for
                                  Computer-Assisted Behavioral Observation
                                  Coding . . . . . . . . . . . . . . . . . 5
        Sivananda Rajananda and   
                 Hakwan Lau and   
                 Brian Odegaard   A Random-Dot Kinematogram for Web-Based
                                  Vision Research  . . . . . . . . . . . . 6
              Maxwell Grady and   
               Zhongwei Dai and   
                   Karsten Pohl   \pkgPLEASE: The Python Low-energy
                                  Electron Analysis SuitE --- Enabling
                                  Rapid Analysis of LEEM and LEED Data . . 7
         Michael Schoeffler and   
           Sarah Bartoschek and   
  Fabian-Robert Stöter and   
              Marlene Roess and   
           Susanne Westphal and   
                Bernd Edler and   
              Jürgen Herre   webMUSHRA --- A Comprehensive Framework
                                  for Web-based Listening Tests  . . . . . 8
                   Xinya Li and   
            Chris R. Vernon and   
          Mohamad I. Hejazi and   
             Robert P. Link and   
             Zhongwei Huang and   
                     Lu Liu and   
                    Leyang Feng   \pkgTethys --- A Python Package for
                                  Spatial and Temporal Downscaling of
                                  Global Water Withdrawals . . . . . . . . 9
             Daniel S. Katz and   
           Kyle E. Niemeyer and   
              Sandra Gesing and   
             Lorraine Hwang and   
          Wolfgang Bangerth and   
             Simon Hettrick and   
                Ray Idaszak and   
                 Jean Salac and   
             Neil Chue Hong and   
Santiago Núñez-Corrales and   
                Alice Allen and   
           R. Stuart Geiger and   
               Jonah Miller and   
                 Emily Chen and   
                Anshu Dubey and   
                  Patricia Lago   Fourth Workshop on Sustainable Software
                                  for Science: Practice and Experiences
                                  (WSSSPE4)  . . . . . . . . . . . . . . . 10
                  Ulrich Matter   \pkgRWebData: A High-Level Interface to
                                  the Programmable Web . . . . . . . . . . 11
           Daniel Michelson and   
               Anders Henja and   
               Sander Ernes and   
         Günther Haase and   
            Jarmo Koistinen and   
  Katarzyna O'sródka and   
            Tuomas Peltonen and   
       Maciej Szewczykowski and   
                     Jan Szturc   BALTRAD Advanced Weather Radar
                                  Networking . . . . . . . . . . . . . . . 12
           Daniel Leightley and   
         Jo-Anne Puddephatt and   
              Laura Goodwin and   
               Roberto Rona and   
                 Nicola T. Fear   \pkgInDEx: Open Source iOS and Android
                                  Software for Self-Reporting and
                                  Monitoring of Alcohol Consumption  . . . 13
                  Nina Heck and   
                Moritz Schubotz   DiViDu --- An Open Source Solution for
                                  Dual Task Experiments with Integrated
                                  Divided Visual Field Paradigm  . . . . . 14
            Chris R. Vernon and   
            Yannick Le Page and   
                   Min Chen and   
                Maoyi Huang and   
        Katherine V. Calvin and   
           Ian P. Kraucunas and   
                 Caleb J. Braun   \pkgDemeter --- A Land Use and Land
                                  Cover Change Disaggregation Model  . . . 15
             Pete Richard Jones   \pkgMyex: A MATLAB Interface for the
                                  Tobii Eyex Eye-Tracker . . . . . . . . . 16
         Jonathan Petticrew and   
               Simon Dimler and   
                    Jo Shien Ng   Simple Monte Carlo Simulator for
                                  Modelling Linear Mode and Geiger Mode
                                  Avalanche Photodiodes in C++ . . . . . . 17
                 Helga Tauscher   \pkgBillie. A Prototypical Framework for
                                  Building Information Model Visualization 18
        Henrik Nygård and   
       Ciarán Murray and   
         Jesper H. Andersen and   
               Georg Martin and   
                 Kaire Torn and   
                Samuli Korpinen   \pkgBEAT 3.0 --- a Tool for Integrated
                                  Biodiversity Assessments . . . . . . . . 19
            Chris R. Vernon and   
              Nino Zuljevic and   
             Jennie S. Rice and   
          Timothy E. Seiple and   
Michael C. W. Kintner-Meyer and   
            Nathalie Voisin and   
           Ian P. Kraucunas and   
               Jin Chunlian and   
               Jarrod Olson and   
             Laurel Schmidt and   
            Scott L. Morris and   
                   Pralit Patel   \pkgCERF --- A Geospatial Model for
                                  Assessing Future Energy Production
