Material and sources to help new lab members get up to speed, or remind current members how to do things we haven’t done recently.
The Yoder Lab Github page, github.com/jbyoderlab, is our central point for project creation, management, and sharing; to start a new project, download or fork our project template. The Yoder Lab Slack channel, yoderlab.slack.com, is the place for coordination and communication among lab members. E-mail Jeremy for access.
The Nobel Institute’s Medicago handbook includes protocols for growing, storing, and experimenting on Medicago truncatula, background on its natural history and the large body of research into its evolution and ecology, and descriptions of some community resources. Poorter et al. (2012), “The art of growing plants for experimental purposes: a practical guide for the plant biologist” is a nice review of considerations in designing and managing greenhouse and growth chamber experiments.
The Medicago Hapmap Project is the clearinghouse for current and past Medicago truncatula genome assemblies and genome-wide sequence and structural variation.
The Joshua Tree Genome Project has an annotated bibliography of research into the evolution of Joshua tree, its interaction with yucca moths, and its projected future under climate change.
There are too many open data and software resources of potential use in the lab’s work to list them all here, but here are a few of the most useful:
Climate: Probably the most widely-used source for historic climate data is BioClim, which can be accessed directly from R. For coverage of North America, ClimateNA has data at a finer spatial and temporal scale, up through 2018; and PRISM draws on NOAA data for fine-scale values at monthly resolution. The Climate Data Guide compiles even more kinds and sources of data, with detailed evaluations of quality and usefulness.
Mapping: Google Earth Pro (the desktop application) provides some very useful functions for creating geospatial datasets, and working with a lot of open-source data on political boundaries, roads, landmarks, and the like. There are a wide range of mapmaking and spatial analysis packages for R.
Genetic and phenotypic data: GenBank is the US-based data repository for DNA sequences; though genetic data, especially non-sequence-based data like microsatellite genotypes, is often posted to Dryad, too. Dryad is primarily geared towards ecological and phenotypic datasets used in ecology and evolutionary biology.
Species identification and occurrences: In California, the canonical source for plant taxonomy and identification is the Jepson Manual, and a version of the manual’s key is entirely online, with links to extensive, expert-identified photo resources in CalPhotos and geo-referenced collection records that draw on a statewide database of herbarium records. Much broader geographic and taxonomic coverage (with some tradeoffs for the quality of data) is available through iNaturalist.
Writing and funding
CSUN Biology’s comprehensive list of intramural funding opportunities gives you a lot of small grants and scholarships to try for, for both graduate and undergraduate students.
Open Grants compiles publicly-available examples of grant proposals to a variety of funders, including many appropriate to the lab’s research. Before starting a new proposal, take a look there to get a feel for formatting and the kinds of ideas that succeed with the funding source.
Rachel Mackelprang, a professor in CSUN Biology’s Microbiology section, has put together a thorough and helpful guide on writing a Master’s thesis proposal.
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