short stories, programming, adventures abroad and more. enjoy!

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projects

long-term optical imaging of the spinal cord in awake, behaving animals
25 may 2023 | neuroscience
How does the spinal cord process sensory stimuli in awake animals? A brief overview of results from our recent preprint describing [...]a spinal implant chamber, fibrosis-inhibiting materials, computational methods, and end-to-end pipeline for large-scale bilateral recording from multiple segments of the spinal cord. This allowed us to conduct long-term (months to over a year) imaging of individual axons, microglia dynamics, and Ca2+ imaging of neurons—all in awake, behaving animals.

Several of the approaches described, such as fibrosis inhibition, are applicable to preparations and experiments beyond the spinal cord.

neuroscience imaging analysis tools
08 november 2021 | neuroscience
Provide new and existing researchers a central location for methods and URLs for calcium imaging data processing and analysis tools. [...]>This table also includes imaging data handling and analysis tools beyond calcium imaging and will be updated going forward.

The table can be sorted by column by clicking each header.

Also found as part of the Brain Initiative Notes post imaging analysis tools or https://github.com/bahanonu/imaging_tools.

on the subject of something: reviving an old website
12 may 2015 | website
On the Subject of Something was my original blog during high-school and early college. My Opera (the site it was hosted on) closed down and[...] I was unaware of this fact during the grace period during which they allowed users to export the content from their website. However, I am extremely grateful to the Internet Archive: Wayback Machine, which allowed me to recover many of the webpages. I've included links to all the relevant posts that I could recover. Enjoy!

interstellar review: was this the final cut?
17 december 2014 | movies
A review of Christopher Nolan's latest movie Interstellar. To put it briefly, rarely has a movie so vastly deviated from my expect[...]ations going in. And not in a good way.

book review: the path to power
29 august 2014 | books
The Path to Power (The Years of Lyndon Johnson) is a sweeping tale about the early years of LBJs life and political career. It is easily on[...]e of the best books I've read in awhile and would heartily recommend to others. Here i'll do a brief review of the book.

book review: the power of myth
11 august 2014 | books
Recently finished The Power of Myth, which covers interviews with Joseph Campbell about myths, and was greatly disappointed. I'll [...]briefly outline why in this review.

evolving actaeon
16 july 2014 | short story
Wanted to quickly turn an idea that came up during a conversation into a short story. Touches on ideas of genetic engineering and cockfight[...]ing.

neuroscience and biology resources
09 may 2014 | science
A continually updated repository of scientific resources (journals, blogs, etc.) in biology with a focus on neuroscience.[...]

an exhaustive search for the truth
18 april 2014 | short story
The project had started out with a simple question: would it be faster to assemble complete knowledge about all truths past, present, and f[...]uture through scientific inquiry or via brute force computation?

sochi olympic stats: medal count
19 february 2014 | america
There have been several articles that re-order the medal count ranking by comparing medals to population or GDP, which then show small coun[...]tries topping the charts. This analysis ignores some obvious facts: small countries are over-represented in the number of athletes they send and the relationship between athletes sent and medals is linear. I present a brief analysis to support and expand on these claims.

coding practices, part 1
10 december 2013 | programming
Some thoughts on coding practices and an outline of a work-flow that i find useful when starting any project. Future posts will focus on co[...]ncrete examples.

excess humanity
26 october 2013 | short story
The point was nearing when humanity needed to optimize the population. And so the question arose: how many humans do we need?[...]

gantis: toward the edge
28 june 2013 | short story
The first in a series of short stories exploring a universe in which our negative space (i.e. space) is turned into their positive space (i[...].e. matter) and vice-versa. Thus, it is like the entire universe is a series of caves that they must excavate. This story introduces a few key characters, explore a bit of the lore, and is an attempt by me to write a story in which a clearer light is shone on a relationship between two characters. More to come, enjoy!

global history of architecture
08 june 2013 | architecture
One of my favorite classes at MIT was 4.605 (Global History of Architecture), which explored various styles and themes found throughout dif[...]ferent buildings and other types of architecture from the beginning of civilization to the present. In the spirit of sharing my enthusiasm for the course i'll discuss some takeaways from, and have included a couple papers i wrote for, the class.

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.

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: 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.

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...

the graphical abstract, part 1
11 november 2012 | science
The graphical abstract is an effective way to convey a complex message in an eye pleasing format that is easily digested. I wanted to creat[...]e a neuroscience-based one as it would be an extension of my work with creating graphic designs and would take advantage of my current studies. From the initial, crowded to the final, clean abstract, I'll go through my thought process and provide links to useful resources.

the nobel prize browser
12 october 2012 | science
Made a small app that allows browsing of Nobel Laureates. Also provides link to their Wikipedia and Pubmed. Might expand to include picture[...]s or some publications. Enjoy!

facebook crawler and youtube api: part 1
07 october 2012 | programming
Created a small app, implemented in python and PHP, that crawls authenticated Facebook page for Youtube videos and adds them to a specified[...] user's Youtube playlist. Useful for groups that post a lot of youtube videos and want a centralized playlist to share with others. I'll go over some of the implementation details in this post.

