Code & Simulation Data References

Code & Simulation Datasets

The following resources are used in workshop examples or exercises.

Adeodu, O., Gee, M., Mahmoudi, B., Vadigepalli, R., & Kothare, M. 2024. “Simulation of the short term impact of atrial fibrillation on hemodynamic variables (Version 1) [Dataset]”. SPARC Portal. DOI: https://doi.org/10.26275/B0LJ-XSTO

Azzolin, L., Eichenlaub, M., Nagel, C., Nairn, D., Sánchez, J., Unger, L., Dössel, O., Jadidi, A., & Loewe, A. 2023. “AugmentA: Patient-specific Augmented Atrial model Generation Tool”. Computerized Medical Imaging and Graphics, 108, 102265.

Bump, Joseph K; Beyer, Dean; O’Neil, Shawn. 2019. “code, data, and metadata document for the manuscript: Territorial landscapes: incorporating density-dependence into wolf resource selection study designs”. Retrieved from the Data Repository for the University of Minnesota, http://hdl.handle.net/11299/201859.

Do, H. X., Smith, J. P., Fry, L. M., Gronewold, A. D. 2020. “Monthly water balance estimates for the Laurentian Great Lakes from 1950 to 2019 (v1.1)” [Data set], University of Michigan - Deep Blue Data. DOI: https://doi.org/10.7302/tx97-nn12

Heuschele, Deborah; Furuta, Daniel; Smith, Kevin; Marchetto, Peter. 2022. Data and analysis code for “Capturing High Resolution Plant Movement in the Field”. Retrieved from the Data Repository for the University of Minnesota (DRUM), DOI: https://doi.org/10.13020/7e6x-8f36.

Jarai, A., Sun, M. 2022. “Simulation data for toppling and height probabilities in sandpiles. Bath: University of Bath Research Data Archive”. DOI: https://doi.org/10.15125/BATH-01088.

Lu, Z., & Ku, Y. 2020. “NeuroRA: A Python toolbox of representational analysis from multi-modal neural data. Frontiers in Neuroinformatics”. 14:563669. DOI: https://doi.org/10.3389/fninf.2020.563669

Matúš Medo, Charlotte K. Y. Ng, Michaela Medová. 2024. “A comprehensive comparison of tools for fitting mutational signatures”. Nature Communications 15, 9467. URL: https://www.nature.com/articles/s41467-024-53711-6

Horna Munoz, Daniel; Constantinescu, George; Rhoads, Bruce ; Lewis, Quinn; Sukhodolov, Alexander. 2020. “Confluence Density Effects Simulation Database. University of Illinois at Urbana-Champaign”. DOI: https://doi.org/10.13012/B2IDB-6257171_V1

Yang, Huang; Waugh, Darryn W. 2019. “Data associated with Yang et al. 2019.”Dependence of Atmospheric Transport into the Arctic on Extent of the Hadley Cell”, Johns Hopkins University Data Archive. DOI: https://doi.org/10.7281/T1/AWJUGZ

Other Resources

“AugmentA/Main.py at Main · KIT-IBT/AugmentA.” n.d. GitHub. Accessed February 27, 2025. https://github.com/KIT-IBT/AugmentA/blob/main/main.py.

Bhandari Neupane, Jayanti, Ram P. Neupane, Yuheng Luo, Wesley Y. Yoshida, Rui Sun, and Philip G. Williams. 2019. “Characterization of Leptazolines A–D, Polar Oxazolines from the Cyanobacterium Leptolyngbya Sp., Reveals a Glitch with the ‘Willoughby–Hoye’ Scripts for Calculating NMR Chemical Shifts.” Organic Letters 21 (20): 8449–53. https://doi.org/10.1021/acs.orglett.9b03216.

“Biomass Scenario Model Energy Analysis NREL.” n.d. Accessed February 17, 2023. https://www.nrel.gov/analysis/bsm/.

“Blooms Taxonomy :: Resource for Educators.” n.d. Accessed January 29, 2023. https://bloomstaxonomy.net/.