                                  Technology Expansion Feasibility . . . . 20
       Rubens Flam-Shepherd and   
              Dev T. Britto and   
          Herbert J. Kronzucker   \pkgvaCATE: A Platform for Automating
                                  Data Output from Compartmental Analysis
                                  by Tracer Efflux . . . . . . . . . . . . 21
       Marc-Antonio Bisotti and   
David Cortés-Ortuño and   
                Ryan Pepper and   
                Weiwei Wang and   
                Marijan Beg and   
             Thomas Kluyver and   
                   Hans Fangohr   \pkgFidimag --- A Finite Difference
                                  Atomistic and Micromagnetic Simulation
                                  Package  . . . . . . . . . . . . . . . . 22


Journal of Open Research Software
Volume 7, Number 1, January 07, 2019

            Chris R. Vernon and   
          Mohamad I. Hejazi and   
          Sean W. D. Turner and   
                 Yaling Liu and   
             Caleb J. Braun and   
                   Xinya Li and   
                 Robert P. Link   A Global Hydrologic Framework to
                                  Accelerate Scientific Discovery  . . . . 1
           Michael Slugocki and   
         Allison B. Sekuler and   
                Patrick Bennett   \pkgBayesFit: a tool for modeling
                                  psychophysical data using Bayesian
                                  inference  . . . . . . . . . . . . . . . 2
              Edward D. Lee and   
               Bryan C. Daniels   Convenient Interface to Inverse Ising
                                  (ConIII): a Python 3 Package for Solving
                                  Ising-Type Maximum Entropy Models  . . . 3
           Christine Harvey and   
                   R. S. Weigel   \pkgTransplant2Mongo: Python Scripts
                                  that Insert Organ Procurement and
                                  Transplantation Network (OPTN) Data in
                                  MongoDB  . . . . . . . . . . . . . . . . 5
          Ben Bond-Lamberty and   
              Kalyn Dorheim and   
                   Ryna Cui and   
           Russell Horowitz and   
             Abigail Snyder and   
           Katherine Calvin and   
                Leyang Feng and   
              Rachel Hoesly and   
                Jill Horing and   
               G. Page Kyle and   
                Robert Link and   
               Pralit Patel and   
          Christopher Roney and   
         Aaron Staniszewski and   
                Sean Turner and   
                   Min Chen and   
               Felip Feijoo and   
             Corinne Hartin and   
             Mohamad Hejazi and   
                 Gokul Iyer and   
                  Sonny Kim and   
                 Yaling Liu and   
                 Cary Lynch and   
              Haewon McJeon and   
               Steven Smith and   
         Stephanie Waldhoff and   
              Marshall Wise and   
                    Leon Clarke   \geonamegcamdata: an R Package for
                                  Preparation, Synthesis, and Tracking of
                                  Input Data for the GCAM Integrated
                                  Human--Earth Systems Model . . . . . . . 6
        Kristoffer Carlsson and   
                   Fredrik Ekre   \pkgTensors.jl --- Tensor Computations
                                  in Julia . . . . . . . . . . . . . . . . 7
              Sean A. Fulop and   
                   Hannah Scott   Vowel System Sandbox: Complex System
                                  Modelling of Language Change . . . . . . 8
              Pierre Augier and   
      Ashwin Vishnu Mohanan and   
                 Cyrille Bonamy   \pkgFluidDyn: a Python Open-Source
                                  Framework for Research and Teaching in
                                  Fluid Dynamics by Simulations,
                                  Experiments and Data Processing  . . . . 9
      Ashwin Vishnu Mohanan and   
             Cyrille Bonamy and   
                  Pierre Augier   \pkgFluidFFT: Common API (C++ and
                                  Python) for Fast Fourier Transform HPC
                                  Libraries  . . . . . . . . . . . . . . . 10
                Paul Walker and   
               Ulrich Krohn and   
                    David Carty   \pkgARBTools: a Tricubic Spline
                                  Interpolator for Three-Dimensional
                                  Scalar or Vector Fields  . . . . . . . . 12
               Zhangqi Chen and   
               Qiaofu Zhang and   
                  Ji-Cheng Zhao   \pkgpydiffusion: a Python Library for
                                  Diffusion Simulation and Data Analysis   13
      Ashwin Vishnu Mohanan and   
             Cyrille Bonamy and   
       Miguel Calpe Linares and   
                  Pierre Augier   \pkgFluidSim: Modular, Object-Oriented
                                  Python Package for High-Performance CFD
                                  Simulations  . . . . . . . . . . . . . . 14
