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Links to projects, articles, reports, and mock websites i'm working on.

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A thought-provoking book that should be read by anyone interested in the study and management of pain.

I provide select passages from the book and will update with additional quotes in the future.

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An updated resource that provides 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.

Also found at https://bahanonu.com/brain/imaging_tools/ or https://github.com/bahanonu/imaging_tools.

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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.

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To visualize the nighttime lights of Eastern Europe, with a focus on times before and after the ongoing Russia-Ukraine conflict, I updated my geoSatView R code originally built to view forest fires in the west coast of the United States to use satellite data from VNP46A1 and other datasets collected from the Suomi NPP VIIRS satellite.

I then created higher-quality movies in MATLAB by using the VNP46A2 Black Marble dataset collected by the same satellite, which has reduced cloud and other artifacts due to additional data processing. This allowed me to quantitate a permanent reduction in nighttime lights within Ukraine (in line with my initial hypothesis) and identify a multi-stage reduction of nighttime lights in Kiev's outer neighborhoods/metropolitan area that was greater than that seen in the city core/center. This highlights the utility of public satellite data to quickly test hypotheses and visualize large-scale changes.

I will go over how the Black Marble dataset is collected and processed along with how I created the movies and the advantages/disadvantages of each data source.

Using this platform and codebase, in follow-up posts I will look at 2021 Texas power crisis during the winter storms, vegetation changes in deforested areas or after conservation efforts, and other events.

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Our book chapter detailing the entire pipeline from surgeries to analysis for calcium imaging of pain-related neural activity has been published.

This can prove a useful reference for those new to calcium imaging (esp. in freely moving animals) or researchers who want to see how others perform certain experimental and analytical steps along with the rationale. Please reach out if you have any specific questions, happy to help!

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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.

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A short dirge that introduces one of the themes of Filugori, my planned book on man's conquest of space.

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I recently became a Howard Hughes Medical Institute Hanna H. Gray Fellow. A brief post thanking my amazing mentors and highlighting (some of) my goals as a Fellow.

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I created geoSatView back in 2018 to visualize fires on the West Coast of the United States. This entry briefly discusses geoSatView along with providing example videos and links to the code.

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San Francisco looks good in red. Select pictures from a Martian-themed bike ride around SF.

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I will briefly discuss properly interpreting data you might see in the mainstream or on social media. The takeaway: if recent data for some measure (e.g. pneumonia deaths) from this year looks to be different than prior years, make sure to check that it is not an artifact of data collection or compilation.

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I am starting a new blog focused on the Origin and Evolution of Life. Here is the first post.

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The North American Pain School (NAPS) is a unique experience. The combination of great faculty and trainees, awesome discussions and talks, and a beautiful location help produce a week that will continue to pay dividends far into the future. In this post I want to give future NAPS attendees an idea of why I loved NAPS so much, interspersed with photos that give a feel for what to expect.

This post can also be found on the PRF website:

https://www.painresearchforum.org/forums/discussion/118414-2019-prf-naps-correspondents-blog#traintopain

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My second blog post as a PRF-NAPS correspondent for the North American Pain School. Briefly talks about how several scientists got into pain research.

This post can also be found on the PRF website: https://www.painresearchforum.org/forums/discussion/118414-2019-prf-naps-correspondents-blog.

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My first blog post as a PRF-NAPS correspondent for the North American Pain School. Explores some thoughts on spiritual, societal, and historical influences on pain perception. More soon!

This post can also be found on the PRF website: https://www.painresearchforum.org/forums/discussion/118414-2019-prf-naps-correspondents-blog#styles-2-0.

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An updated spatiotemporal domain of neuroscience methods graphic, inspired by from Sejnowski, 2014. More changes will be added in time.

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I will begin posting again on the BRAIN initiative notes running webpage/blog that I started while ago. There is a lot going on in neuroscience and many questions of how it relates to society at large. Below I have included the first of the new posts that goes over methods for identifying cells and reconstructing neural activity traces from calcium imaging movies.

Find article on BRAIN webpage at Calcium imaging cell identification and fluorescence activity trace reconstruction, part 1.

Look forward to more postings!

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Who We Are and How We Got Here is an excellent book that, even with its flaws, is worth reading for the great overview it gives into the emerging ancient DNA field that could have profound impacts on culture, politics, and science. Goodreads review at https://www.goodreads.com/review/show/2343817531.

