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@article{kerr2021covasim,
title={Covasim: an agent-based model of COVID-19 dynamics and interventions},
author={Kerr, Cliff C and Stuart, Robyn M and Mistry, Dina and Abeysuriya, Romesh G and Rosenfeld, Katherine and Hart, Gregory R and N{\'u}{\~n}ez, Rafael C and Cohen, Jamie A and Selvaraj, Prashanth and Hagedorn, Brittany and others},
journal={PLOS Computational Biology},
volume={17},
number={7},
pages={e1009149},
year={2021},
publisher={Public Library of Science San Francisco, CA USA},
doi={10.1371/journal.pcbi.1009149}
}
@InProceedings{kerr2022python,
title={Python vs.\ {t}he pandemic: a case study in high-stakes software development},
author={Kerr, Cliff C and Stuart, Robyn M and Mistry, Dina and Abeysuriya, Romesh G and Cohen, Jamie A and George, Lauren and Jastrzebski, Micha{\l} and Famulare, Michael and Wenger, Edward and Klein, Daniel J},
year={2022},
booktitle={Proceedings of the 21st {P}ython in Science Conference ({SciPy} 2022)},
doi={10.25080/majora-212e5952-00e}
}
@article{kerr2015optima,
title={Optima: a model for HIV epidemic analysis, program prioritization, and resource optimization},
author={Kerr, Cliff C and Stuart, Robyn M and Gray, Richard T and Shattock, Andrew J and Fraser-Hurt, Nicole and Benedikt, Clemens and Haacker, Markus and Berdnikov, Maxim and Mahmood, Ahmed Mohamed and Jaber, Seham Abdalla and others},
journal={Journal of Acquired Immune Deficiency Syndromes},
volume={69},
number={3},
pages={365--376},
year={2015},
publisher={LWW}
}
@Incollection{kerr2020optima,
author = {Kerr, Cliff C and Stuart, Robyn M and Kedziora, David J and Brown, Amber and Abeysuriya, Romesh and Chadderdon, George L and Nachesa, Anna and Wilson, David P},
title = {Optima HIV methodology and approach},
booktitle = {Tackling the World’s Fastest-Growing HIV Epidemic},
chapter = {},
publisher = {The World Bank},
year = {2020},
editor = {Zhao, Feng and Benedikt, C and Wilson, David},
address = {Washington, DC},
pages = {291},
doi = {10.1596/978-1-4648-1523-2_ch13}
}
@article{kedziora2019cascade,
title={The {C}ascade {A}nalysis {T}ool: software to analyze and optimize care cascades},
author={Kedziora, David J and Abeysuriya, Romesh and Kerr, Cliff C and Chadderdon, George L and Harbuz, Vlad-Ștefan and Metzger, Sarah and Wilson, David P and Stuart, Robyn M},
journal={Gates Open Research},
volume={3},
year={2019},
publisher={Gates Foundation-Open Access},
doi={10.12688/gatesopenres.13031.2}
}
@misc{atomica,
author = {{The Atomica Team}},
title = {Atomica: a simulation engine for compartmental models.},
year = {2020},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://github.com/atomicateam/atomica}
}
@article{pearson2018optima,
title={Optima Nutrition: an allocative efficiency tool to reduce childhood stunting by better targeting of nutrition-related interventions},
author={Pearson, Ruth and Killedar, Madhura and Petravic, Janka and Kakietek, Jakub J and Scott, Nick and Grantham, Kelsey L and Stuart, Robyn M and Kedziora, David J and Kerr, Cliff C and Skordis-Worrall, Jolene and others},
journal={BMC Public Health},
volume={18},
number={1},
pages={1--12},
year={2018},
publisher={Springer},
doi={10.1186/s12889-018-5294-z}
}
@article{gosce2021optima,
title={Optima TB: A tool to help optimally allocate tuberculosis spending},
author={Gosc{\'e}, Lara and Abou Jaoude, Gerard J and Kedziora, David J and Benedikt, Clemens and Hussain, Azfar and Jarvis, Sarah and Skrahina, Alena and Klimuk, Dzmitry and Hurevich, Henadz and Zhao, Feng and others},
journal={PLOS Computational Biology},
volume={17},
number={9},
pages={e1009255},
year={2021},