          Paul F. Petrowski and   
          Elizabeth G. King and   
          Timothy M. Beissinger   An R Framework for the Partitioning of
                                  Linkage Disequilibrium between and
                                  Within Populations . . . . . . . . . . . 15
                 Will Usher and   
                    Tom Russell   A Software Framework for the Integration
                                  of Infrastructure Simulation Models  . . 16
              Heidi Seibold and   
              Achim Zeileis and   
                Torsten Hothorn   \pkgmodel4you: an R Package for
                                  Personalised Treatment Effect Estimation 17
               Hagen Radtke and   
        Florian Börgel and   
   Sandra-Esther Brunnabend and   
                Anja Eggert and   
          Madline Kniebusch and   
         H. E. Markus Meier and   
             Daniel Neumann and   
             Thomas Neumann and   
                   Manja Placke   \pkgValidator --- a Web-Based
                                  Interactive Tool for Validation of Ocean
                                  Models at Oceanographic Stations . . . . 18
               Markus Quade and   
                Julien Gout and   
                    Markus Abel   \pkgGlyph: Symbolic Regression Tools . . 19
           Johannes Brenner and   
              Guilio Genova and   
           Giacomo Bertoldi and   
             Georg Niedrist and   
           Stefano Della Chiesa   \pkgSWCalibrateR: Interactive, Web-Based
                                  Calibration of Soil Moisture Sensors . . 20
                     Y. Q. Wang   An Open Source Software Suite for
                                  Multi-Dimensional Meteorological Data
                                  Computation and Visualisation  . . . . . 21
             Thomas B. Wild and   
           Daniel P. Loucks and   
            George W. Annandale   \pkgSedSim: a River Basin Simulation
                                  Screening Model for Reservoir Management
                                  of Sediment, Water, and Hydropower . . . 22
              Michael Clerx and   
            Martin Robinson and   
                Ben Lambert and   
               Chon Lok Lei and   
             Sanmitra Ghosh and   
             Gary R. Mirams and   
              David J. Gavaghan   Probabilistic Inference on Noisy Time
                                  Series (PINTS) . . . . . . . . . . . . . 23
        Abdelrahman Abouali and   
         Domingos Xavier Viegas   \pkgFire ROS Calculator: a Tool to
                                  Measure the Rate of Spread of a
                                  Propagating Wildfire in a Laboratory
                                  Setting  . . . . . . . . . . . . . . . . 24
               Julian Stieg and   
                Peter Marks and   
                  Lasse Gerrits   \pkgUN-CODE: Software for Structuring
                                  and Visualizing Collective
                                  Decision-Making Based on Qualitative
                                  Data . . . . . . . . . . . . . . . . . . 25
             Ewout van den Berg   The Ocean Tensor Package . . . . . . . . 26
Jose Luis García del Castillo y López   \pkgMachina.NET: a Library for
                                  Programming and Real-Time Control of
                                  Industrial Robots  . . . . . . . . . . . 27
            James F. Varner and   
              Noor Eldabagh and   
                Derek Volta and   
              Reem Eldabagh and   
           Jonathan J. Foley IV   \pkgWPTherml: a Python Package for the
                                  Design of Materials for Harnessing Heat  28
             Daniel Wheeler and   
              Trevor Keller and   
          Stephen J. DeWitt and   
        Andrea M. Jokisaari and   
              Daniel Schwen and   
          Jonathan E. Guyer and   
           Larry K. Aagesen and   
           Olle G. Heinonen and   
           Michael R. Tonks and   
          Peter W. Voorhees and   
                James A. Warren   \pkgPFHub: The Phase-Field Community Hub 29
              Luuk Van Waes and   
      Mariëlle Leijten and   
               Tom Pauwaert and   
            Eric Van Horenbeeck   A Multilingual Copy Task: Measuring
                                  Typing and Motor Skills in Writing with
                                  Inputlog . . . . . . . . . . . . . . . . 30
           Katherine Calvin and   
                Robert Link and   
                  Marshall Wise   \pkggcamland v1.0 --- an R Package for
                                  Modelling Land Use and Land Cover Change 31
              Paul van Gent and   
               Haneen Farah and   
             Nicole van Nes and   
                  Bart van Arem   Analysing Noisy Driver Physiology
                                  Real-Time Using Off-the-Shelf Sensors:
                                  Heart Rate Analysis Software from the
                                  Taking the Fast Lane Project . . . . . . 32
               Lyndon White and   
