Employment
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2022-Present Associate Professor, Department of Environmental Science, Policy and Management, University of California, Berkeley.
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2015-2022 Assistant Professor, Department of Environmental Science, Policy and Management, University of California, Berkeley.
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2013-2015 NSF Post-doctoral Scholar in the Department of Applied Mathematics and Statistics, University of California, Santa Cruz. Mentors: Marc Mangel, Stephan Munch
Education
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2012 Ph.D Population Biology, University of California, Davis. Mentor: Alan Hastings
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2007 A.B in Physics, Princeton University, with honors and certificates in biophysics and applied and computational mathematics.
Publications
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James J. Wray, Neta A. Bahcall, Paul Bode, Carl Boettiger, Phillip Hopkins (2006). The Shape, Multiplicity, and Evolution of Superclusters in Lambda-CDM Cosmology, The Astrophysical Journal 652 (2) 907-916. doi:10.1086/50860. (preprint)
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Carl Boettiger, Jonathan Dushoff, Joshua S Weitz (2010). Fluctuation domains in adaptive evolution, Theoretical Population Biology 77 (1) 6-13. doi:10.1016/j.tpb.2009.10.003. (preprint, code, data)
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Carl Boettiger, Graham Coop, Peter Ralph (2012). Is your phylogeny informative? Measuring the power of comparative methods, Evolution 66 (7) 2240-51. doi:10.1111/j.1558-5646.2011.01574.x, (preprint, code, data)
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Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger, Brian O’Meara, (2012). Modeling Stabilizing Selection: Expanding the Ornstein-Uhlenbeck Model of Adaptive Evolution, Evolution 66 (8) 2369-2383. doi:10.1111/j.1558-5646.2012.01619.x (software)
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Carl Boettiger, Alan Hastings (2012). Quantifying Limits to Detection of Early Warning for Critical Transitions, Journal of the Royal Society: Interface 9 (75) 2527-2539. doi:10.1098/rsif.2012.0125. (preprint, code)
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Carl Boettiger, Duncan Temple Lang (2012). Treebase: An R package for discovery, access and manipulation of online phylogenies, Methods in Ecology and Evolution 3 (6) 1060–1066. doi:10.1111/j.2041-210X.2012.00247x. (code, software)
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Carl Boettiger, Duncan Temple Lang, Peter Wainwright (2012). rfishbase: exploring, manipulating and visualizing FishBase data from R, Journal of Fish Biology. 81 (6) 2030–2039. doi:10.1111/j.1095-8649.2012.03464.x. (code, software)
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Carl Boettiger, Alan Hastings (2012). Early Warning Signals and the Prosecutor’s Fallacy, Proceedings of the Royal Society B 279 (1748) 4734-4739. doi:10.1098/rspb.2012.2085. (preprint, code, data)
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Carl Boettiger, Alan Hastings (2013). Tipping points: From patterns to predictions, Nature 493, 157–158. doi:10.1038/493157a.
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Carl Boettiger, Noam Ross, Alan Hastings (2013). Early warning signals: The charted and uncharted territories. Theoretical Ecology doi:10.1007/s12080-013-0192-6. (preprint, code)
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Carl Boettiger, Alan Hastings (2013). No early warning signals for stochastic transitions: insights from large deviation theory. Proceedings of the Royal Society B. doi:10.1098/rspb.2013.1372. (preprint, code)
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Carl Boettiger, Marc Mangel, Stephan Munch (2015). Avoiding tipping points in fisheries management through Gaussian process dynamic programming. Proceedings of the Royal Society B 282(1801), 8–11. doi:10.1098/rspb.2014.1631. (preprint, code, data). F1000 recommended
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Carl Boettiger (2015). An introduction to Docker for reproducible research. ACM SIGOPS Operating Systems Review 49(1), 71-79. doi:10.1145/2723872.2723882. (preprint)
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Carl Boettiger, Scott Chamberlain, Edmund Hart, Karthik Ram (2015). Building Software, Building Community: Lessons from the rOpenSci Project. Journal of Open Research Software 3: e8, doi:10.5334/jors.bu.
