Vol. 5 No. 1 (2017)

Published: 2017-01-09

Software Metapapers

pycalphad: CALPHAD-based Computational Thermodynamics in Python

Richard Otis, Zi-Kui Liu

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Gridsampler – A Simulation Tool to Determine the Required Sample Size for Repertory Grid Studies

Mark Heckmann, Lukas Burk

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RMPCDMD: Simulations of Colloids with Coarse-grained Hydrodynamics, Chemical Reactions and External Fields

Pierre de Buyl, Mu-Jie Huang, Laurens Deprez

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Matlab Code for the Discrete Hankel Transform

Natalie Baddour, Ugo Chouinard

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Cambridge Rocketry Simulator – A Stochastic Six-Degrees-of-Freedom Rocket Flight Simulator

Willem J. Eerland, Simon Box, András Sóbester

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Tadarida: A Toolbox for Animal Detection on Acoustic Recordings

Yves Bas, Didier Bas, Jean-François Julien

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Alida – Advanced Library for Integrated Development of Data Analysis Applications

Stefan Posch, Birgit Moeller

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The Matlab Radial Basis Function Toolbox

Scott A. Sarra

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preconfig: A Versatile Configuration File Generator for Varying Parameters

Francois Nedelec

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xarray: N-D labeled Arrays and Datasets in Python

Stephan Hoyer, Joe Hamman

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mma: An R Package for Mediation Analysis with Multiple Mediators

Qingzhao Yu, Bin Li

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Generalized Sampling in Julia

Robert Dahl Jacobsen, Morten Nielsen, Morten Grud Rasmussen

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MEDINA: MECCA Development in Accelerators – KPP Fortran to CUDA source-to-source Pre-processor

Michail Alvanos, Theodoros Christoudias

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Teetool -- a probabilistic trajectory analysis tool

Willem Eerland, Simon Box, Hans Fangohr, András Sóbester

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DifferentialEquations.jl – A Performant and Feature-Rich Ecosystem for Solving Differential Equations in Julia

Christopher Rackauckas, Qing Nie

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ML-Ask: Open Source Affect Analysis Software for Textual Input in Japanese

Michal Ptaszynski, Pawel Dybala, Rafal Rzepka, Kenji Araki, Fumito Masui

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VaMpy: A Python Package to Solve 1D Blood Flow Problems

Alexandra K. Diem, Neil W. Bressloff

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HydroCloud: A Web Application for Exploring Stream Gage Data

Martin C. Roberge, Michael P. McGuire, Jie Lian

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NeuroCharter: A Neural Networks Software to Visually Discover the Effects and Contributions between Interrelated Features

Mohammad N. Elnesr, A. A. Alazba

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Web Tool for Navigating and Plotting SomaLogic ADAT Files

Foo Cheung, Giovanna Fantoni, Maria Conner, Brian A. Sellers, Yuri Kotliarov, Julián Candia, Katherine Stagliano, Angélique Biancotto

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Xanthos – A Global Hydrologic Model

Xinya Li, Chris R. Vernon, Mohamad I. Hejazi, Robert P. Link, Leyang Feng, Yaling Liu, Lynn T. Rauchenstein

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Picasso: A Modular Framework for Visualizing the Learning Process of Neural Network Image Classifiers

Ryan Henderson, Rasmus Rothe

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VScope — Data Acquisition and Analysis for Voltage-sensitive Dye Imaging Using Multiple Cameras and Electrophysiology

Daniel A. Wagenaar

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GENESIS – The GENEric SImulation System for Modelling State Transitions

Matthew S. Gillman

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ATUS-Commuting: Stata Code to Calculate Commuting Time in the American Time Use Survey

Gray Kimbrough

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The Giles Ecosystem – Storage, Text Extraction, and OCR of Documents

Julia Damerow, B. R. Erick Peirson, Manfred D. Laubichler

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GIFT-Grab: Real-time C++ and Python multi-channel video capture, processing and encoding API

Dzhoshkun Ismail Shakir, Luis Carlos García-Peraza-Herrera, Pankaj Daga, Tom Doel, Matthew J. Clarkson, Sébastien Ourselin, Tom Vercauteren

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DSCImageCalc – Software for Determining Similarity Coefficients for the Analysis of Image Segmentations

Tom Lawton

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OpenOpticalFlow: An Open Source Program for Extraction of Velocity Fields from Flow Visualization Images

Tianshu Liu

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Jug: Software for Parallel Reproducible Computation in Python

Luis Pedro Coelho

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ImageSURF: An ImageJ Plugin for Batch Pixel-Based Image Segmentation Using Random Forests

Aidan O'Mara, Anna E. King, James C. Vickers, Matthew T. K. Kirkcaldie

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BayesTwin: An R Package for Bayesian Inference of Item-Level Twin Data

Inga Schwabe

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Issues in Research Software

Reproducibility in Research: Systems, Infrastructure, Culture

Tom Crick, Benjamin A. Hall, Samin Ishtiaq

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