Vita

employment

2013 NSF post-doctoral scholar in the Center for Stock Assessment Research at the University of California, Santa Cruz. Mentors: Marc Mangel, Stephan Munch

education

2012 Ph.D Population Biology, University of California, Davis. Mentor: Alan Hastings
2007 A.B in Physics Princeton University, with honors and certificates in biophysics and applied and computational mathematics.

publications

Carl Boettiger. (2015) An introduction to Docker for reproducible research. ACM SIGOPS Operating Systems Review, Special Issue on Repeatability and Sharing of Experimental Artifacts. 49(1), 71-79. doi:10.1145/2723872.2723882 (pdf) (arXiv)
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 (pdf) (arXiv) (repository) (data)
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 (pdf) (arXiv) (repository)
Carl Boettiger*, Noam Ross*, Alan Hastings. (2013) Early warning signals: The charted and uncharted territories. Theoretical Ecology doi:10.1007/s12080-013-0192-6 (pdf) (arXiv) (repository)
Carl Boettiger, Alan Hastings (2013). Tipping points: From patterns to predictions, Nature 493, 157–158. doi:10.1038/493157a (pdf)
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 (pdf) (arXiv) (code) (data)
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 (pdf) (preprint) (code) (R package)
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.2012.00247.x (pdf) (preprint) (code) (R package)
Carl Boettiger and 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 (pdf) (arXiv) (code)
Jeremy M. Beaulieu, Dwueng-Chwuan Jhwueng, Carl Boettiger and 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 (pdf) (R package)
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 (pdf) (arXiv) (code) (data)
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 (pdf) (arXiv) (code) (data)
James J. Wray, Neta A. Bahcall, Paul Bode, Carl Boettiger, Phillip Hopkins. (2006) The Shape, Multiplicity, and Evolution of Superclusters in ΛCDM Cosmology, The Astrophysical Journal 652 (2) 907-916. doi:10.1086/508600 (pdf) (arXiv)

presentations

Berkeley Initiative for Global Change Biology, student organized symposium. (Oct 2014) Invited speaker.
Ecological Society of America, Sacramento CA. (Aug 2014).
DIMACS Global Change, Berkeley CA (May 2014) Invited speaker
Zoology Seminar, Wisconsin-Madison. (April 2014). Invited speaker
Department of Environmental Science, Policy & Management, UC Berkeley. (March 2014)
American Society of Naturalists, Asilomar, CA (Jan 2014)
Woods Hole Oceanographic Institute (July 2013). Invited speaker
Ecological Society of America Conference, Minneapolis, MN. (Aug 2013)
UC Davis Dept of Environmental Resources and Economics; Davis, CA (May 2013). Invited speaker
Ecological Society of America Conference, Portland, OR. (Aug 2012) (slides)
Computational Science Graduate Fellows Conference, Washington DC. (July 2012) (video recording) (slides) (doi)
Evolution Conference, Ottawa, CAN. Invited speaker for the annual SSB Symposium. (July 2012) (slides)
Ecological Society of America Conference; Austin, TX. (Aug 2011) In Nature Precedings (doi) (slides)
Evolution Conference; Norman, OK. (June 2011) In Nature Precedings, (doi) (slides)
iEvoBio Conference; Norman, OK. (June 2011) In Nature Precedings, (doi) (slides)
Science Online; Durham, NC. (Jan 2011) In Nature Precedings, (doi) (slides)
Society for Integrative and Comparative Biology. Salt Lake City, Utah. (Jan 2011) In Nature Precedings, (doi) (slides)
iEvoBio Conference; Portland, OR. (June 2010) In Nature Precedings (doi) (slides)
Evolution Conference; Portland OR. (June 2010) In Nature Precedings (doi) (slides)
University of Tennessee, Knoxville, TN. (Nov 2009)
Center for Population Biology, Davis, CA. (Nov 2009) (slides)
International Institute of Applied Systems Analysis, Vienna; Austria. (Aug 2009) In Nature Precedings, (doi) (slides)
Cornell Probability Summer School, Ithaca, NY. (June 2008) In Nature Precedings, (doi) (slides)

theses

Carl Boettiger (2012). Regime shifts in ecology and evolution (PhD Dissertation). doi: 10.6084/m9.figshare.97218
Carl Boettiger, Stephen Pacala, David Huse (2007) Ensemble Behavior from Individual Dynamics in Multispecies Forest Populations. Princeton Physics Dept. doi: 10.6084/m9.figshare.678304 (pdf)
Carl Boettiger, Joshua Weitz, Simon Levin (2007) Adaptive Dynamics: Branching Phenomena and the Canonical Equation Princeton Physics Dept. doi: 10.6084/m9.figshare.678306 (pdf)
Carl Boettiger, David Huse (2006) Clonal Interference Models in Population Genetics. Princeton Physics Dept. doi: 10.6084/m9.figshare.678305 (pdf)

