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COMPASS-DOE / data-workflows

Sensor data workflows and processing scripts
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References for SP paper #83

Open bpbond opened 9 months ago

bpbond commented 9 months ago

Just saw this, so opening an issue to log it.

Nature 4.0: A networked sensor system for integrated biodiversity monitoring https://onlinelibrary.wiley.com/doi/10.1111/gcb.17056?af=R

Chu et al.: AmeriFlux BASE data pipeline to support network growth and data sharing, Sci Data, 10, 614, 2023. https://www.nature.com/articles/s41597-023-02531-2

bpbond commented 9 months ago

More data workflows

Stoudt, S., Vásquez, V. N., and Martinez, C. C.: Principles for data analysis workflows, PLoS Comput. Biol., 17, e1008770, 2021. http://dx.doi.org/10.1371/journal.pcbi.1008770

Liu, J., Cichota, R., Langer, S., Burgueño, E., and Michel, A.: Data pipeline for managing field experiments, MethodsX, 10, 102031, 2023. http://dx.doi.org/10.1016/j.mex.2023.102031

Open science

Lowndes, J. S. S., Best, B. D., Scarborough, C., Afflerbach, J. C., Frazier, M. R., O’Hara, C. C., Jiang, N., and Halpern, B. S.: Our path to better science in less time using open data science tools, Nat Ecol Evol, 1, 160, 2017. http://dx.doi.org/10.1038/s41559-017-0160

Wilkinson et al.: The FAIR Guiding Principles for scientific data management and stewardship, Sci Data, 3, 160018, 2016. http://dx.doi.org/10.1038/sdata.2016.18

Models-data

Dietze, M. C., LeBauer, D. S., and Kooper, R.: On improving the communication between models and data, Plant Cell Environ., 36, 1575–1585, 2012. http://dx.doi.org/10.1111/pce.12043

Fer et al.: Beyond ecosystem modeling: A roadmap to community cyberinfrastructure for ecological data-model integration, Glob. Chang. Biol., 27, 13–26, 2021. http://dx.doi.org/10.1111/gcb.15409

bpbond commented 9 months ago

Importance of good data management etc.:

Improper data practices erode the quality of global ecological databases and impede the progress of ecological research https://onlinelibrary.wiley.com/doi/10.1111/gcb.17116?af=R

bpbond commented 8 months ago

Tools

Ram, K.: Git can facilitate greater reproducibility and increased transparency in science, Source Code Biol. Med., 8, 7, 2013. http://dx.doi.org/10.1186/1751-0473-8-7

Braga, P. H. P., Hébert, K., Hudgins, E. J., Scott, E. R., Edwards, B. P. M., Sánchez Reyes, L. L., Grainger, M. J., Foroughirad, V., Hillemann, F., Binley, A. D., Brookson, C. B., Gaynor, K. M., Shafiei Sabet, S., Güncan, A., Weierbach, H., Gomes, D. G. E., and Crystal-Ornelas, R.: Not just for programmers: How GitHub can accelerate collaborative and reproducible research in ecology and evolution, Methods Ecol. Evol., 14, 1364–1380, 2023. http://dx.doi.org/10.1111/2041-210x.14108

bpbond commented 5 months ago

Flags in other model workflows

Jung, M., Nelson, J., Migliavacca, M., El-Madany, T., Papale, D., Reichstein, M., Walther, S., and Wutzler, T.: Technical note: Flagging inconsistencies in flux tower data, Biogeosciences, 21, 1827–1846, 2024. https://bg.copernicus.org/articles/21/1827/2024/

bpbond commented 2 weeks ago

Networking the forest infrastructure towards near real-time monitoring – A white paper https://www.sciencedirect.com/science/article/pii/S0048969723007830

The Integrated Carbon Observation System in Europe https://journals.ametsoc.org/view/journals/bams/103/3/BAMS-D-19-0364.1.xml