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Carl Boettiger, Scott Chamberlain, Rutger Vos and Hilmar Lapp (2016). RNeXML: a package for reading and writing richly annotated phylogenetic, character, and trait data in R. Methods in Ecology and Evolution. doi:10.1111/2041-210X.12469. (preprint, code, software)
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Carl Boettiger, Michael Bode, James N. Sanchirico, Jacob LaRiviere, Alan Hastings, and Paul Robert Armsworth (2016). Optimal management of a stochastically varying population when policy adjustment is costly. Ecological Applications 26 (3) 808-817.
doi:10.1890/15-0236. (preprint, code) -
T Alex Perkins, Carl Boettiger, Benjamin L. Philips. (2016) After the games are over: life-history trade-offs drive dispersal attenuation following range expansion. Ecology and Evolution 6 (18) 6425-6434. doi:10.1002/ece3.2314. (preprint, code)
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Hampton, Jones, Wasser, Schuldhauer, Supp, Brun, Herandez, Boettiger, Collins, Gross, Fernandez, Budden, White, Teal, Labou, Aukema (2017). Skills and Knowledge for Data Intensive Research. BioScience. doi:10.1093/biosci/bix025. (preprint)
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Ben Marwick, Carl Boettiger, Lincoln Mullen (2017). Packaging data analytical work reproducibly using R (and friends). The American Statistician. doi:10.1080/00031305.2017.1375986. (preprint)
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Getz, Marshall, Carlson, Giuggioli, Ryan, Romañach, Boettiger, Chamberlain, Larsen, D’Odorico, O’Sullivan (2017). Making ecological models adequate. Ecology Letters. doi:10.1111/ele.12893
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Carl Boettiger (2017). Generating Codemeta Metadata for R Packages.
The Journal of Open Source Software 2 (19), 454, doi:10.21105/joss.00454 -
Carl Boettiger, Dirk Eddelbuettel (2018). An Introduction to Rocker: Docker Containers for R. The R Journal. doi:10.32614/RJ-2017-065
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Carl Boettiger (2018). From noise to knowledge: how randomness generates novel phenomena and reveals information. Ecology Letters. doi:10.1111/ele.13085 (preprint, code, data)
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Milad Memarzadeh, Carl Boettiger (2018). Adaptive management of ecological systems under partial observability. Biological Conservation. 224, 9-15. doi:10.1016/j.biocon.2018.05.009. (software)
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Carl Boettiger (2018). Managing Larger Data on a GitHub Repository. Journal of Open Source Software, 3(29), 971, doi:10.21105/joss.00971. (software).
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Karthik Ram, Carl Boettiger, Scott Chamberlain, Noam Ross, Maelle Salmon, & Stephanie Butland (2018). A Community of Practice Around Peer-review for Long-term Research Software Sustainability. Computing in Science & Engineering, 9615(c), 1–1. doi:10.1109/MCSE.2018.2882753
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Katz, Allen, Barba, Berg, Bik, Boettiger, et al. (32 co-authors.) (2018). The principles of tomorrow’s university. F1000Research, 7:1926 doi:10.12688/f1000research.17425.1.
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Carl Boettiger (2019). Ecological Metadata as Linked Data. Journal of Open Source Software, 4(34), 1276, doi:10.21105/joss.01276 (software).
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Dan Sholler, Karthik Ram, Carl Boettiger, Daniel S Katz (2019). Enforcing public data archiving policies in academic publishing: A study of ecology journals. Big Data & Society 6(1) 1-18. doi:10.1177/2053951719836258. (preprinthttps://doi.org/10.48550/arXiv.1810.13040)
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Milad Memarzadeh, Carl Boettiger (2019). Resolving the Measurement Uncertainty Paradox in Ecological Management. American Naturalist. doi:10.1086/702704. (preprint, code, data). F1000 recommended
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Carl Boettiger, Ryan Batt (2019). Bifurcation or state tipping: assessing transition type in a model trophic cascade. Journal of Mathematical Biology. doi:10.1007/s00285-019-01358-z (preprint, code)
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Milad Memarzadeh, Gregory L. Britten, Boris Worm, Carl Boettiger (2019). Rebuilding global fisheries under uncertainty. Proceedings of the National Academy of Sciences. doi:10.1073/pnas.1902657116
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de Aguiar, Newman, Pires, Yeakel, Boettiger, Burkle, Gravel, Guimarães Jr, O’Donnell, Poisot, Fortin, Hembry (2019). Revealing biases in the sampling of ecological interaction networks, PeerJ, doi:10.7717/peerj.7566. (software).
