Biafra Ahanonu, PhD

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r functions: ggplot barplot with errorbars
06 june 2013 | programming

The best way to create a barplot with errorbars using ggplot in R is not obvious. I'll show a super simple solution.[...]

brain initiative notes
27 may 2013 | neuroscience

This is a continually updated collection of news, ideas/findings, and other tidbits related to the [...]n/' target='_blank'>BRAIN initiative, promising biotechnologies, and neuroscience/biology in general. This is a really exciting time in neuroscience and I hope to capture a bit of that here.

¿qué es la calle?
24 may 2013 | short story | spanish

Había terminado y salé para mi cocina. Tenía hambre pero este día no había comida dentro de mi despensa. Me fui y caminé hacienda[...] la Tport—una máquina que puede transportar una persona a otro lugar sin energía y tiempo. Cuando entré la máquina, toqué algunos botónes y esperé. Pero nada ocurrió y lo hice las mismas acciones otra vez—y nada ocurrió.

How would the disappearance of streets affect the social fabric? This short story briefly (in castellano!) explores a world in which instantaneous, free transport is possible. Meant mainly to practice my spanish, i plan to follow-up with a more detail story in the future.

bash scripting: youtube downloading macro
17 may 2013 | programming

<p> Once again, the command line is the root of all that is good in the world. This time, it has helped improve on a long[...]-standing issue for me: what is the easiest way to get a copy of all the <a href='http://www.youtube.com/playlist?list=PLmku2swCXQpqWAZSscjV4h9bcLennVcif' target='_blank'>luscious melodies</a> i hear on youtube? Courtesy of <a href='http://rg3.github.io/youtube-dl/' target='_blank'>youtube-dl</a>, a nifty little command line utility, this problem has been solved. However, every once in awhile it throws errors and i wanted a wrapper bash script to take care of this and some other processing. I'll briefly go over the code. </p>

bioc218: predicting co-translational pausing with neural networks
14 may 2013 | science

Wanted to share my final paper for bioc218, a computational biology class i t[...]ook this winter 2013. We were tasked with choosing a particular technique, algorithm, or any material discussed in the class and exploring it in more detail. Neural networks seemed particularly interesting—and not just because i'm a neuroscientist. I wanted to use machine learning algorithms to improve predictions for the project i am working on in Judith Frydman's lab.

bio42: notes
12 may 2013 | teaching

While teaching bio42 (cell biology and animal physiology) I created weekly notes to help students in my section study and focus on the impo[...]rtant materials presented in the class. I built off of the latex boilerplate that I have been improving over time to create weekly notes. This highlights why I love LaTeX so much, especially for larger projects that are heavily linked—it allows easy annotation, indexing, creation of new document styles, and other related processes rapidly and consistently. Plus, separating content and style is always a plus and images stay uncoupled from a propriety source (e.g. Word files).

I really love the resulting notes and student feedback was quite positive. I thought sharing them might be useful for others in the future. The source latex files and raw images can be sent upon request (I'm considering making a Github repository in the future). I'll briefly talk about the document below and certain decisions that were made to get it to its current state.

cheyne-stoke respiration
12 april 2013 | programming

One can create art with data, many have proven that with beautiful infographics or dazzling[...] company reports. I thought using R to create an artistic rendering of a normally mundane process would be neat. I developed a graphic based on Cheyne-Stokes respiration using ggplot. Code is included at the end.

sharing minds
26 march 2013 | short story

We had just met and she knew everything about me: where I'd come from, job, favorite books, hideaway where I went to think, special Sun[...]day bike routes, time of day I woke and slept, first time abroad, family members' names, secret hobbies, wants, desires, people I abhorred, my first love...everything.

What if you could access all of another's memory? What would you do?

from the archives: poems, part 1
24 march 2013 | poems

A couple of my old poems from way back when, with minor edits. Enjoy.[...]

bash scripting: playlist maker
23 march 2013 | programming

Decided to take another stab at converting small programs to bash. This time, the python playlist maker was updated to bash and greatly sim[...]plified, no longer need to do sketchy recursions.

bash scripting: batch file renamer
25 february 2013 | programming

Bit by bit, I have replaced repetitive tasks completed using downloaded programs with scripts that do the same thing more efficiently, with[...]out the residual registry and file junk many programs leave, and with the flexibility to allow me to modify the script to suite specific needs in the future. This was the case with batch renaming files. I've included the script and briefly go over the code.

bio42: diagrams, part 1
25 january 2013 | teaching

Had a couple minutes to spare before leaving lab, so decided to throw together some diagrams to help explain a couple biological pathways s[...]tudents of bio42, a bio class at Stanford I'm TAing. Hoping to make a set for each system we study. Started with vesicle budding and fusion along with muscle contraction in smooth and skeletal muscles.

r functions: pca
10 january 2013 | programming

Started a github repository to put online R functions I've create for some common types of analysis and plots. Aim to have a core set of fu[...]nctions to make figures look prettier, even on preliminary analysis. A couple examples are included focusing on the first function: principal component analysis.

A GitHub repository can be found at: R plotting functions.

latex boilerplate
27 december 2012 | programming

LaTeX Boilerplate is for those starting a project or more experienced users who want an organized structure to their documents. All code (e[...].g. \newcommand, pgfkeys) and packages included are commented. The boilerplate contains examples for common tasks: figures, tables, BibTeX, index, new commands (including some using pgfkeys), and more.

A GitHub repository can be found at: LaTeX Boilerplate. I briefly explain the layout; installation and usage can be found in the repository readme.

stanford bing concert hall: first impressions
15 december 2012 | stanford

Designed by architect Richard Olcott (Ennead Architects) and sound designer Dr. Yasuhisa T[...]oyota (Nagata Acoustics), the Bing Concert Hall is stunning. Robert Campbell (Fisher Dachs Associates) was on hand during the second sound check (along with Richard and Dr. Toyota) to discuss the philosophy behind the building, a bit of history, and where they hope it will be in the future. This post is my impressions of the place along with notes from their interview.

freedom in a dying world
01 december 2012 | short story

Flash, crackle, bang. Pit-pat, pit-pat, pit-pat. The flare skidded down the long, narrow tunnel that appeared to stretch downward forev[...]er. Another corridor, if you want to call the passages in this labyrinth of a make-shift cave that, ran to our right. Behind us, a sliver of light, flickering on and off, spilling in from the opening from whence we came. We all gave each other the look-n-nod, donned our breathing masks then proceeded to attach the hooks and ropes. Minutes later, one by one, we rappelled down into the abyss below...