grants

2013-2014 Co-PI on Sloan Foundation grant for the rOpenSci Project $ 180,000.
2013-2015 NSF Postdoctoral Fellow, Intersections of Biology and Mathematical and Physical Sciences and Engineering DBI-1306697. $138,000. Link to proposal: doi: 10.6084/m9.figshare.652970
2011, 2012 PI on Department of Energy Grant No. DE-AC02-05CH11231. 50,000 hr on NERSC supercomputing resources.
2009 IIASA YSSP fellowship. National Academy of Sciences, NSF Grant No. OISE-0738129, $8,000. proposal: doi: 10.6084/m9.figshare.678310
2008-2012 Computational Science Graduate Fellowship. Department of Energy, Grant No: DE-FG02-97ER25308, 4 yrs x $36,000/yr

awards

2011 Mendeley & PLoS Binary Battle software competition award, $1,000
2011 Volterra Award (Best student talk, ESA 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
2006 Plasma Physics Fellow, PPPL

service

NCEAS Scientific Advisory Board
rOpenSci Leadership team

Reviewer for:

2015 Proceedings of the National Academy of Sciences, Journal of Statistical Software, Bioinformatics, Chapman & Hall, Ecology Letters
2014 Theoretical Ecology, Biodiversity Data Journal, Ecology Letters, Journal of Theoretical Biology, American Naturalist, Proceedings of the National Academy of Sciences, Proceedings of the Royal Society B
2013 Theoretical Ecology, Francis & Taylor, Ideas in Ecology and Evolution, The R Journal, National Science Foundation, Proceedings of the Royal Society B, Journal of Open Research Software, Canadian Journal of Fisheries and Aquatic Sciences
2012 Theoretical Ecology, Evolution, Methods in Ecology and Evolution, Proceedings of the Royal Society B, PLoS ONE, Ecology, Conservation Letters, Ecology Letters
2011 Theoretical Ecology, Ecological Modelling, Evolution, Methods in Ecology and Evolution, Ecosphere
2010 & prior Theoretical Ecology, Journal of Mathematical Biology, Ecological Modelling, Ecology

other service

Student member for the CBS Dean search. 2011
Co-chaired the student group on Open Science. 2010-12
Co-chaired the Graduate Teaching Community. 2009-10
Student member for the CPB program review. 2010

selected software

Carl Boettiger (2013). knitcitations: Dynamic citations for dynamic documents. Stable version on CRAN.
Carl Boettiger, Scott Chamberlain, Karthik Ram, Edmund Hart (2013). rfigshare: Programmatic access to the figshare data repository. Stable version on CRAN.
Carl Boettiger (2012). pmc: Phylogenetic Monte Carlo. current version.
Carl Boettiger & Duncan Temple Lang (2011). treebase: An R interface to TreeBASE. Stable version on CRAN.
Carl Boettiger (2011). rfishbase: Programmatic access to FishBase. Stable version on CRAN.
I am also a founding member of the rOpenSci project under which I have written several additional software projects

See my Github page for a more complete list of my software packages.

workshops

Reproducible Science Hackathon: Curriculum & Workflow Development. National Evolutionary Synthesis Center (NESCent), Durham, North Carolina.
2014 Second Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE 2.0). New Orleans, LA.
2014 co-organizer “rOpenSci Hackathon (#rOpenHack)”, Github HQ in San Fransisco, CA. (summary, video documentary)
2014 invited to “A toolbox for analysis of long-term ecological dynamics using the Kepler Workflow System.” A Working group of the National Ecological Analysis and Synthesis Center (NCEAS), Santa Barbara, CA.
2013 Mathematical Biology Institute (MBI) invited speaker, Sustainable Management of Living Natural Resources, Columbus, OH.
2013 invited to Workforce development, a planning workshop for an NSF software sustainability center: Institute for Sustainable Earth and Environmental Software. Oakland CA.
2013 invited to Software Lifecycle, a planning workshop for an NSF software sustainability center: Institute for Sustainable Earth and Environmental Software. National Ecological Analysis and Synthesis Center (NCEAS), Santa Barbara, CA.
2011-2013 National Institute for Mathematical and Biological Synthesis (NIMBioS) working group: Pretty Darn Good Control, Knoxville, TN
2009 American Institute for Mathematics, Stochastic and deterministic spatial modeling in population dynamics, Palo Alto, CA

media interviews

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