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Carl Boettiger (2020). Ecological management of stochastic systems with long transients. Theoretical Ecology. doi:10.1007/s12080-020-00477-4, (code)
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Kari Norman, Scott Chamberlain, Carl Boettiger (2020). taxadb: A high‐performance local taxonomic database interface. Methods in Ecology and Evolution. doi:10.1111/2041-210X.13440 (software)
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Pascal, Memarzadeh, Boettiger, Lloyd, Chadès (2020). A Shiny r app to solve the problem of when to stop managing or surveying species under imperfect detection Methods in Ecology and Evolution. doi:10.1111/2041-210X.13501 (software)
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Carl Boettiger (2020). [Rp] Fluctuation domains in adaptive evolution. ReScience C 6, 1, #15, doi:10.5281/zenodo.4081202, (pdf, code)
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Caleb Scoville, Melissa Chapman, Razvan Amironesei, Carl Boettiger (2021). Algorithmic conservation in a changing climate. Current Opinion in Environmental Sustainability 51, 30-35, doi:10.1016/j.cosust.2021.01.009.
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Reimer, Arroyo-Esquivel, Jiang, Scharf, Wolkovich, Zhu, Boettiger (2021). Noise can create or erase long transient dynamics. Theoretical Ecology doi:10.1007/s12080-021-00518-6, (code, data)
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Karatayev, Baskett, Kushner, Shears, Caselle, Boettiger (2021). Grazer behavior can regulate large-scale patterning of community states. Ecology Letters doi:10.1111/ele.13828 (preprint)
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Chapman, Oestreich, Frawley, Boettiger, Diver, Santos, Scoville, Armstrong, Blondin, Chand, Haulsee, Knight, Crowder (2021). Promoting equity in the use of algorithms for high seas conservation. One Earth doi:10.1016/j.oneear.2021.05.011, (preprint, code)
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Lapeyrolerie, Boettiger. (2021) Teaching machines to anticipate catastrophes. Proceedings of the National Academy of Sciences doi:10.1073/pnas.2115605118
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Chapman, Scoville, Lapeyrolerie, Boettiger. (2021). Power and Accountability in Reinforcement Learning Applications to Environmental Policy. 35th Conference on Neural Information Processing Systems (NeurIPS 2021) (preprint, pdf)
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Chapman, Wiltshire, Baur, Bowles, Carlisle, Castillo, Esquivel, Gennet, Iles, Karp, Kremen, Liebert, Olimpi, Ory, Ryan, Sciligo, Thompson, Waterhouse, Boettiger. (2022). Social-ecological feedbacks drive tipping points in farming system diversification. One Earth doi:10.1016/j.oneear.2022.02.007 (preprint, code)
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Boettiger (2022). The Forecast Trap. Ecology Letters 25, 1655-1664, doi:10.1111/ele.14024 (preprint, code)
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Lapeyrolerie, Chapman, Norman, Boettiger (2022). Deep Reinforcement Learning for Conservation Decisions. Methods in Ecology and Evolution. doi:10.1111/2041-210X.13954 (preprint, code)
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Laperoleryie, Boettiger. (2022). Limits to Ecological Forecasting: Estimating Uncertainty for Critical Transitions with Deep Learning. Methods in Ecology and Evolution. doi:10.1111/2041-210X.14013 (preprint, code)
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Benjamin S. Halpern, Carl Boettiger, Michael C. Dietze, Jessica A. Gephart, Patrick Gonzalez, Nancy B. Grimm, et al. (116 co-authors). (2023). Priorities for synthesis research in ecology and environmental science. Ecosphere. doi:10.1002/ecs2.4342
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Chapman, Boettiger, Brashares. (2023). Leveraging private land conservation to meet 2030 biodiversity targets in the United States. Conservation Science and Practice. doi:10.1111/csp2.12897 (preprint,
code) -
Thomas, Boettiger, Carey, Dietze, Johnson, Kenney, Mclachlan, Peters, Sokol, Weltzin, Willson, Woelmer, and Challenge Contributors (2023). The NEON Ecological Forecasting Challenge. Frontiers in Ecology and the Environment. 21, (3) pp 112-113. doi:10.1002/fee.2616 (preprint)