publisher={Public Library of Science San Francisco, CA USA},
doi={10.1371/journal.pcbi.1009255}
}
@inproceedings{o2022fpsim,
title={{FPSim}: An Agent-Based Model of Family Planning for Informed Policy Decision-making},
author={O'Brien, Michelle L and Valente, Annie and Chabot-Couture, Guillaume and Proctor, Joshua and Klein, Daniel and Kerr, Cliff and Zimmermann, Marita},
booktitle={PAA 2022 Annual Meeting},
year={2022},
organization={PAA}
}
@article{fraser2021using,
title={Using allocative efficiency analysis to inform health benefits package design for progressing towards Universal Health Coverage: Proof-of-concept studies in countries seeking decision support},
author={Fraser-Hurt, Nicole and Hou, Xiaohui and Wilkinson, Thomas and Duran, Denizhan and Abou Jaoude, Gerard J and Skordis, Jolene and Chukwuma, Adanna and Lao Pena, Christine and Tshivuila Matala, Opope O and Gorgens, Marelize and others},
journal={PLOS {O}ne},
volume={16},
number={11},
pages={e0260247},
year={2021},
publisher={Public Library of Science San Francisco, CA USA},
doi={10.1371/journal.pone.0260247}
}
@article{nust2020ten,
title={Ten simple rules for writing Dockerfiles for reproducible data science},
author={N{\"u}st, Daniel and Sochat, Vanessa and Marwick, Ben and Eglen, Stephen J and Head, Tim and Hirst, Tony and Evans, Benjamin D},
journal={PLOS {C}omputational {B}iology},
volume={16},
number={11},
pages={e1008316},
year={2020},
publisher={Public Library of Science San Francisco, CA USA},
doi={10.1371/journal.pcbi.1008316}
}
@article{kerr2019epidemiology,
title={Is epidemiology ready for Big Software?},
author={Kerr, Cliff C},
journal={Pathogens and {D}isease},
volume={77},
number={1},
pages={ftz006},
year={2019},
publisher={Oxford University Press},
doi={10.1093/femspd/ftz006}
}
@article{esteban2019fmriprep,
title={fMRIPrep: a robust preprocessing pipeline for functional MRI},
author={Esteban, Oscar and Markiewicz, Christopher J and Blair, Ross W and Moodie, Craig A and Isik, A Ilkay and Erramuzpe, Asier and Kent, James D and Goncalves, Mathias and DuPre, Elizabeth and Snyder, Madeleine and others},
journal={Nature {M}ethods},
volume={16},
number={1},
pages={111--116},
year={2019},
publisher={Nature Publishing Group},
doi={10.1038/s41592-018-0235-4}
}
@misc{nilearn,
author = {{The Nilearn Team}},
title = {Nilearn: a library for easy statistical and machine-learning analysis of brain volumes.},
year = {2010-2022},
publisher = {GitHub},
journal = {GitHub repository},
url = {https://nilearn.github.io/stable/index.html}
}
@article{hadfield2018nextstrain,
title={Nextstrain: real-time tracking of pathogen evolution},
author={Hadfield, James and Megill, Colin and Bell, Sidney M and Huddleston, John and Potter, Barney and Callender, Charlton and Sagulenko, Pavel and Bedford, Trevor and Neher, Richard A},
journal={Bioinformatics},
volume={34},
number={23},
pages={4121--4123},
year={2018},
publisher={Oxford University Press},
doi={10.1093/bioinformatics/bty407}
}
@article{waskom2021seaborn,
title={Seaborn: statistical data visualization},
author={Waskom, Michael L},
journal={Journal of Open Source Software},
volume={6},
number={60},
pages={3021},
year={2021},
doi={10.21105/joss.03021}
}
@article{halchenko2021datalad,
title={DataLad: distributed system for joint management of code, data, and their relationship},
author={Halchenko, Yaroslav and Meyer, Kyle and Poldrack, Benjamin and Solanky, Debanjum and Wagner, Adina and Gors, Jason and MacFarlane, Dave and Pustina, Dorian and Sochat, Vanessa and Ghosh, Satrajit and others},
journal={Journal of Open Source Software},
volume={6},
number={63},
year={2021},
