Data Sharing & Management Snafu

It is old, but I just found this amazing little video that explains so many of the challenges related to data sharing. Proper data management practices are important not only for these sorts of unexpected data sharing situations but for reproducibility as well. How can you or anyone else build …


Open Science from the NIH

This is a well-made and very informative explanation of the motivation behind efforts at enhancing reproducibility and openness in scientific research. This is a worthy goal and efforts toward achieving it should be applauded and given our full support.


Freeing research data

As a scientist, my job is to produce new knowledge. I get paid to think new thoughts, create hypotheses, perform experiments, and hopefully uncover new truths about the world that no one has ever seen before. The basic idea of science and being a scientist is beautiful, even romantic. Unfortunately …


Searching Flybase with Alfred

Just want to share a quick tip today for speeding up a site-specific search I use all the time. As a fly geneticist, I find myself constantly searching the Drosophila community resource Flybase for specific genes, transgenic stocks, and references. By leveraging the power of custom searches in my application …


Tiny six-legged animals

I noticed a fun little Twitter trend today under the hash tag #UpGoerFive. Inspired by Randal Munroe’s xkcd comic on the Saturn V rocket entitled Up Goer Five, which explained the workings of the rocket using only the “ten-hundred words people use the most often,” parasitologist Theo Sanderson built …


Triggering the academic scientist

Recently, Chase over at Studies in Semicolons started putting together a GTD-style trigger list for academics. I was inspired and took his invitation to modify the list for my own purposes. I think this will be quite useful in my weekly mind dumps as I try to get everything …


Getting geeky with research tools

Gabe of Macdrifter fame and I recently recorded an episode of his Generational podcast together. It really was a blast.

Go listen to us geek out on the tools I use for searching and organizing my notes on scientific literature. Hopefully you will hear something useful.

Link: Research Materials and …


An animated guide to open access

The always amusing PhD Comics just posted an animated explanation of the issues surrounding academic publishing and the open access movement. This is an incredibly important issue in acadmia. We have allowed academic publishing to remain mired in the same basic business model for hundreds of years. This business model …


Writing better than you normally do

As a research scientist and professor, presentations and publications are both the banes of my existence and the primary metrics by which I am evaluated. I know I need to write more to hone my craft. I know there is no perfect time to write. I know that I have …


The Life of a Nature Paper

Nice and quick summary of the steps a manuscript goes after submission to Nature

(via Claudia Scholz)


Science or screwing around

Science gif

(via Craig Robertson)


Fun with regular expressions

If you have every done anything with regular expressions you know what I am feeling now. They have this weird way of inducing giddiness in a fully grown nerd-man. Even when the task at hand is incredibly mundane, regular expressions can make you feel like Superman. Oh, the power!

I …


Creating a custom url scheme via AppleScript and Python

I wrote recently about my somewhat obsessive notetaking strategies that include a personal wiki and summary pages for each of the scientific articles I read. Well, if you thought that was crazy, please avert your eyes because things are about to get geeky.

My frustration began when I wanted the …


An academic notetaking workflow

As an scientist, I read lots of journal articles in the form of PDF files. I wrote recently about how I find papers related to my field of interest (i.e., sensory neurobiology in insects) and I thought it would also be fun to write a bit more about the …


Cleaning up the “Open with” menu

If you are someone who regularly right-clicks on files and uses the “Open with” command to open them in anything other than the default app, you will be happy to know what I am about to tell you. You may have noticed a lot of weird duplicate listings in the …


Big meetings can be useful

Normally, I am not a fan of really large scientific conferences. You arrive in a crowd of hundreds or even thousands of other scientists all hoping the meeting won’t be a waste of their time. The talks are organized into sessions, some of which you hope will be at …


Setting up Dropbox on a remote host

In the “news to me” column, Dropbox1 apparently has a command line interface. Although that may not sound cool at first, let me tell you what I have done with it. Inspired by Macdrifter, I have recently been fiddling with the static site generator Pelican. This site, meager as …


Welcome to Science

Welcome to Science

Zen Pencils by Gavin Aung Than is a comic illustrating inspirational quotes.
The new one from Phil Plait on the wonder of being a scientist made me smile.
“Welcome to Science. You’re gonna like it here.”


Watching a fly develop

A new microscopy technique was just published in a couple of back-to-back papers in Nature Methods by Tomer et al. and Krzic et al. that uses multi-angle imaging and massive computing power to reconstruct 3D videos of your specimen of interest. These particular papers used their fancy new technique to …


Staying afloat

Staying on top of new research developments is a very important aspect of survival in academia. For most of us, this means we can never read enough papers. I am not sure if it is fortunate or unfortunate, but there are so many new papers being published everyday, keeping up …


Why Korea?

Whenever I meet new people, they always ask “Why Korea? What made you settle down here?” The truth is that when I moved to Korea in early 2007, it was impossible to imagine what was about to happen. Right after college, I entered the highly competitive Tri-Institutional MD-PhD Program …