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Sydne Record, Carl Boettiger and Christine R Rollinson. (2023). Synthesizing forecasts to inform decision-making and advance ecological theory. Methods in Ecology and Evolution, 14: 728-731. doi:10.1111/2041-210X.14070
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Thomas, McClure, Moore, Woelmer, Boettiger, Figueiredo, Hensley, Carey (2023). Near-term forecasts of NEON lakes reveal gradients of environmental predictability across the U.S. Frontiers in Ecology and the Environment. 21, (5) pp 220-226. doi:10.1002/fee.2623 (preprint, code, data)
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Melissa Chapman, Lily Xu, Marcus Lapeyrolerie & Carl Boettiger (2023). Bridging adaptive management and reinforcement learning for more robust decisions. Philosophical Transactions of the Royal Society B 378, 2022-0195, doi:10.1098/rstb.2022.0195. (preprint)
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David Moreau, Krisina Wiebels, & Carl Boettiger. (2023). Containers for computational reproducibility. Nature Reviews Methods Primers 3, (50). doi:10.1038/s43586-023-00236-9
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Montealegre-Mora, Lapeyrolerie, Chapman, Keller, Boettiger. Pretty Darn Good Control: When are Approximate Solutions Better than Approximate Models. (2023) Bulletin of Mathematical Biology. doi:10.1007/s11538-023-01198-5 (preprint, code)
Grants
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Examining Environmental Justice through Open Source, Cloud Native Tools. NASA National Aeronautics and Space Administration (2022-2025). UCB Award ID: 055956-001. Carl Boettiger, PI. Total: $134,596.
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Collaborative Research: Frameworks: DeCODER (Democratized Cyberinfrastructure for Open Discovery to Enable Research). (2022-2026) National Science Foundation #OAC-2209865, UCB sub-award ID: 054904-001; PI $102,984
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A decision framework for managing European Green Crab infestations on the coast of Washington and Salish Sea shorelines. US Geological Survey (2022 - 2025). UCB Award ID: 054356-001. Carl Boettiger, PI. Total: $174,577.
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CAREER: Harnessing the data revolution for predicting and managing ecosystem regime shifts. Carl Boettiger. (2020-2025). National Science Foundation #DBI-1942280. $504,335.00
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The Rocker Project. Carl Boettiger, Noam Ross, Dirk Eddelbuettel. (2019 - 2021). Chan-Zuckerberg Initiative: Essential Open Source Software for Science. $75,912
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The Influence of Conflicting Policies and Supply-Chain Pressures on Farmers’ Decisions and Tradeoffs with Respect to Biodiversity, Profitability, and Sustainability. Timothy Bowles (PI), Alastair Iles, Claire Kremen, Carl Boettiger. (2018-2022). National Science Foundation #CNH-1824871 $1,301,737
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The rOpenSci Project. Karthik Ram, Carl Boettiger, Scott Chamberlain. (renewal, 2019-2021). Helmsley Charitable Trust, award 2016PG-BRI004. $1,000,000
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Detecting Change in Global Biodiversity through Large Scale Network Analysis. Carl Boettiger, Rosemary Gillespie, Rasmus Nielsen. (2018). Berkeley Institute for Data Science, $67,000
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Big Data, Big Uncertainty: Ecological Decision- Making in the 21st Century. (2018-2020). Hellman Fellows Award, The Hellman Foundation. $37,600
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Berkeley Collegium Award for Narrowing the Gap Between Teaching and Research. (2018-2019) $16,867.50
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Managing ecosystems under extreme uncertainty. (2016 - 2019) NSF XSEDE TG-DEB160003. NSF Estimated value of computing resources: $34,558
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Reproducible and Collaborative Data Science. NSF XSEDE TG-DEB160021. (2016 - 2019) NSF Estimated value of computing resources: $20,028
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James S McDonnell Foundation Post-doctoral Fellowship in Complex Systems (Awarded to post-doctoral scholar Allison Barner, who then chose to bring this award to my group at UC Berkeley) $200,000.