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Chinese conquests of Venus, cats fighting off extra-dimensional dragons, Soviet telepathic experiments gone wrong, and much much more! Cordwainer's The Rediscovery of Man is a grand, unique vision of Mankind's future and is a must read for anyone interested in a delightful journey that will both get them to ponder many new ideas and leave a smile on their face.

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I spent the past year leading the Stanford Biosciences Student Association (SBSA) as President. This post consist of the letter to the community I sent out at the end of my term giving some highlights of the past year, those who have helped out, and thoughts on future directions.

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A review of Private Empire: ExxonMobil and American Power, a book that provides an excellent view of how a large multinational corporation deals with adversity, planning on horizons unheard of in political or other arenas, and deals with hostile, often unstable governments in far flung reaches of the world. This review was written back in December 2016, but I am posting it here largely unchanged.

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I have created an updated and corrected E-book version of Johannes V. Jensen's The Long Journey. It is easier to use on ebook readers and when using text-to-speech since header/footers and other errata have been removed from the PDF converted text. I've included HTML, EPUB, and MOBI files along with an explanation of major fixes/changes made. Enjoy!

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How do you disentangle the period in which Don Quixote was written, it's stature as a literary classic, and all the other baggage that accompany this epic? Forget all about it and just enjoy the reading experience.

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An old review of The Revolution: A Manifesto, a book that is well worth revisiting from time to time.

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For those willing to take the plunge, The Road to Serfdom is endlessly rewarding and well worth the intellectual effort.

A re-post of a book review I did back in July 2008.

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Barbarians at the Gate is an excellent journalistic endeavor and a non-stop thrill from start to finish; highly recommended.

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All the President's Men offers a compelling description of Woodward and Bernsteins investigative journalism but suffers from a narrow presentation of the events surrounding Watergate and its exposure.

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What an adventure. In short, the book describes the key players, their personalities, ambitions, and background, along with the financial forces at work that created the culture of Enron and thus the seeds for its dramatic rise and fall. Highly recommended.

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The Revenant is a beautiful, haunting, and brutal tale of a man's struggle against nature, himself, and his fellow man. And at the same time, it is one of those brilliantly conceived movies that uses screen time to allow the audience to meditate and reflect on what they have just witnessed. Go see this movie.

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Harmony Black starts with an old premise, there is a normal and magical world, and barely builds on it. If you are looking for a fun weekend read, this book will fit the bill. But don't expect to come away with a novel view on the world or a new set of wondrous ideas to mull over.

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Star Wars: The Force Awakens is an okay movie when viewed through the eyes of an adult, but is a fun, entertaining movie if you go in with a twelve year old's mindset. It pushes the right buttons and has a good amount of fan service. But it ultimately fails as a standalone movie—with its boring/predictable plot, rehashed characters and concepts, and other flaws—that will ultimately be remembered as good or bad depending on how episodes VIII and IX turn out.

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Black Mirror is a unique and ever timely experience. The vignettes are spot on and while each explores a different aspect of our interaction with technology, the internet, and social media, there is an underlying dystopian view of the world that unifies the whole series. Watch it.

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Walter Isaacson has done an admirable job of trying to tackle such a complicated biographical subject. But for many aspects of his life, from his childhood upbringing to his relationship with Patty Jobs to his time at NeXT, the book is lacking.

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As has been stated many times, Robert Caro has written a tome that will show you in minute detail how a man manipulated the law, people, and money to obtain, use, and abuse power in quest to reshape NYC. It is absorbing, thrilling, informative, and much more. Read this book.

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Providing links to some articles and other resources that I have found useful while in graduate school. I'll continually update the list as I find more.

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A flawed and deceitful rant against free markets in the guise of an objective analysis about the dynamics of capital. Piketty focuses almost exclusively on the inequality of wealth/capital and its accumulation. He then spends vast portions of the book attempting to put this inequality in a bad light without clearly articulating why. Couple that with a tendency to qualify every claim so as to avoid taking a definitive stand and you have a book that leaves you more confused and less informed about the topic, the dynamics of capital, than you entered with.

I'll update this review as I continue to chew over the book's many claims/assertions.

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A gorgeously shot film that is hampered by a spartan story that never really goes anywhere and action that becomes repetitive by the end of the first act.

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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!

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A short review of the excellent Zero to One, mostly analyzing an important question it ask early on: "What important truth do very few people agree with you on?"

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A brilliant science fiction novel that raises many questions and sets up an intriguing universe.