            Roberto Togneri and   
                    Wei Liu and   
             Mohammed Bennamoun   \pkgDataDeps.jl: Repeatable Data Setup
                                  for Reproducible Data Science  . . . . . 33
                Iain Emsley and   
         Torò Graven and   
                Nicola Bird and   
            Susan Griffiths and   
              Jessica Suess and   
                      Lucy Shaw   Please Touch the Art: Experiences in
                                  Developing for the Visually Impaired . . 4
             Daniel S. Katz and   
            Stephan Druskat and   
              Robert Haines and   
               Caroline Jay and   
               Alexander Struck   The State of Sustainable Research
                                  Software: Learning from the Workshop on
                                  Sustainable Software for Science:
                                  Practice and Experiences (WSSSPE5.1) . . 11


Journal of Open Research Software
Volume 8, Number 1, January 15, 2020

        Alan V. Di Vittorio and   
            Chris R. Vernon and   
                     Shijie Shu   \pkgMoirai Version 3: a Data Processing
                                  System to Generate Recent Historical
                                  Land Inputs for Global Modeling
                                  Applications at Various Scales . . . . . 1
          Tobias Stål and   
                Anya M. Reading   A Grid for Multidimensional and
                                  Multivariate Spatial Representation and
                                  Data Processing  . . . . . . . . . . . . 2
          V. Gonzalez-Perez and   
                    P. Keil and   
                      Y. Li and   
              A. Zülke and   
                  R. Burrel and   
                   D. Csala and   
                      H. Hoster   A Python Package to Preprocess the Data
                                  Produced by Novonix High-Precision
                                  Battery-Testers  . . . . . . . . . . . . 3
            Alexander Raß   High Precision Particle Swarm
                                  Optimization Algorithm (HiPPSO)  . . . . 4
   A. F. M. Kamal Chowdhury and   
                Jordan Kern and   
             Thanh Duc Dang and   
                Stefano Galelli   \pkgPowNet: a Network-Constrained Unit
                                  Commitment/Economic Dispatch Model for
                                  Large-Scale Power Systems Analysis . . . 5
                 Foo Cheung and   
             The CHI Consortium   A Figure One Web Tool for Visualization
                                  of Experimental Designs  . . . . . . . . 6
            Hari Nandakumar and   
            Shailesh Srivastava   \pkgABC-OCT --- a Cross-Platform
                                  Implementation of Real-Time
                                  Fourier-Domain Optical Coherence
                                  Tomography . . . . . . . . . . . . . . . 7
           Stephen Thompson and   
             Thomas Dowrick and   
               Goufang Xiao and   
     João Ramalhinho and   
                 Maria Robu and   
                 Mian Ahmad and   
                 Dan Taylor and   
            Matthew J. Clarkson   \pkgSnappySonic: an Ultrasound
                                  Acquisition Replay Simulator . . . . . . 8
               Kashif Shaad and   
                     Howard Alt   An Open Source Toolbox for Integrating
                                  Freshwater Social-Ecological Indicators
                                  in Basin Management  . . . . . . . . . . 9
                Zarrar Khan and   
                Thomas Wild and   
               Chris Vernon and   
                Andy Miller and   
             Mohamad Hejazi and   
                Leon Clarke and   
  Fernando Miralles-Wilhelm and   
        Raul Munoz Castillo and   
              Fekadu Moreda and   
    Julia Lacal Bereslawski and   
            Micaela Suriano and   
                    Jose Casado   \pkgMetis --- a Tool to Harmonize and
                                  Analyze Multi-Sectoral Data and Linkages
                                  at Variable Spatial Scales . . . . . . . 10
        Robin A. Richardson and   
            David W. Wright and   
             Wouter Edeling and   
        Vytautas Jancauskas and   
             Jalal Lakhlili and   
               Peter V. Coveney   \pkgEasyVVUQ: a Library for
                                  Verification, Validation and Uncertainty
                                  Quantification in High Performance
                                  Computing  . . . . . . . . . . . . . . . 11
       Antonia Hadjimichael and   
                 David Gold and   
                David Hadka and   
                   Patrick Reed   \pkgRhodium: Python Library for
                                  Many-Objective Robust Decision Making
                                  and Exploratory Modeling . . . . . . . . 12
                    Martin Rabe   \pkgSpectram: a MATLAB\reg and GNU
                                  Octave Toolbox for Transition Model
