Dispatches

How much was the Japanese Imperial Palace worth?

With the Japanese Emperor attempting to abdicate the throne this week, it is a good time to reflect on the significance of the event. While not odd historically (the Emperors in Heian Era resigned fairly often), this is the first resignation in the modern era. Whether he will actually be ...

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Computer Models in History: Soviet Political Realism

Stepping into a slightly different pool than usual, let’s look at something from history: VRYAN (Russian acronym for Surprise Nuclear Missile Attack)

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Scientific Utopias: Or How I Learned to Stop Worrying and Love the h-index

tl;drThe h-index isn’t boiling a person down into a single number, we are. Also, people in power are the worst and will act as such even if they’re scientists

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A Man Walks into a Bar: A Computational Scientist’s Nightmare

There’s the old joke: “A man walks into a bar. He says ‘ow’ “.

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Setting up a new development environment

Setting up your development environment on a new computer can be a pain. This guide will show you how you can take your existing environment and put them into an installer script.

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Andrew Jennings wins 3rd prize in the Poster competition at Northwestern Computational Research Day

At the second annual Northwestern Computational Research day the Amaral Lab was well represented, with undergraduate students Andrew Jennings and Aaron Stern presenting their research. Both did an excellent job, not only in crafting their posters but also presenting their work to all of the symposium attendees. Despite the stiff ...

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Computational research, no longer a red-headed stepchild!

This week I had the, almost obscene, pleasure of participating in Northwestern’s Computational Research Day as a chairperson and poster judge.I typically cringe at the thought of attending conferences and symposia, since I am mainly a homebody (I love my desk, computer, research, and daily schedule), but at the symposium ...

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Filippo Radicchi receives Complex Systems Society's Junior Scientific award

Professor Radicchi (Indiana University), a lab alumnus, is part of the new generation of scientists that are making significant contributions to the study of complex systems and networks. His many important contributions span from theoretical studies of structural and dynamical properties of networks, to analyses of large-scale empirical data about ...

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Troubleshooting the Pyenv/Homebrew Combination

When first starting to use pyenve with homebrew, there are a couple things you can do to horribly mess things up. Or you could avoid doing them, if you’d prefer to have things functional. I tried both approaches.

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Using pyenv

Pyenv is a simple, yet powerful, tool that manages different python versions all from within a user’s home directory.

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I wish I knew then what I know now (reproducible methods are awesome!)

I started working in computational research with no meaningful experience. I spent two years in high school “programming” in C++ on a Windows 98 machine with an IDE that made the programs run (sometimes) through what must have been magic. The past five years have been a constant refinement of ...

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Annoying things about conferences (Part II)

There is something about big faceless crowds that always feels intimidating, hostile, even if we know it is not real, and make us act accordingly. Scientist and fourth-graders alike.

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Stand up and make a retraction

A Nature paper from 2005 that reported a connection between body symmetry and dancing ability was recently retracted. Whatever for? I Investigate.

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Negative results are boring

A few weeks ago, The Economist ran an interesting series of articles chronicling “How science goes wrong.” While most of their points were – or should be – painfully obvious to academics, seeing it in writing has its merits, and helping to educate the general public on some of these ...

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Mean to the Regression

A recent PNAS paper teaches us a lot about data fitting, specifically, how not to do it.

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The Amaral lab website is changing

Our website is being upgraded. Learn about the changes that are coming.

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Workshop organization 101.

Last March I was program chair for CompleNet2013 after attending as a speaker the previous year. I thought that my experience might help others understand what are the different organization roles, and also how the whole process looks like behind the scenes.

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Can a physicist fix a cell?

For those of you who haven’t read the article “Can a biologist fix a radio?” allow me to summarize: physicists and engineers are awesome, biologists are idiots.

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Biologists hate math and other citation database stories

The conclusions reached by a study published in a recent issue of PNAS may not be entirely trustworthy. Well, maybe I need to be more specific so as to narrow it down to just one study. The paper I’m referring to is "Heavy use of equations impedes communication among biologists" ...

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A biologist goes to the doctor

On Medical Diagnosis: who is ill, the individual who lost its robustness to compensate for deformations or the deviant from the population mean? — Nicolás Peláez

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