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Putting up some code that might be useful to others when formatting Goodreads widgets using dynamic class creation in SASS.

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A review of Christopher Nolan's latest movie Interstellar. To put it briefly, rarely has a movie so vastly deviated from my expectations going in. And not in a good way.

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Earlier this year I created a webpage to list various labs, websites, and other resources related to neuroscience and biotechnology. Decided to expand on this and create a living document of various technologies currently used in neuroscience.

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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 one 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.

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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.

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Wanted to quickly turn an idea that came up during a conversation into a short story. Touches on ideas of genetic engineering and cockfighting.

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Below is the current crop of books I'm reading along with ratings and mini-reviews for other novels I've recently finished. I'm always excited to start a new book, so recommendations are welcome!

NOTE! The ratings are a combination of how impactful the book was on my thinking about a particular topic or how well I think it was written/got its point across. Thus, at times whether I agree or disagree with the content/thesis/etc. of the book, it could still get 5 stars if the point it makes gets me to think about the subject in a new way or changes how I interpret the world around me.

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A continually updated repository of scientific resources (journals, blogs, etc.) in biology with a focus on neuroscience.

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A function to easily create custom colormaps in Matlab.

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The project had started out with a simple question: would it be faster to assemble complete knowledge about all truths past, present, and future through scientific inquiry or via brute force computation?

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There have been several articles that re-order the medal count ranking by comparing medals to population or GDP, which then show small countries 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.

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There are various ways to handle variable input arguments (varargin) in Matlab. I present the standard getOptions method I developed that is simple, flexible, and allows for more readable code.

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An artistic rendering of Boston's skyline using R. Code and source data are included.

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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 concrete examples.

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The point was nearing when humanity needed to optimize the population. And so the question arose: how many humans do we need?

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The processes of passing command-line parameters to ImageJ plugins isn't the most direct. Illustrated is a simple solution to this problem, full code included.

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How much effort would you expend to abstract man?

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Thought i'd share the wrapper function i use to knit files using the excellent knitr package in R. This allows easy creation of an html page that integrates commentary, R code, and the resulting plots (which are base64 encoded, so the html file is fully portable).

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A revised Declaration of Independence I did awhile ago (i.e. high school) for a writing class. It is slightly a mockery of the style of writing sometimes used back then, e.g. finding unnecessarily complicated ways of saying a simple concept; long, ponderous sentences; and an abuse of the Capital.

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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!

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Small script to enable quick randomization of files in a directory and conversion back to original names later. Original inspiration was a way to blind data analysis, e.g. if studying images from an experiment and don't want to be biased by the conditions applied.

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One of my favorite classes at MIT was 4.605 (Global History of Architecture), which explored various styles and themes found throughout different 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.

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

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This is a continually updated collection of news, ideas/findings, and other tidbits related to the 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.

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Hab�a terminado y sal� para mi cocina. Ten�a hambre pero este d�a no hab�a comida dentro de mi despensa. Me fui y camin� hacienda la Tport—una m�quina que puede transportar una persona a otro lugar sin energ�a y tiempo. Cuando entr� la m�quina, toqu� algunos bot�nes y esper�. Pero nada ocurri� y lo hice las mismas acciones otra vez—y nada ocurri�.

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.

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<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>

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Wanted to share my final paper for bioc218, a computational biology class i took 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.

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While teaching bio42 (cell biology and animal physiology) I created weekly notes to help students in my section study and focus on the important 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.

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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.

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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 Sunday 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?

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

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

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Bit by bit, I have replaced repetitive tasks completed using downloaded programs with scripts that do the same thing more efficiently, without 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.

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Had a couple minutes to spare before leaving lab, so decided to throw together some diagrams to help explain a couple biological pathways students 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.

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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 functions 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.

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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.

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Designed by architect Richard Olcott (Ennead Architects) and sound designer Dr. Yasuhisa Toyota (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.

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Flash, crackle, bang. Pit-pat, pit-pat, pit-pat. The flare skidded down the long, narrow tunnel that appeared to stretch downward forever. 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...

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Now that I've gotten back in the python groove somewhat, wanted to make a playlist script that recursively went through a folder, found all files in a sub-folder and create a playlist from them. Implementation described and link to github repository.

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The graphical abstract is an effective way to convey a complex message in an eye pleasing format that is easily digested. I wanted to create 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.