                                  Guided Deconvolution of Dynamic
                                  Spectroscopic Data . . . . . . . . . . . 13
                    Riko Kelter   \pkgbayest: an R Package for Effect-Size
                                  Targeted Bayesian Two-Sample $t$-Tests   14
               K. E. Kaiser and   
               A. N. Flores and   
                   C. R. Vernon   \pkgJanus: a Python Package for
                                  Agent-Based Modeling of Land Use and
                                  Land Cover Change  . . . . . . . . . . . 15
            Jagir R. Hussan and   
                Peter J. Hunter   \pkgComfort Simulator: a Software Tool
                                  to Model Thermoregulation and Perception
                                  of Comfort . . . . . . . . . . . . . . . 16
               Gabriele Gentile   \pkgCURSAT ver. 2.1: a Simple,
                                  Resampling-Based, Program to Generate
                                  Pseudoreplicates of Data and Calculate
                                  Rarefaction Curves . . . . . . . . . . . 17
                 Adam Pluta and   
            Ontje Lünsdorf   \pkgesy-osmfilter --- a Python Library
                                  to Efficiently Extract OpenStreetMap
                                  Data . . . . . . . . . . . . . . . . . . 19
             Robert Jackson and   
               Scott Collis and   
               Timothy Lang and   
               Corey Potvin and   
                    Todd Munson   \pkgPyDDA: a Pythonic Direct Data
                                  Assimilation Framework for Wind
                                  Retrievals . . . . . . . . . . . . . . . 20
              Marc Lavielle and   
             Philip D. Waggoner   Exploring and Comparing Unsupervised
                                  Clustering Algorithms  . . . . . . . . . 21
               Paige Fisher and   
                 Wentao Cao and   
                    Qingzhao Yu   Using SAS Macros for Multiple Mediation
                                  Analysis in R  . . . . . . . . . . . . . 22
           Brendan Williams and   
                Michael Lindner   \pkgpyfMRIqc: a Software Package for Raw
                                  fMRI Data Quality Assurance  . . . . . . 23
           Ulrike Grömping   \pkgDoE.MIParray: an R Package for
                                  Algorithmic Creation of Orthogonal
                                  Arrays . . . . . . . . . . . . . . . . . 24
              Corey Schimpf and   
               Brian Castellani   \pkgCOMPLEX-IT: a Case-Based Modelling
                                  and Scenario Simulation Platform for
                                  Social Inquiry . . . . . . . . . . . . . 25
             Vladyslav Oles and   
                Anton Kukushkin   \pkgBoolSi: a Tool for Distributed
                                  Simulations and Analysis of Boolean
                                  Networks . . . . . . . . . . . . . . . . 26
             Thomas Dowrick and   
                James Avery and   
              Mayo Faulkner and   
               David Holder and   
              Kirill Aristovich   \pkgEIT-MESHER --- Segmented FEM Mesh
                                  Generation and Refinement  . . . . . . . 27
   Jordi Figueras i Ventura and   
              Martin Lainer and   
          Zaira Schauwecker and   
            Jacopo Grazioli and   
                    Urs Germann   \pkgPyrad: a Real-Time Weather Radar
                                  Data Processing Framework Based on
                                  Py-ART . . . . . . . . . . . . . . . . . 28
              Lisa Sahlmann and   
             Christian B. Mendl   \pkgGuiTeNet: a Graphical User Interface
                                  for Tensor Networks  . . . . . . . . . . 29
                 Drew Paine and   
           Devarshi Ghoshal and   
           Lavanya Ramakrishnan   Experiences with a Flexible User
                                  Research Process to Build Data Change
                                  Tools  . . . . . . . . . . . . . . . . . 18


Journal of Open Research Software
Volume 9, Number 1, February 02, 2021

                     Hyemin Han   \pkgBayesFactorFMRI: Implementing
                                  Bayesian Second-Level fMRI Analysis with
                                  Multiple Comparison Correction and
                                  Bayesian Meta-Analysis of fMRI Images
                                  with Multiprocessing . . . . . . . . . . 1
           Isabelle Mirouze and   
                   Sophie Ricci   Smurf: System for Modelling with
                                  Uncertainty Reduction, and Forecasting   2
                Tianshu Liu and   
               David M. Salazar   \pkgOpenOpticalFlow\_PIV: an Open Source
                                  Program Integrating Optical Flow Method
                                  with Cross- Correlation Method for
                                  Particle Image Velocimetry . . . . . . . 3
                Ian Edhlund and   