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The rOpenSci Project (2015-2018, Co-PI). Karthik Ram, Carl Boettiger, Scott Chamberlain. Helmsley Charitable Trust, award 2016PG-BRI004. $2,875,071
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The CodeMeta Project (2015). National Science Foundation #ACI-1549758 $165,782. (proposal link)
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The rOpenSci Project, Phase II funding (2014, Co-PI). Karthik Ram, Carl Boettiger, Scott Chamberlain. Alfred P. Sloan Foundation $300,000
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NSF Biology Post-doc (2013-2015). National Science Foundation #DBI-1306697, $138,000 (proposal link)
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The rOpenSci Project Phase I funding (2013 Co-PI). Karthik Ram, Carl Boettiger, Scott Chamberlain. Alfred P. Sloan Foundation $180,000
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IIASA YSSP fellowship (2009). National Academy of Sciences, OISE-0738129, $8,000. (proposal link)
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Computational Science Graduate Fellowship (2008). United States Department of Energy, #DE-FG02-97ER25308, $149,000. (proposal link)
Book Chapters
- Carl Boettiger (2017). A Reproducible R Notebook Using Docker. In J. Kitzes, D. Turek, & F. Deniz (Eds.), The Practice of Reproducible Research: Case Studies and Lessons from the Data-Intensive Sciences (1st ed., pp. 109–117). Oakland, CA: UC Press. https://www.ucpress.edu/book.php?isbn=9780520294752
Teaching
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ESPM-157: Data Science for Global Change Ecology. UC Berkeley. Upper-division undergraduate course, 4 units. Offered every Fall.
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ESPM-288: Reproducible and Collaborative Data Science. UC Berkeley. Graduate-level course, 3 units. Offered every Spring.
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ESPM-88B: Data Science in Ecology and the Environment. UC Berkeley. Freshman level Data-8 connector; not currently offered.
Invited Talks & Workshops
2023
- Invited seminar speaker, University of Southern California, Biology Department, CA
- Invited seminar speaker, University of California, Davis, Department of Mathematics, CA
- Invited seminar speaker, Virginia Polytechnic Institute and State University (Virginia Tech), VA
- Invited workshop speaker, Critical Transitions, Princeton University, NJ
- Invited seminar speaker, Data Sciences, University of New South Wales, Sydney, Australia
- Invited talk, Gordon Conference on Predictive Ecology, Stonehill College, MA
- Co-organizer, Ecological Forecasting Unconference, NEON Headquarters, Boulder, CO
- Invited workshop speaker, Australian Mathematical Sciences (AMSI) Winter School, Brisbane, Australia
- Invited seminar speaker, University of Queensland, Brisbane, Australia
2022
- Ecological Forecasting Initiative workshop (online)
- Invited speaker, International Institute of Applied Systems Analysis (IIASA) conference, Boston University, Boston MA.
2021
- Workshop on the Future of Synthesis, National Center for Ecological Analysis and Synthesis (co-organizer).
- National Ecological Observatory Network (NEON) Workshop on Complex Landscapes at Scale.
- Ecological Forecasting Initiative (EFI) Workshop on Empowering Development of the Next Generation of Educational Materials for Forecasting.
2020
- Invited seminar speaker, University of Oregon, Eugene, OR.
- Chan-Zuckerberg Initiative Essential Open Source Software for Science Workshop.
- Invited seminar speaker, DataONE data repository network.
- Ecological Forecasting Initiative Research Coordination Network Workshop.
- Invited seminar speaker, Concordia University, Montreal, CA.
2019
- Invited Biodiversity Research Center seminar speaker, University of British Columbia, Vancouver, Canada.
- Ecological Forecasting Oral Session, American Geophysical Union, San Fransisco, CA.
- Advancing Theory in Ecology, NSF Workshop. Pennsylvania State University, State College, PA.
- Biodiversity Data Workshop, invited speaker, Arizona State University, Tempe, AZ.
- Transients in Ecology, Organized Oral Session, Ecological Society of America Annual Meeting, Louisville, KY.
- Ecological Forecasting Initiative Conference, AAAS Headquarters, Washington DC.
- NIMBioS Transient Dynamics Workshop, University of Tennessee, Knoxville, TN.
- Project EDDIE keynote speaker, Carlton College, Northfield MN.
- US Research Software Sustainability Institute Workshop, NCEAS, Santa Barbara, CA.
- COMPASS Workshop for scientific communication, Asilomar, CA.
2018
- NSF SI2 PIs Meeting, Washington, DC.
- rOpenSci unconference, Seattle, WA.
- Faculty Learning Program Fellows Workshop Berkeley, CA.
- GraphXD, Berkeley, CA.