archive everything!
01 october 2012 | notes
Archived everything in my inbox. It's awesome. Continues my general trend of simplifying. Logging off websites, only checking the news for [...]brief periods, and focusing on a core set of hobbies. Eliminating distractions and reducing information overload are doing wonders to fight off stress and keep me humming along.

when darkness falls
18 september 2012 | short story
"You can't prove other stars exist!" We lived in fear. Those in the past cannot understand this fear. Swirling un[...]der the sea of anxiety is hatred, a deep abhorrence for the past and all it held. I skittered along the barren floor, my features obscure and hidden by the dearth of light. A hundred, thousand, countless years ago there was light, said the old text. But none was to be found. They warned of a time when no 'stars' would twinkle in the sky, but they were wrong. There were never stars.

What happens when the universe changes, forever hiding information about its past.

who needs oxygen?
31 august 2012 | short story
We have entered into unknown territory, the nebula around us swirls with shades of pink, purple and orange and the light of stars long[...] dead. It is a breathtaking sight. There are several young stars drifting through the ether that flare and burn the sky. It has been two years since our last encounter with a solid planet and some of the crew was starting to lose it. Luckily for us, we'd been given some ridiculous suits.

A tale that examines that pressing question of all explorers: How far would you go, and what would you sacrifice, for knowledge?

flesh and blood
22 august 2012 | short story
Like many people, I was programmed to like my job, least I grow bored or suicidal. But this was the future! The biologist were supposed[...] to engineer out man's desires and policy makers slowly outlaw this barbaric practice. But it is hardly surprising that didn't happen.

A story about the future of prostitution.

ted talks
01 august 2012 | essay
Reflections on a couple TED talks.[...]

killing time
27 july 2012 | short story
I killed Time. And now I stand trial for my crimes. A short story about laziness and the pitfalls of language.[...]

weatherman's god
10 july 2012 | short story
"You know Harry, I don't understand this God." "What about him Bob?" "He went through all the trouble of creating lif[...]e, only to make it mortal."
"Yes, and...?"
"Well, why did he go through all the trouble of making us, if only to let us die. Seems like a waste."
"There's a lot of waste in the world Bob, this ain't no different."
"No, but think about it. He's omnipresent, no? He sees and knows all. Past, present and future. The whole shebang. But he can't make us immortal?"
"Maybe he can't. Or doesn't want to. That ever cross ya mind?"

A short story about God.

short story collection
24 june 2012 | short story
The short stories that I have written will now include a link to a pdf containing all the short stories on this website and a couple others[...]. The link will stay the same, I'll just update the file from time-to-time.

countdown to equality
10 june 2012 | short story
It was December 31st, 2089 and I was feeling a bit hungry. The neighbors down the street were throwing a New Year’s p[...]arty; they were a superstitious bunch and assumed all their savings would disappear on New Year’s Day due to a computer glitch. I decided to pitch in, though I’m not the superstitious type, just to show my appreciation. The parties from past years, after all, were quite a hoot.

A look at an extreme take on conservation and were it could take us.

putting the customer first
09 june 2012 | short story
“So, Mr. Paterson, I have heard great things about your business. The earnings reports you gave me look stellar. But there arenâ[...]€™t any real details about what your business does. I couldn’t find specific information on your considerable series A funding. As a series B investor, I would like to know a little more before investing.”

We listen in on a business meeting between the founder of a company and a potential investor. What is the business? Well, that fact may surprise you.

setting the record straight
02 june 2012 | short story
The sun beat down and I raised my hand to cover my eyes. It had been days, weeks, maybe even years. Who knew? I surely didn’t. T[...]he dry sands whipped our faces, blurring our vision and making us believe we saw things. Water, chief among them. Haha, it’s funny how that most abundant always seems to be the end of us. You either drown in it or die from not having it. No one wins. Someone told me that they’d managed to survive a month without water. I don’t believe it, but guess I’m about to find out. We’d seen other things. Silver buildings that rose into the sky, it blinded us and as we got close, a sandstorm would appear and when it was gone, so was the house. It is incredible what you imagine when under stress…

A return to writing short stories, this one focuses on the surreal memories of two hapless 'heroes'...

designing icons
25 may 2012 | design
How do you design an icon for a website? This question arose once I'd finished writing the back-end of this website. There is a great [...]book called Creative Workshop: 80 Challenges to Sharpen Your Design Skills that helped me answer this question.

This essay focuses on the icon I designed for the website and the thinking process behind it.

filugori reboot
15 may 2012 | filugori
Several months ago I took a hard look at Filugori: The Long Tale, the story I started in grade school that was meant to be a mash-[...]up of my favorite books and fictional universes. However, it lacked a certain vision. The story was fun, frantic and fanciful, but there was no heart. It lacked cohesion and the universe did not appear to justify its own existence. Why should someone care to read this tale? What would they gain from it? While fleshing out the background of the universe, providing details on the four major epochs that define the story, I came to realize that I wanted to tell a very different tale than originally planned.

the evolving style
29 march 2012 | design
This website was built from scratch using only Notepad. While it would have been easier to create the site in Dreamweaver or another pr[...]ogram and then upload it, I wanted to learn first-hand about the steps involved in web development. The site has allowed me to hone my design skills, both aesthetically and organizationally. This is an essay detailing the evolution of the website.