           Matthew Macauley and   
                      Cindy Lee   \pkgPBTK Optimizer: an Open Source
                                  Application for PBTK Model Parameter
                                  Optimization in Python . . . . . . . . . 4
         Philippe Apparicio and   
              David Maignan and   
      Jérémy Gelb   \pkgVIFECO: an Open-Source Software for
                                  Counting Features on a Video . . . . . . 7
             Konstantin Stadler   \pkgPymrio --- a Python Based
                                  Multi-Regional Input-Output Analysis
                                  Toolbox  . . . . . . . . . . . . . . . . 8
      Christoph G. Hoffmann and   
          George N. Kiladis and   
                Maria Gehne and   
          Christian von Savigny   A Python Package to Calculate the
                                  OLR-Based Index of the
                                  Madden--Julian-Oscillation (OMI) in
                                  Climate Science and Weather Forecasting  9
            Eugenio Piasini and   
 Alexandre L. S. Filipowicz and   
            Jonathan Levine and   
                 Joshua I. Gold   \pkgEmbo: a Python package for empirical
                                  data analysis using the Information
                                  Bottleneck . . . . . . . . . . . . . . . 10
          Florian Riefstahl and   
                    Felix Gross   \pkgFastGAPP --- a MATLAB Based Program
                                  Supports Earth Scientists Interpreting
                                  Geochemical, Petrological and
                                  Sedimentological Data  . . . . . . . . . 11
          William Thielicke and   
            René Sonntag   Particle Image Velocimetry for MATLAB:
                                  Accuracy and enhanced algorithms in
                                  PIVlab . . . . . . . . . . . . . . . . . 12
          Christopher Kadow and   
           Sebastian Illing and   
       Etor E. Lucio-Eceiza and   
           Martin Bergemann and   
            Mahesh Ramadoss and   
          Philipp S. Sommer and   
               Oliver Kunst and   
           Thomas Schartner and   
              Klaus Pankatz and   
               Jens Grieger and   
           Mareike Schuster and   
              Andy Richling and   
            Hannes Thiemann and   
              Ingo Kirchner and   
             Henning W Rust and   
              Thomas Ludwig and   
             Ulrich Cubasch and   
                    Uwe Ulbrich   Introduction to \pkgFreva --- a Free
                                  Evaluation System Framework for Earth
                                  System Modeling  . . . . . . . . . . . . 13
            Valentin Sulzer and   
           Scott G. Marquis and   
               Robert Timms and   
            Martin Robinson and   
                 S. Jon Chapman   \pkgPython Battery Mathematical
                                  Modelling (PyBaMM) . . . . . . . . . . . 14
                Tiger Cross and   
           Rasika Navarange and   
                Joon-Ho Son and   
               William Burr and   
                Arjun Singh and   
               Kelvin Zhang and   
                Miruna Rusu and   
      Konstantinos Gkoutzis and   
             Andrew Osborne and   
               Bart Nieuwenhuis   \pkgSimple RGC: ImageJ Plugins for
                                  Counting Retinal Ganglion Cells and
                                  Determining the Transduction Efficiency
                                  of Viral Vectors in Retinal Wholemounts  15
          Christos Kotsalos and   
                 Jonas Latt and   
                Bastien Chopard   \pkgPalabos-npFEM: Software for the
                                  Simulation of Cellular Blood Flow
                                  (Digital Blood)  . . . . . . . . . . . . 16
             Thomas Dowrick and   
                 Mian Ahmad and   
           Stephen Thompson and   
         James Hetherington and   
            Jonathan Cooper and   
                  Matt Clarkson   \pkgCMakeCatchTemplate: a C++ template
                                  project  . . . . . . . . . . . . . . . . 17
                 Aruna Jayasena   Register Transfer Level Disparity
                                  generator with Stereo Vision . . . . . . 18
      Brandon P. M. Edwards and   
                  Adam C. Smith   \pkgbbsBayes: an R Package for
                                  Hierarchical Bayesian Analysis of North
                                  American Breeding Bird Survey Data . . . 19
                  Dan Barry and   
               Qijian Zhang and   
           Pheobe Wenyi Sun and   
                   Andrew Hines   \pkgGo Listen: an End-to-End Online
                                  Listening Test Platform  . . . . . . . . 20
Gáspár Lukács   \pkgSmaRT-CIT: Smartphone App for the
                                  Response Time Concealed Information Test
                                  with Ready-to-Use Android Deployment . . 21
               Rune Barnkob and   