- Digital Data in Biodiversity UC Berkeley. (co-organizer)
- Ecological Society of America Invited Symposium Addressing Outstanding Challenges to Operationalizing Resilience (Organizer). New Orleans, LA.
- Nonlinear Forecasting for Fisheries Applications, NOAA Southwest Fisheries Science Center, Santa Cruz, CA.
2017
- CROSS Symposium Speaker Santa Cruz, CA.
- Imagining Tomorrow’s University Chicago, IL.
- rOpenSci unconference, Los Angeles, CA.
- Prov-a-thon: Practical Tools for Reproducible Science, Tamaya, NM.
- NSF Translational Data Science Workshop, Berkeley Institute for Data Science, Berkeley, CA.
2016
- Force16 Codemeta Workshop, Portland OR (organizer).
- CodeMeta NSF Workshop Portland, OR (organizer).
- rOpenSci unconference, San Francisco, CA.
2015
- Empirical Dynamical Modeling and Forecasting in Nonlinear Systems, NTU, Taiwan.
- Moore-Sloan Data Science Environments: Second Annual Data Science Summit (Workshop)
- Data Intensive Training Workshop, NCEAS, Santa Barbara, CA.
- NSF Big Data Hubs Design Charette, Western Region.
- rOpenSci unconference, San Francisco CA.
- Pretty Darn Good Control Working group, NIMBIOS, Knoxville TN.
2014
- Berkeley Initiative for Global Change Biology Workshop (student organized), UC Berkeley, CA.
- DIMACS Global Change, Berkeley CA.
- Zoology Seminar, University of Wisconsin, Madison, WI.
- ESPM Seminar, UC Berkeley, CA.
- rOpenSci unconference, San Francisco CA.
- Reproducible Science: Curriculum & Workflow Workshop, NESCent, Durham, NC.
- WSSSPE 2.0 Meeting. New Orleans, LA.
- Workflows Working Group, NCEAS, Santa Barbara, CA.
2013 & prior
- invited speaker, MBI, Sustainable Management of Living Natural Resources, Columbus, OH.
- invited seminar speaker, WHOI, Woods Hole, MA.
- invited seminar speaker, UC Davis Dept of Environmental Resources and Economics; Davis, CA.
- invited speaker, SSB Symposium, Evolution Conference, Ottawa, CAN.
- Sustainable Management of Living Natural Resources Workshop, MBI Columbus, OH.
- Academic software & workforce development Workshop, ISEES. Oakland, CA.
- Software Lifecycle Workshop, ISEES, Santa Barbara, CA.
- Pretty Darn Good Control Working group, NIMBIOS, Knoxville, TN.
- Stochastic spatial modeling in population dynamics Workshop, AIM, Palo Alto, CA.
Awards
- 2020 CAREER Award, National Science Foundation
- 2020 Early Career Fellow, Ecological Society of America
- 2020 Winkler Family Foundation Scholar
- 2018 Hellman Fellow, Hellman Foundation
- 2011 Volterra Award, Ecological Society of America, Theory Section
- 2007 Elected to Membership in the Society of Sigma Xi
- 2007 Allen G. Shenstone Prize in Physics, Princeton University
- 2007 The Class of 1870 Old English Prize, Princeton University
- 2006 Kusaka Memorial Prize in Physics, Princeton University
Service
Campus
- 2018 - current. Governance Committee for Data Science Programs
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- Faculty Working Group for the formation of the Division of Data Science & Information
- 2018 - 2019. Faculty Task Force for Data Science Minor Design
- 2018 - 2019. Faculty Advisory Committee of the Vice Chancellor for Undergraduate Education
- 2017 - 2018. ESPM Remote Sensing Faculty Search, committee member & equity liaison
- 2017 - 2018. ad hoc Data Science Degree Proposal Committee
- 2017 - 2020. Steering Committee for NSF Research Traineeship (NRT): Environment and Society: Data Science for the 21st Century (DS421)
- 2015 - 2019. Berkeley Research Computing Advisory Committee
Extra-campus
- 2019 - current. Associate Editor, Ecology Letters
- 2010 - current. rOpenSci Leadership Team
- 2014 - 2020. NCEAS Scientific Advisory Board
- 2016 - 2019. Jetstream Cloud Computing Stakeholder Advisory Board, XSEDE.