doi={10.21105/joss.03262}
}
@misc{pytorch-research,
author = {Lorica, Ben},
title = {Why AI and machine learning researchers are beginning to embrace PyTorch},
year = {2017},
url = {oreilly.com/radar/podcast/why-ai-and-machine-learning-researchers-are-beginning-to-embrace-pytorch}
}
@article{maciver2019hypothesis,
title={Hypothesis: A new approach to property-based testing},
author={MacIver, David R and Hatfield-Dodds, Zac and others},
journal={Journal of Open Source Software},
volume={4},
number={43},
pages={1891},
year={2019},
doi={10.21105/joss.01891}
}
@article{synthpops,
author = {Mistry, Dina and Kerr, Cliff C and Abeysuriya, Romesh G and Wu, Meikang and Fisher, Mary and Thompson, Ace and Skrip, Laura and Cohen, Jamie A and Klein, Daniel J},
title = {SynthPops: a generative model of human contact networks.},
year = {in preparation}
}
@article{burden-codereview,
title={Easing the burden of code review},
author={{Nature Editorial Board}},
journal={Nature Methods},
volume={15},
number={9},
pages={641},
year={2018},
doi={10.1038/s41592-018-0137-5}
}
@article{robitaille2013astropy,
title={Astropy: A community {P}ython package for astronomy},
author={Robitaille, Thomas P and Tollerud, Erik J and Greenfield, Perry and Droettboom, Michael and Bray, Erik and Aldcroft, Tom and Davis, Matt and Ginsburg, Adam and Price-Whelan, Adrian M and Kerzendorf, Wolfgang E and others},
journal={Astronomy \& Astrophysics},
volume={558},
pages={A33},
year={2013},
publisher={EDP Sciences}
}
@article{vallat2018pingouin,
title={Pingouin: statistics in Python.},
author={Vallat, Raphael},
journal={Journal of Open Source Software},
volume={3},
number={31},
pages={1026},
year={2018},
doi={10.21105/joss.01026}
}
@article{benureau2018re,
title={Re-run, repeat, reproduce, reuse, replicate: transforming code into scientific contributions},
author={Benureau, Fabien CY and Rougier, Nicolas P},
journal={Frontiers in {N}euroinformatics},
volume={11},
pages={69},
year={2018},
publisher={Frontiers Media SA},
doi={10.3389/fninf.2017.00069}
}
@article{ramachandran2011mayavi,
title={Mayavi: 3D visualization of scientific data},
author={Ramachandran, Prabhu and Varoquaux, Ga{\"e}l},
journal={Computing in Science \& Engineering},
volume={13},
number={2},
pages={40--51},
year={2011},
publisher={IEEE},
doi={10.1109/mcse.2011.35}
}
@article{sullivan2019pyvista,
title={PyVista: 3D plotting and mesh analysis through a streamlined interface for the Visualization Toolkit (VTK)},
author={Sullivan, C and Kaszynski, Alexander},
journal={Journal of Open Source Software},
volume={4},
number={37},
pages={1450},
year={2019},
publisher={The Open Journal},
doi={10.21105/joss.01450}
}
@article{perkel2020challenge,
title={Challenge to scientists: does your ten-year-old code still run?},
author={Perkel, Jeffrey M},
journal={Nature},
volume={584},
number={7822},
pages={656--659},
year={2020},
publisher={Nature Publishing Group},
doi={10.1038/d41586-020-02462-7}
}
@article{kerr2018optimization,
title={Optimization by adaptive stochastic descent},
author={Kerr, Cliff C and Dura-Bernal, Salvador and Smolinski, Tomasz G and Chadderdon, George L and Wilson, David P},
journal={PloS one},
volume={13},
number={3},
pages={e0192944},
year={2018},
publisher={Public Library of Science San Francisco, CA USA}
}
@InProceedings{rocklin2015dask,
author = { Matthew Rocklin },
title = { Dask: Parallel Computation with Blocked algorithms and Task Scheduling },
booktitle = { Proceedings of the 14th {P}ython in Science Conference ({SciPy} 2015) },
pages = { 130 - 136 },
year = { 2015 },
editor = { Kathryn Huff and James Bergstra },
doi = { 10.25080/Majora-7b98e3ed-013 },
}