             Massimiliano Rossi   \pkgDefocusTracker: a Modular Toolbox
                                  for Defocusing-based, Single-Camera, 3D
                                  Particle Tracking  . . . . . . . . . . . 22
               Tulio Molina and   
                Juan Ortega and   
              Juan Muñoz   \pkgHELMpy, Open Source Package of Power
                                  Flow Solvers, Including the Holomorphic
                                  Embedding Load Flow Method (HELM),
                                  Developed on Python 3  . . . . . . . . . 23
                   Adrian Moore   \pkgautoAPI --- a Web-Based Tool for
                                  Specification of an API Endpoint to
                                  Return JSON Data From an XML Source  . . 24
               Ales Jelinek and   
               Adam Ligocki and   
                    Ludek Zalud   Robotic Template Library . . . . . . . . 25
             Angela Herring and   
         Charles Ferenbaugh and   
         Christopher Malone and   
             Daniel Shevitz and   
            Evgeny Kikinzon and   
                 Gary Dilts and   
         Hoby Rakotoarivelo and   
            Jan Velechovsky and   
        Konstantin Lipnikov and   
               Navamita Ray and   
                  Rao Garimella   \pkgPortage: a Modular Data Remap
                                  Library for Multiphysics Applications on
                                  Advanced Architectures . . . . . . . . . 26
         Saras M. Windecker and   
              Peter A. Vesk and   
Stacey M. Trevathan-Tackett and   
                   Nick Golding   \pkgmixchar: an R Package for the
                                  Deconvolution of Thermal Decay Curves    27
            Robin Champseix and   
            Laurent Ribiere and   
      Clément Le Couedic   A Python Package for Heart Rate
                                  Variability Analysis and Signal
                                  Preprocessing  . . . . . . . . . . . . . 28
             Ross J. Turner and   
           Rebecca B. Latto and   
                Anya M. Reading   An ObsPy Library for Event Detection and
                                  Seismic Attribute Calculation: Preparing
                                  Waveforms for Automated Analysis . . . . 29
            Jacques Muthusi and   
             Peter W. Young and   
                 Samuel Mwalili   \pkg%svy\_freqs: a Generic SAS Macro for
                                  Creating Publication-Quality Three-Way
                                  Cross-Tabulations  . . . . . . . . . . . 30
         Claudio S. Ravasio and   
             Lyndon Da Cruz and   
              Christos Bergeles   \pkgoflibnumpy and \pkgoflibpytorch:
                                  Optical Flow Handling and Manipulation
                                  in Python  . . . . . . . . . . . . . . . 31
                  Diogo Ferrari   \pkgCESER: an R Package to Compute
                                  Cluster Estimated Standard Errors  . . . 32
            Maarten Plieger and   
                Ernst de Vreede   \pkgAdaguc-Server: Interactive Access to
                                  Heterogeneous Meteorological and
                                  Climatological Datasets Using Open
                                  Standards  . . . . . . . . . . . . . . . 33
               James R. Schmidt   \pkgCSVDataMerge: a Simple and Free
                                  Program for Concatenating Experimental
                                  Data Files . . . . . . . . . . . . . . . 34
   M. Bekker-Nielsen Dunbar and   
            Thomas J. R. Finnie   \pkgbayesint: a Python Package for
                                  Calculating Bayesian Credible Intervals
                                  of Ratios of Beta Distributions  . . . . 35
                    J. Fehr and   
                   C. Himpe and   
                    S. Rave and   
                        J. Saak   Sustainable Research Software Hand-Over  5
              Simon Hilpert and   
       Stephan Günther and   
              Martin Söthe   \pkgoemof.tabular --- Introducing Data
                                  Packages for Reproducible Workflows in
                                  Energy System Modeling . . . . . . . . . 6


Journal of Open Research Software
Volume 10, Number 1, March 02, 2022

            Rémi Cresson   \pkgSR4RS: a Tool for Super Resolution
                                  of Remote Sensing Images . . . . . . . . ??
             Vanessa Sochat and   
               Nicholas May and   
                 Ian Cosden and   
      Carlos Martinez-Ortiz and   
              Sadie Bartholomew   The Research Software Encyclopedia: a
                                  Community Framework to Define Research
                                  Software . . . . . . . . . . . . . . . . ??
             Johannes N. Hansen   \pkgnd --- a Framework for the Analysis
                                  of $n$-dimensional Earth Observation
                                  Data . . . . . . . . . . . . . . . . . . ??