- Reviewer for over 40 journals, NSF review panelist, ad hoc reviewer for UC CCGA, NSF, NERSC.
Software
R Packages
minioclient
: A High Performance Interface to S3-based Object Stores. Carl Boettiger (2023).gbifdb
: A High Performance Interface to GBIF. Carl Boettiger (2022).neonstore
: A Fast and Provenance Aware Local NEON Data Store. Carl Boettiger, Quinn Thomas, Christine Laney, Claire Lunch (2020).contentid
: An Interface for Content-Based Identifiers. Carl Boettiger and Jorrit Poelen (2020).taxalight
: A Lightweight and Lightning-Fast Taxonomic Naming Interface. Carl Boettiger and Kari Norman (2020)sarsop
: Approximate POMDP Planning Software. Carl Boettiger and Jeroen Ooms and Milad Memarzadeh (2020).taxadb
: A High-Performance Local Taxonomic Database Interface. Carl Boettiger and Kari Norman and Jorrit Poelen and Scott Chamberlain, (2020).emld
: Ecological Metadata as Linked Data. Carl Boettiger (2019).virtuoso
: Interface to Virtuoso using ODBC. Carl Boettiger (2019).rdflib
: Tools to Manipulate and Query Semantic Data. Carl Boettiger (2018).codemetar
: Generate CodeMeta Metadata for R Packages. Carl Boettiger, Maëlle Salmon (2018).EcoNetGen
: Simulate and Sample from Ecological Interaction Networks. Marcus de Aguiar, Erica Newman, Mathias Pires, Carl Boettiger (2018).piggyback
: Managing Larger Data on a GitHub Repository. Carl Boettiger (2018).arkdb
: Archive and Unarchive Databases Using Flat Files. Carl Boettiger (2018).EML
: Read and Write Ecological Metadata Language File. Carl Boettiger, Matt Jones (2016; v2 2019).RNeXML
: Semantically Rich I/O for the NeXML Phylogenetics Format. Carl Boettiger, Scott Chamberlain, Hilmar Lapp, Rutger Voss (2014).pmc
: Phylogenetic Monte Carlo. Carl Boettiger (2012).knitcitations
: Citations for Knitr Markdown Files. Carl Boettiger (2012).rfishbase
: R Interface to FishBase. Carl Boettiger, Scott Chamberlain, Duncan Temple Lang, Peter Wainwright (2011; v2 2015; v3 2019).
Python Modules
- gym_fishing: A Simulation Environment for Deep Reinforcement Learning for sustainable fisheries management. Carl Boettiger and Marcus Lapeyrolerie (2021).
- gym_conservation A Simulation Environment for Deep Reinforcement Learning for conservation scenarios. Carl Boettiger (2021)
Other Software
- Carl Boettiger, Dirk Eddelbuettel. The Rocker Project: Docker images for the R environment. https://rocker-project.org. (Language: Dockerfile)
- Carl Boettiger, Matt Jones, et al. The CodeMeta Project: Software Metadata Exchange https://codemeta.github.io (Language: JSON-LD)
Media interviews
- Martin, Glen. (2019).“How Algorithms Could Save the Planet.” California Magazine). https://alumni.berkeley.edu/california-magazine/just-in/2019-02-01/how-algorithms-could-save-planet
- Seltenrich, N. (2016). “Scaling the Heights of Data Science.” Breakthroughs Magazine. https://nature.berkeley.edu/breakthroughs/opensci-data
- Tachibana, C. (2014). “The paperless lab” Science 345(6195) pp. 468-470. 10.1126/science.opms.p1400087
- Mascarelli, A. (2014) “Research tools: Jump off the page.” Nature 507, 523–525. doi:10.1038/nj7493-523a
- Check Hayden E (2013). “Mozilla Plan Seeks to Debug Scientific Code.” Nature, 501, pp. 472-472. doi:10.1038/501472a
- Van Noorden R (2013). “Data-Sharing: Everything on Display.” Nature, 500, pp. 243-245. doi:10.1038/nj7461-243a
- Gewin, Virginia (2013). “Turning Point: Carl Boettiger” Nature, 493 p 711 doi:10.1038/nj7434-711a
- Wald, Chelsea (2010). “Scientists Embrace Openness” Science. doi:10.1126/science.caredit.a1000036