This was an internal document for me to keep track of what I was changing and why, but decided to reword it and make it an article. Hope you like it.

humanism in european art and society
06 january 2012 | essay
One of the main themes of the renaissance was the rebirth in the interest of classical themes or greco-roman culture. Many artist, eit[...]her through paintings, sculptures or architecture, portrayed this general movement by using Greek/roman themes, such as pillars, and integrating it into their works. But it wasn?t just an interest in greek/roman architecture or appearance but also their cultures.

An essay looking at various European paintings and how they were used to capture the essence of European culture, both old and new.

killer's army
21 december 2009 | short story
The trees flew past us, the wind almost drowning out the roars, hisses, and howls that permeated the area. The gun felt cold in my han[...]d; it weighed me down and got in the way of my agile attempts to slip through the undergrowth. To my left was Marsha, like a sly fox she twisted and turned to avoid everything Nature did to obstruct her path. To my right was Judy, her movements labored owing to the gash running down the side of her leg. It oozed green and yellow puss—we may have to kill her before she turns. The twigs and branches continued to rip through my clothes and skin, yet it was nothing compared to the terror that drove us forward. The howls grew louder and the falling of trees could be heard behind us.

Perhaps the pinnacle of my horror stories, it is a relentless, fast-paced tale of zombies, an accident in the making and a mysterious man. There are two independent stories being told, but drawing the link makes everything much more satisfying.

humanity's gold
20 november 2009 | short story
Captain’s Log 1.25.2838 My eyes watered at the sight. We had finally discovered what we had spent all these years wandering[...] aimlessly for. Shifting and moving, the silvery substance coated the land, its beauty enticing and dicing. There were several who ventured over its smooth surface, dying one by one. Out in the distance could be seen the splendorous pinnacle, atop its peak a mountain of gold. Men still strove for that most holy of materials, still killed and maimed for a chance to hold and possess it; some said that gold had become more than a sign of wealth and power.

Another story that ended up inspiring my book-in-progress Filugori, it is a focus on humanity's lust for something, anything, that will bring him fame and glory. It uses a character more obsessed with the adventure as a counter-backdrop to the drama unfolding around him.

broken
11 november 2009 | short story
“Haha, my brother, how have you been?” “Great. Times are good, money is flowing, bitches crawl all over me—wh[...]at more could a man desire?”
I sat in the corner through blurred vision, watching them hug and chat. Grrrrrrr. There were many things I hated about this house, least of which was the rats. I went to work every day, but that can wait. I got up and was immediately dragged back down. The chains, how could I forget?

Inspired by a series of articles on sexual slavery in Eastern Europe, this is a surreal, sad tale of a girl and her abusers. This took my experimentation with more suspenseful, fear-driven stories to another level. Unfortunately, not all stories have a fairy-tale ending...

filugori
27 december 2008 | short story
The pair looked out across the gorgeous vista, the golden plans below waiting to be harvested, the mountains in the distance yearning [...]to be explored, the hidden structures and stories aching to be discovered. The sky was auburn green; owing to the transition between ecosystems as the planet was terraformed. The suits were itchy, their bright white exterior blinding those foolish enough to stare at them. They reminded him of the astronaut suits they used to see from the late 20th century photos.

Possibly the best short, it focuses on the attack by an unknown entity on an alien city. The fear, anticipation and rapidly switching perspective were an experiment in a new style for me. I think it paid off.

up next!
16 september 2007 | short story
Click I walked down the streets of New York, my skin reflective and my shirt discoloured near the armpits. The subway ticket stil[...]l in my hand almost slipped out and I shoved it into my pocket. My vision blurred for a bit, but my tired body and my sticky hands prevented me from relieving my eyes of the salt and water. My sister walked slightly ahead of me, the clunk of her luggage a soothing melody compared to the rancor the rest of the city seemed to have for my ears.

A slightly fictional look at several events in my life with a story style reminiscent of watching TV.

death takes no bribes
27 august 2007 | short story
The ball whizzed past the net and bounced on the very edge of the service box. I reached out with Herculean effort to hit the ball as [...]it tried to curve away from me. Relief! My return sped towards the middle of the court, only to see him already at the net, Apollo at his back. He sliced the ball to my forehand, I rushed and managed to get to the ball, and turned, waiting for the succeeding surge of energy to do battle with against this unstoppable foe.

A mythical take on a tennis match that I had during high school. Part of a "Kernal Writing" assignment in my high school writing class.

55 fiction
02 march 2006 | short story
Collection of three short pieces of fiction that contain only fifty-five words. They are all play on words.[...]
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