I’m a PhD candidate in the Snitkin Lab at the University of Michigan. I use computational biology approaches and bioinformatics tools to conduct my research. My thesis research focuses on the genomics of the bacterial species C. difficile. To support my genomic analyses I wrote a software package to perform bacterial genome-wide association studies called hogwash. I also contributed to the development of prewas, a software package that preprocesses SNPs after variant calling but before running GWAS.
If I’m not in lab I’m probably at UM’s Ross School of Business helping out at the Wolverine Venture Fund, quilting, or roller skating.
I’m currently applying for computational biology internships for summer 2020.
Christine Marie Bassis, Kaylie A. Bullock, Daniel E. Sack, Katie Saund, Ali Pirani, Evan S Snitkin, Veronica I. Alaniz, Elisabeth H. Quint, Vincent B. Young, Jason Bell
R Package Submission to CRAN I just submitted an R package, prewas, that I wrote with my colleagues Zena and Stephanie. The whole process took many more hours than I had anticipated. This post details the snags I ran into and their fixes. Hopefully, this will help other package submission newbies!
General resources: There are many resources that spell most of what you need to know to submit a package.
Market Sizing I created an interactive dashboard to facilitate with market sizing. Here is a static image of the dashboard: Users can estimate the market size of a product, company or industry using a bottom up approach. The dashboard dynamically generates the plot with the relative sizes of the total available market (TAM), serviceable available market (SAM), and serviceable obtainable market (SOM). Users can download a .png of the plot.
Emoji DNA Generate a DNA string of two random emoji each time your terminal starts, like this adorable koala-bear DNA:
Download the script from my github page.
To use emoji_dna.sh:
1) Download emoji_dna.sh
2) From your terminal add to your bash_profile (nano ~/.bash_profile) the line:
bash /path/to/emoji_dna.sh
3) Source your bash_profile: source ~/.bash_profile
4) Open a new terminal window and enjoy!
This little script was a challenge put to me by Ryan Crawford while we discussed both the elegant Bonsai tree generator for terminal by John Allbritten and the goofy twitter account @emojiDNA.
Locations in The Dresden Files The Dresden Files are an amazing, silly fantasy series about magic in modern day Chicago. This tutorial will walk through how to makes maps in R using locations from The Dresden Files.
Getting location data I had a ton of fun clicking around this interactive map of The Dresden Files locations. I wanted to expand on it by including more locations and adding metadata onto the locations.
If you’re nervous about an upcoming poster session it may help to articulate your specific concerns, develop a strategy to address each one, and then proceed to have a great poster session. Here are some common concerns and my suggested strategies.
Concerns about presenting unpublished or unfinished work Fear 1: The project is unfinished so people will ask questions I can’t answer. You are presenting work that isn’t yet published so there will be gaps in your research.