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Justified text is awesome. Clean lines align well with other elements and it doesn't produce a crazy jagged edge. But without hyphens, problems quickly arise. Some lines have super large spaces between words and the end look is quite ugly. There are several solutions: css, server-side, and javascript.

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And here it seemed I'd forgotten to write about the last exhilarating weeks in Singapore. Fear not! Beautiful buildings, a Hong Kong speed-run, and more food await the eager reader.

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Made a small app that allows browsing of Nobel Laureates. Also provides link to their Wikipedia and Pubmed. Might expand to include pictures or some publications. Enjoy!

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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.

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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.

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James J. Polk expanded the territory of the United States by about one-third during his tenure. A remarkable feat. Not only that, but it was done through an astonishing three ways: territorial conquest, gold and negotiation.

Some thoughts on why we should demand less rhetoric and more pragmatism/details from our presidents.

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"You can't prove other stars exist!"
We lived in fear. Those in the past cannot understand this fear. Swirling under 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.

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Before finishing my adventures in Singapore, I was asked to put together a final report describing my experiences and where the program could improve. Rather than bore you with details, I've included a link to download the report. This is a draft form and I'll update the link with a finished version in the future.

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Scott Adams recently wrote about citizenship and how the Internet will bring the fall of territory-based national governments, and by extension wars. In this post I briefly highlight where he errs and give reasons why country divides will only grow sharper in the coming decades, in part due to competition for dwindling water, oil and other resources along with increasingly fraught intranational civil relations.

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The chef's ingredients are scattered throughout the Guild Wars 2 map, but the profession is a cheap way to get 10 levels quickly. Because I am OCD and would rather not read text when I can browse a spreadsheet, compiled information from a couple of sources that is more easily searchable.

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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?

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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.

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Marina Bay Sands, Sydney, Haw Pa Villa and more! The good times keep rolling in Singapore.

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When coding, writing up blog post, or doing any other task, I generally have used Notepad++. It is a great program that automatically detects, based on the extension, the type of code you are writing and parses the file accordingly. It is light and gets the job done, but it always felt like it could be taken to the next level. Enter Sublime Text 2, a program that seems to have everything I am looking for in a text editor and then some.

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quicklinks is a new homepage for those looking for efficiency over lavish use of big buttons commonly seen in Firefox, Opera and other browser's homepages. As quicklinks is still a little rough around the edges and needs to be updated, I've added it to GitHub to allow me to update it easier.

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Many default PowerPoint themes are too outlandish and graphics heavy for my taste. So over the last year or so, I have begun designing my own themes for PowerPoint. I'll go over the design decisions behind a couple and provide links to download the themes.

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Wanted to add the ability for people to comment on this website, but delayed adding the feature until I could write the code myself. There are many pre-built PHP solutions on the market (like commentator), but the original purpose of this site was to allow me to learn how to build a website from scratch. So I've implemented the comment system using about a hundred lines of code to access the MySQL database, verify inputs and display all the comments for a particular article.

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Reflections on a couple TED talks.

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I killed Time. And now I stand trial for my crimes.

A short story about laziness and the pitfalls of language.

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Sometimes it feels like life should have a record button that nicely parses the endless stream of awesomeness that comes at you. Not a camecorder or microphone, but a program that understands the world, can automatically find and retrieve the most useful links then type-up a nicely formatted document to present to others. Alas, while some of this technology exist, it isn't in one nice little package. Plus, writing about Singapore is almost as fun as experiencing it. Below are some finds from my fifth and sixth week in Singapore, from adventures in Bali to savouring the taste of Ayam Goreng Pedas Ramen (super spicy!).

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"You know Harry, I don't understand this God."
"What about him Bob?"
"He went through all the trouble of creating life, 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.

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Massive artificial trees, beautiful orchid gardens, clubbing till late and learning about Singapore from students and labmates--this week was a blast.

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I have been recording down many recent and very old dreams in a Word document, which has swelled to over 7,000+ words and contains near one hundred stories. The plan is to clean-up and compile all these stories into one novella that has several characters exploring the dream-worlds with some overarching story to tie it all together. Should be a fun experiment.

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Allowed a bit of a breather this week, but nonetheless still full of adventures: getting an equivalent of Montezuma's revenge (but still trudging on), visiting the awesome Mustafa Indian centre, a trip to Malaysia, biking and plenty more. Let's dive in.

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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.

