Attending JSM Conference 2016 in Chicago

This weekend I'm headed to Chicago to the big, annual conference for statisticians in North America: the Joint Statistical Meetings (JSM). I'll be there Sunday through Wednesday afternoon and I'm giving a talk on Tuesday in Session #405 titled 'Statistical Challenges in the Analysis of Single-Cell RNA-Seq Data'. In preparation for the conference, I started a set of notes on GitHub of the sessions I'm mostly interested in attending. As I attend various sessions, I'll add more notes of software, papers and links from the talks.  Looking forward to catching up with some old friends and meeting new friends!

Problems installing latest R version on cluster

For my research, I often need to access R on a cluster instead of on my personal laptop. This week I tried to update to the latest version of R-3.3.1 and I found out it is no longer as simple as it used to be. Previously, I would just follow my notes on installing R and R packages locally which is posted on GitHub. To install the latest R (currently version 3.3), I needed to access newer versions of some libraries (zlib, bzip2, curl, pcre and xz). The './configure' step would fail without access to the updated libraries. Usually these types of packages would be included in the installation of R on linux, but it is no longer included. Instead, it assumes these libraries are already installed and updated.

This led to some frustration. Then a postdoc in our lab (Mike Love) sent me this wonderful step-by-step tutorial on getting the updated libraries and successfully installing the latest R. As the tutorial mentions, if the system admins update these libraries, you won't run into this problem. If they don't keep this libraries up-to-date, then you will find this tutorial to be very helpful.

P.S. I tweeted the link and Gabe Becker responded that he had a more complicated set up. His solution was to statically link to the libraries.

@stephaniehicks Ive been going through this, but our R has to live in larger ecosystems, so had to statically link libz, bz2, pcre and curl

— Gabe Becker (@groundwalkergmb) July 20, 2016

Advice on Following an Academic Career Path

I've been putting together some general advice on following an academic career path. This ranges from being a graduate student to faculty at a university or institution. I put the information in a GitHub repo, so more information could be added be me and others (pull requests are welcomed!) over time.  The advice generally comes from being in an applied statistics / genomics field, but I think it mostly applies to a broader set of fields. As I move through my career, I will continue to add resources, links and notes to it.  Hopefully others will find it useful!

Maryland-Style Crab Cakes

  

After recently visiting Baltimore, we wanted to learn more about the local food culture.  For anyone who has been there, you'll know that crab cakes and Old Bay seasoning are staples of the area.

Old Bay was originally developed by a Jewish man named Gustav Brunn, who fled Germany in 1939.  After establishing himself on the Chesapeake Bay (which stretches from Virginia Beach to the Pennsylvania border), his seasoning took the name "Old Bay" from the iconic overnight mail service that ran from Baltimore, MD to Norfolk, VA.  The Baltimore Steam Packet Company was nicknamed "the Old Bay Line," which survived attacks during the The Civil War and government requisition for WWII.  After reopening as an automobile ferry service, the company went under... but the Old Bay seasoning continued to gain popularity as a seafood seasoning, since it kept tavern-goers thirsty.  In 1990, McCormick & Co bought the Old Bay brand (with Zatarain's and Lowry's following).

Contents of Old Bay seasoning are:

• celery salt (ground celery seed and salt)
• paprika
• black pepper
• cayenne pepper
• ground mustard powder
• bay leaf powder
• other trace spices (cinnamon, allspice, nutmeg, ginger, clove, cardamom, etc)

Today's recipe is based on one developed by Jenn @ Once Upon A Chef:  LINK

• 2 large eggs
• 2-1/2 tablespoons mayonnaise
• 1 teaspoon Worcestershire sauce
• 1 teaspoon Old Bay seasoning
• 1 teaspoon garlic powder
• 1/2 teaspoon chili powder
• 1/2 teaspoon black pepper
• 1/4 teaspoon salt
• pinch of ground mustard
• 1 large stalk of celery, finely diced
• 1/4 large onion, finely diced
• 2 tablespoons celery leaves, finely chopped
• 1 pound lump crab meat
• ~1 cup panko
• Vegetable or canola oil, for cooking

To the chopping block!

Finely chop celery and onion.

Mix together all ingredients.

Scoop the melange into patties.

Shallow fry the patties in canola oil.

Flip when they are golden brown (and delicious).

Choose your favorite sauce and enjoy!