Boulesteix, Anne-Laure, Rolf Hh Groenwold, Michal Abrahamowicz, Harald Binder, Matthias Briel, Roman Hornung, Tim P Morris, Jörg Rahnenführer, and Willi Sauerbrei. 2020. “Introduction to Statistical Simulations in Health Research.” BMJ Open 10 (12): e039921. https://doi.org/10.1136/bmjopen-2020-039921.

Burt, Andrew, Brenda Leong, and Stuart Shirrell. n.d. “Beyond Explainability: A Practical Guide to Managing Risk in Machine Learning Models.”

“Computer Simulation.” 2022. Wikipedia. https://en.wikipedia.org/w/index.php?title=Computer_simulation&oldid=1129408483.

“Contribute Data FITBIR.” n.d. Accessed March 7, 2025. https://fitbir.nih.gov/content/contribute-data.

Cosmo, Roberto Di, Sabrina Granger, Konrad Hinsen, Nicolas Jullien, and Daniel Le Berre. 2025. “CODE Beyond FAIR.” https://inria.hal.science/hal-04930405/document.

“DCN CURATED Modules - Github.” n.d. Accessed January 29, 2023. https://datacurationnetwork.github.io/CURATED/modules/.

“DCN Data Primers - Github.” 2023. https://github.com/DataCurationNetwork/data-primers.

Denholm, P, and R Margolis. 2008. “Supply Curves for Rooftop Solar PV-Generated Electricity for the United States.” Technical Report.

Dietrich, Dianne. 2025. “Readme Template for Software.” https://doi.org/10.7298/H85A-QZ91.

“FAIR Data Podcast RSpace.” n.d. Accessed January 29, 2023. https://www.researchspace.com/fair-data-podcast.

Fejer, Bela. 2020. “Data from: Anomalous Electron Temperature.” Browse All Datasets, December. https://doi.org/https://doi.org/10.26078/ZERJ-B751.

Gebru, Timnit, Jamie Morgenstern, Briana Vecchione, Jennifer Wortman Vaughan, Hanna Wallach, Hal Daumé III, and Kate Crawford. 2021. “Datasheets for Datasets.” arXiv. http://arxiv.org/abs/1803.09010.

“Gridded Population of the World (GPW), V3 SEDAC.” n.d. Accessed February 3, 2023. https://sedac.ciesin.columbia.edu/data/collection/gpw-v3.

“Gridded Population of the World (GPW), V4 SEDAC.” n.d. Accessed February 3, 2023. https://sedac.ciesin.columbia.edu/data/collection/gpw-v4.

Gruenpeter, Morane, Daniel S. Katz, Anna-Lena Lamprecht, Tom Honeyman, Daniel Garijo, Alexander Struck, Anna Niehues, et al. 2021. “Defining Research Software: A Controversial Discussion.” Zenodo. https://doi.org/10.5281/ZENODO.5504016.

Hinsen, Konrad. 2019. “Dealing With Software Collapse.” Computing in Science & Engineering 21 (3): 104–8. https://doi.org/10.1109/MCSE.2019.2900945.

“Home FITBIR.” n.d. Accessed March 7, 2025. https://fitbir.nih.gov/.

Kambezidis, Harry D. 2017. “Solar Radiation Modelling: The Latest Version and Capabilities of MRM.” Journal of Fundamentals of Renewable Energy and Applications 07 (02). https://doi.org/10.4172/2090-4541.1000e114.

Kanda, Ravi, Anthony Lowry, and Susanne Buiter. 2021. “2D Thermo-Mechanical Simulations of Flat Subduction - Supporting Data for Research Manuscript.” Browse All Datasets, November. https://doi.org/https://doi.org/10.26078/3BQS-9029.

Kozlowski, Wendy Anne. 2025. “Readme Template for Data.” https://doi.org/10.7298/MHNS-ZM71.

Lee, Sean, Aamir Shakir, Darius Koenig, and Julius Lipp. 2024. “Open Source Strikes Bread - New Fluffy Embeddings Model.” https://www.mixedbread.ai/blog/mxbai-embed-large-v1.

Mullendore, Gretchen L., Matthew S. Mayernik, and Douglas C. Schuster. 2021. “Open Science Expectations for Simulation-Based Research.” Frontiers in Climate 3. https://www.frontiersin.org/articles/10.3389/fclim.2021.763420.

