I originally used OpenWetWare to host my lab notebooks. My lab notebooks have since moved to a wordpress platform to leverage particular features, give a greater flexibility and a more permissive license. From wordpress I have migrated to a Jekyll-based lab notebook, giving even more flexibility and a faster platform. For more information, see the introduction to my lab notebook.
Research interests: Open Lab Notebooks
Phylogenetically based comparative methods are an established and rapidly expanding area of research in macroevolution. Existing approaches may produce misleading results when the traits under consideration reflect different niche specialization across the taxa in question. I propose a method that addresses these difficulties and extends our ability to ask new questions using phylogenetic comparative data, such as the inferring number of niches represented in the data and rate of evolutionary transitions between niches.
Mathematical population models play an essential role in management of natural resources such as fisheries, forecasting disease dynamics or controlling invasive species. Understanding uncertainty and quantifying risk are crucial to effective management decisions -- a plan with a higher expected recovery rate of fish stocks may not be preferable if it also has a higher probability of possible extinction of the stock. Stochasticity is an intrinsic part of natural systems, and rather than view it always as noise that must be filtered out, it can become a source of information about the system itself. I am currently working on two inter-related projects in stochastic population dynamics.
I focus primarily on influence of stochastic dynamics on the canonical equation and adaptive branching . I spent the summer 2009 working with Ulf Dieckmann at IIASA calculating the waiting time until evolutionary branching. Also see my Mendeley collection on papers in Adaptive Dynamics.
Note: Links in topic titles will take you to my Lab Notebooks which have current overview of the research on the cover page and entries day by day.
For a full list of my software, please visit my Github page.
Though due to my fellowship I have no TA positions, I am interested in effective approaches to teaching and learning, including model-based reasoning, peer learning, experiential learning, and the use of technology in education. I formerly served as TA and mentor for the collaborative learning at the interface of mathematics and biology (CLIMB) program. I am an active member of the Graduate Teaching Community at UC Davis, a network of graduate students and postdocs who meet weekly to discuss and practice approaches to education. You can follow our community on our blog. I also occasionally have the chance to teach a session in a seminar or group meeting, which I often use to test out ideas. I maintain a teaching notebook through openwetware to keep track of the successes and failures of the things I explore.
My Other Internet Habitats
- Github Profile. Home to all my current software development. Follow my activity and related projects, connect to other coders.
- Mendeley Profile. Home to my literature collections.
- FriendFeed/sciencefeed Aggregation of my reading, web activity. Several groups here are a great source of news on Science 2.0 tools and ideas. Occasionally cc posts to my twitter.
- Social bookmarking: google reader for journals and blogs, and delicious for other sites. citeUlike.
- Forums: biostar profile, stackoverflow profile, Ubuntu
- General social networking sites: Profiles on LinkedIn, Facebook.
- Academic social networking platforms: epernicus, researchGate, academia.edu. So far I haven't found these of any use. profile at myExperiment, site for Bioinformatics workflows.
- I follow and contribute to several technical help mailing lists, including help-gsl, r-sig-phylo, r-sig-ecology, r-sig-hpc
- CSGF profile, my current fellowship.
- I am helping create an Open Science Community at UC Davis. We are building our group page around OpenWetWare.
- Graduate Teaching Community
- StatSciComp UC Davis based user group for statistical scientific computing in R.
- I'm a director on the board of the nonprofit Solar Community Housing Association, Davis CA.
- I'm a trip leader for Sacramento Inner City Outings
- I'm a guide with UC Davis Outdoor Adventures rock climbing, backpacking and winter programs.