        Thi-Ngoc-Thu Nguyen and   
        Andreas Höfter and   
            Kevin Leonardic and   
         Stefanie Rosenhain and   
           Fabian Kiessling and   
           Wannida Sae-Tang and   
                Uwe Naumann and   
                   Felix Gremse   A Micro-computed Tomography Database and
                                  Reference Implementation for Parallel
                                  Computations of Trabecular Thickness and
                                  Spacing  . . . . . . . . . . . . . . . . ??
             Nikolay Petrov and   
             Vasil Atanasov and   
                Trevor Thompson   Open-Source MUltiple Tests Corrections
                                  and FOrmatted Tables Software (MUFOS)    ??
                Gabi Wethor and   
                Matthew L. Hale   \pkgStudySandboxx: a Tool for Scraping,
                                  Sandboxing, Preserving, and Preparing
                                  Interactive Web Sites for Use in
                                  Human-computer Interaction and
                                  Behavioral Studies . . . . . . . . . . . ??
                   Xin Tong and   
          Sou-Cheng T. Choi and   
                 Yuhan Ding and   
         Fred J. Hickernell and   
                  Lan Jiang and   
Lluís Antoni Jiménez Rugama and   
   Jagadeeswaran Rathinavel and   
                  Kan Zhang and   
                Yizhi Zhang and   
                      Xuan Zhou   \pkgGuaranteed Automatic Integration
                                  Library (GAIL): an Open-Source MATLAB
                                  Library for Function Approximation,
                                  Optimization, and Integration  . . . . . ??
                Nils Rosjat and   
                    Silvia Daun   \pkgDST (Dynamic Synchronization
                                  Toolbox): a MATLAB Implementation of the
                                  Dynamic Phase-Locking Pipeline from
                                  Stimulus Transformation into Motor
                                  Action: Dynamic Graph Analysis Reveals a
                                  Posterior-to- Anterior Shift in Brain
                                  Network Communication of Older Subjects  ??
                 Brena Lima and   
               Nuno Fachada and   
                  Rui Dinis and   
            Daniel B. Costa and   
                     Marko Beko   \pkgUavnoma: a UAV-NOMA Network Model
                                  under Non-Ideal Conditions . . . . . . . ??
             Meryem Berrada and   
               Richard A. Secco   \pkgRho: Application to Analyze
                                  Electrical Resistivity . . . . . . . . . ??
        Anna-Lena Lamprecht and   
      Carlos Martinez-Ortiz and   
            Michelle Barker and   
       Sadie L. Bartholomew and   
              Justin Barton and   
             Neil Chue Hong and   
               Jeremy Cohen and   
            Stephan Druskat and   
              Jeremy Forest and   
        Jean-Noël Grad and   
             Daniel S. Katz and   
           Robin Richardson and   
               Robert Rosca and   
              Douwe Schulte and   
           Alexander Struck and   
               Marion Weinzierl   What Do We (Not) Know About Research
                                  Software Engineering?  . . . . . . . . . ??


Journal of Open Research Software
Volume 11, Number 1, 2023

             Magnus Hagdorn and   
                 Noel Gourmelen   \pkgTaskfarm: a Client/Server Framework
                                  for Supporting Massive Embarrassingly
                                  Parallel Workloads . . . . . . . . . . . ??
  Adéla\"\ide Raguin and   
             Ian Stansfield and   
            Maria Carmen Romano   \pkgExpressInHost: a Codon Tuning Tool
                                  for the Expression of Recombinant
                                  Proteins in Host Microorganisms  . . . . ??
     João Ramalhinho and   
             Thomas Dowrick and   
              Ester Bonmati and   
            Matthew J. Clarkson   \pkgFan-Slicer: a Pycuda Package for
                                  Fast Reslicing of Ultrasound Shaped
                                  Planes . . . . . . . . . . . . . . . . . ??
       Md. Manjurul Hussain and   
             Ishtiak Mahmud and   
             Sheikh Hefzul Bari   \pkgpyHomogeneity: a Python Package for
                                  Homogeneity Test of Time Series Data . . ??
               Simon Christ and   
        Daniel Schwabeneder and   
     Christopher Rackauckas and   
  Michael Krabbe Borregaard and   
                 Thomas Breloff   \pkgPlots.jl --- a User Extendable
                                  Plotting API for the Julia Programming
                                  Language . . . . . . . . . . . . . . . . ??
             Vanessa Sochat and   
           Matthieu Muffato and   
               Audrey Stott and   
         Marco De La Pierre and   
                 Georgia Stuart   Automated Discovery of Container
                                  Executables  . . . . . . . . . . . . . . ??