“Open Spatial Demographic Data and Research.” n.d. WorldPop. Accessed February 2, 2023. https://www.worldpop.org/.

“OpenPMD Standard for Simulation Data (and Metadata) Further Developed in PaNOSC WP5 News CORDIS European Commission.” n.d. Accessed February 22, 2023. https://cordis.europa.eu/article/id/413169-openpmd-standard-for-simulation-data-and-metadata-further-developed-in-panosc-wp5.

“ORNL LandScan Viewer - Oak Ridge National Laboratory.” n.d. Accessed February 2, 2023. https://landscan.ornl.gov/.

“ParaView.” n.d. Accessed February 2, 2023. https://www.paraview.org/about/.

“ParaView Companion Tools.” n.d. Accessed February 2, 2023. https://www.paraview.org/companion-tools/.

“Physical Solar Model (PSM) V3 API NREL: Developer Network.” n.d. Accessed February 17, 2023. https://developer.nrel.gov/docs/solar/nsrdb/psm3-download/.

“Reference Documents.” n.d.a. Accessed July 7, 2023. https://www.sisostds.org/ProductsPublications/ReferenceDocuments.aspx.

———. n.d.b. Accessed July 7, 2023. https://www.sisostds.org/ProductsPublications/ReferenceDocuments.aspx.

Sengupta, Manajit, Andrew Weekley, Aron Habte, and Anthony Lopez. n.d. “Validation of the National Solar Radiation Database (NSRDB) (2005‒2012): Preprint.”

Sengupta, Manajit, Yu Xie, Anthony Lopez, Aron Habte, Galen Maclaurin, and James Shelby. 2018. “The National Solar Radiation Data Base (NSRDB).” Renewable and Sustainable Energy Reviews 89 (June): 51–60. https://doi.org/10.1016/j.rser.2018.03.003.

“Software Tools – OHDSI.” n.d. Accessed February 27, 2025. https://www.ohdsi.org/software-tools/.

“Supporting Software Preservation Services in Research and Memory Organizations • CLIR.” n.d. Accessed January 29, 2023. https://www.clir.org/pubs/reports/supporting-software-preservation-services-in-research-and-memory-organizations/.

“SWAT Soil & Water Assessment Tool.” n.d. Accessed February 3, 2023. https://swat.tamu.edu/.

Thurgood, Jaden. 2021. “Aircraft Input Files for Pylot and MachUpX.” Browse All Datasets, February. https://doi.org/https://doi.org/10.26078/d71p-9a11.

Ullrich, Oliver, Victor Potapenko, and Naphtali Rishe. 2020a. “Examining Repositories for Simulation Data.” SNE Simulation Notes Europe 30 (2): 61–66. https://doi.org/10.11128/sne.30.tn.10513.

———. 2020b. “Examining Repositories for Simulation Data.” SNE Simulation Notes Europe 30 (2): 61–66. https://doi.org/10.11128/sne.30.tn.10513.

“What About Model Data? Best Practices for Preservation and Replicability.” n.d. Accessed January 29, 2023. https://zoidy.shinyapps.io/ModelDataRubric/#.

White House Office of Science and Technology Policy (OSTP). 2022. “Desirable Characteristics of Data Repositories for Federally Funded Research.” Executive Office of the President of the United States. https://doi.org/10.5479/10088/113528.

Wickett, Karen M. 2023. “Critical Data Modeling and the Basic Representation Model.” Journal of the Association for Information Science and Technology online (early release). https://doi.org/10.1002/asi.24745.

Xu, L., R. D. Pyles, K. T. Paw U, S. H. Chen, and E. Monier. 2014. “Coupling the High-Complexity Land Surface Model ACASA to the Mesoscale Model WRF.” Geoscientific Model Development 7 (6): 2917–32. https://doi.org/10.5194/gmd-7-2917-2014.

Yang, Huang, Darryn W. Waugh, Clara Orbe, and Gang Chen. 2020. “Dependence of Atmospheric Transport Into the Arctic on the Meridional Extent of the Hadley Cell.” Geophysical Research Letters 47 (20): e2020GL090133. https://doi.org/10.1029/2020GL090133.