more user craziness with docker
Should do something about rstudio script when running as a non-root user…. Fixed! Requires changing user more carefully; we cannot simply delete the existing user.
When using a docker image with a non-root default user, we can launch a container as root by giving root’s UID instead with the --user 0 flag. (Note that we can do this with other UIDs as well, though it produces a troublesome unnamed user when the userid hasn’t been assigned to a user name).
- RStudio image now completely configures default user in the Dockerfile, such that userconf.sh need only configure custom users. See userconf.sh. We now do:
usermod -l rstudio docker \
&& usermod -m -d /home/rstudio rstudio \
&& groupmod -n rstudio docker instead of userdel which causes issues if we launch as that user. Note, this means containers built on rstudio have only the user rstudio available and not the docker user, unless explicitly added/renamed. Avoids issues like multiple home directories/unpredictable home directory name as well (Since RStudio-server wants to open in home dir and not in a user-owned root directory like /data like most other apps would use.) - RStudio must still be launched as root (see RStudio issue), so a Dockerfile with non-root user must use the --user 0 flag or run rserver or the default supervisord using sudo.
- Configure supervisord.conf configuration not to throw erroneous error messages (e.g. userconf.sh is expected to exit with 0, users explicitly declared, config file explicitly declared to avoid security vulnerability of custom conf in working dir, etc).
Reading list notes
Sebastian has a very nice reading list for his upcoming seminar on evolution in stochastic environments that I wanted to make note of for my own reference as well.
Reading: Ruel, Jonathan J., and Matthew P. Ayres. “Jensen’s inequality predicts effects of environmental variation.” Trends in Ecology & Evolution 14.9 (1999): 361-366. Optional Reading: Frank, Steven A., and Montgomery Slatkin. “Evolution in a variable environment.” American Naturalist (1990): 244-260.
BETWEEN-GENERATION BET-HEDGING
Week 2: Historical perspective and overview
Readings: Stearns, Stephen C. “Daniel Bernoulli (1738): evolution and economics under risk.” Journal of biosciences 25.3 (2000): 221-228. Childs, Dylan Z., C. J. E. Metcalf, and Mark Rees. “Evolutionary bet-hedging in the real world: empirical evidence and challenges revealed by plants.” Proceedings of the Royal Society B: Biological Sciences (2010): rspb20100707. Optional Reading: Simons, Andrew M. “Modes of response to environmental change and the elusive empirical evidence for bet hedging.” Proceedings of the Royal Society B: Biological Sciences (2011): rspb20110176.
Week 3: Seedbanks in annual plants Readings: Venable, D. Lawrence. “Bet hedging in a guild of desert annuals.” Ecology 88.5 (2007): 1086-1090; Gremer, Jennifer R., and D. Lawrence Venable. “Bet hedging in desert winter annual plants: optimal germination strategies in a variable environment.” Ecology letters 17.3 (2014): 380-387.
Week 4: Stochastic switches, epigenetics, and bacteria
Readings: Beaumont, Hubertus JE, et al. “Experimental evolution of bet hedging.” Nature 462.7269 (2009): 90-93; Veening, J. et al. “Bistability, Epigenetics, and Bet-Hedging in Bacteria.” Annual Reviews of Microbiology (2008)
Week 5: Bet-hedging in structured populations
Potential readings: Carja, Oana, Uri Liberman, and Marcus W. Feldman. “The evolution of phenotypic switching in subdivided populations.” Genetics 196.4 (2014): 1185-1197; Pfister, Catherine A. “Patterns of variance in stage-structured populations: evolutionary predictions and ecological implications.” Proceedings of the National Academy of Sciences 95.1 (1998): 213-218.; Schreiber, Sebastian J. “The evolution of patch selection in stochastic environments.” The American Naturalist 180.1 (2012): 17-34.
WITHIN-GENERATION BET-HEDGING
Week 6: The idea and a perspective Readings: Gillespie, John H. “Natural selection for within-generation variance in offspring number.” Genetics 76.3 (1974): 601-606; Hopper, Keith R., et al. “Within-generation bet hedging: a seductive explanation?.” Oikos 101.1 (2003): 219-222.
Week 7: Multiple matings in wasps and cooperative breeding in birds Readings: Sarhan, Alia, and Hanna Kokko. “Multiple mating in the glanville fritillary butterfly: A case of within-generation bethedging?” Evolution 61.3 (2007): 606-616; Rubenstein, Dustin R “Spatiotemporal environmental variation, risk aversion, and the evolution of cooperative breeding as a bet-hedging strategy.” Proceedings of the National Academy of Sciences 108.Supplement 2 (2011): 10816-10822.
Week 8: Synthesis of between- and within-generation bet-hedging Readings: Starrfelt, Jostein, and Hanna Kokko. “Bet-hedging: a triple trade-off between means, variances and correlations.” Biological Reviews 87.3 (2012): 742-755; Frank, Steven A. “Natural selection. I. Variable environments and uncertain returns on investment*." Journal of evolutionary biology 24.11 (2011): 2299-2309.
RESOURCE VARIATION AND RISK AVERSION
Week 9: Multiple limiting factors and ovule packaging in angiosperms Readings: Rosenheim, Jay A., Uri Alon, and Guy Shinar. “Evolutionary Balancing of Fitness-Limiting Factors.” The American Naturalist 175.6 (2010): 662-674. Burd, Martin, et al. “Ovule number per flower in a world of unpredictable pollination.” American Journal of Botany 96.6 (2009): 1159-1167.