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This pace can't keep up. Saw some crazy animals at a night safari, wandered around NUS's campus late at night (the place is chaotic, beautiful and slightly eerie at night), met with SUTD's president and more. It seems that staying in Singapore for most of the summer is a go, there is so much here to find out and explore. That might also be because I severely underestimated the size of the country (e.g. don't glance at a map's scale and assume 20 miles = 2 miles, haha). Anyhow, here goes, another eventful week summarized in small snippets.

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Wow, what a week. Ran around Hong Kong, learned a couple new things in the lab, meet a bunch of awesome MIT/SUTD students, went clubbing twice, ate a different type (Indian, Indonesian, Muslim, etc.) of food each meal, wandered around Singapore several of the nights and so much more. To top it all off, I was able to learn a ton about Singapore's culture. This place is awesome.

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It was December 31^st, 2089 and I was feeling a bit hungry. The neighbors down the street were throwing a New Year’s party; 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.

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“So, Mr. Paterson, I have heard great things about your business. The earnings reports you gave me look stellar. But there aren’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.

Summary

I fly out to Singapore today. Two days, 11,459 miles and (hopefully) one A Song of Fire and Ice book later, I'll be in my dream city. Can't wait!

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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. The 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'...

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The new-tab page on most browsers inefficiently uses screen real estate by giving each website a picture and large button. While useful for tablets, it prevents addition of many websites and can't be organized into groups without increasing the number of clicks required. Also, often only one search site is accessible, with the rest found in a drop-down menu. To alleviate this, I created quicklinks. It uses javascript to create a row of categories (that you choose), which when hovered over show associated links. Further, there are several search bars readily avaliable, no extra clicking needed. Enjoy.

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Quantized art. The idea came about while reading how the music industry assembles top-liners, producers, artists, performers, etc. to create top 40 hits. For example, there has been a recent trend in pop music to use 'drops', when the song builds to a crescendo and then a crazy, catchy bass line is released that causes everyone to dance. This has been perfected to the point where even an okay song can become popular because the producers know when to build, at what moment to intersperse catchy, meaningless lyrics and how to end the song on a high. I like the idea that art (as in paintings, drawings, etc.) can be dissected and quantified.

My first pass at developing an algorithm to break art down to its details and then use this knowledge to generate art that people would consider 'great'. We'll see how this evolves.

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First post about Singapore lays out some of the background surrounding the trip and Singapore itself. This summer is going to be awesome!

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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.

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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.

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This website was built from scratch using only Notepad. While it would have been easier to create the site in Dreamweaver or another program 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.

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One of the main themes of the renaissance was the rebirth in the interest of classical themes or greco-roman culture. Many artist, either 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.

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My terms as social chair during Fall 2011 went quite well, but there were several things I was unsatisfied with. This presentation outlines several different areas I would like to see improved.

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The Janelia Undergrad program ended with a all-day Symposium during which each undergrad had around 15 minutes to present the results of their project. It was a fun way to end the summer and see what the others had been up to.

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The second presentation that Alyson and I gave during the Janelia Undergrad program, it was a brilliant paper that used Hidden Markov models to build a predictive algorithm that could tell you what chromatin states you were in.

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At the beginning of the Janelia Undergrad program we had to give a presentation on what we planned to do. It was a worthwhile experiences that made one really focus on the different aspects of your project and get feedback.

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Alyson Yee and I gave the first presentation of the Janelia Undergrad program. The paper tried to tease apart the different aspects of a songbird's appearance that most influenced behavior of other birds.

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I spent January 2011 in Cuernavaca, Mexico and worked on a project to model the Notch and JAK/STAT signaling pathways. This is part of one presentation, which I gave in Spanish.

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An educational presentation I gave in Spanish about the differential equation model used in several papers to predict biological pathways.

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Presentation I gave in 9.29, the computational neuroscience class at MIT. They attempted to build a model that could use the information obtained from recordings in the prefrontal cortex and other areas of a monkey brain to predict their behavior based on the 'state' their neuron groups were in.

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One of the presentations I had to give during my stay in Barcelona. Detailed some of the progress made in characterizing the response of different Drosophila species to a set of odors.

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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 hand; 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.

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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.

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“Haha, my brother, how have you been?”
“Great. Times are good, money is flowing, bitches crawl all over me—what 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...

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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.

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Click
I walked down the streets of New York, my skin reflective and my shirt discoloured near the armpits. The subway ticket still 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.

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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.

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Collection of three short pieces of fiction that contain only fifty-five words. They are all play on words.