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Posts tagged “computer

Flexible coding for data visualization

My main-PI has an odd habit of wanting us to edit things as we’re presenting them. I’ve watched this happen and had to do it myself. Suddenly you find yourself editing a paper/grant/etc. and forgetting how to spell your name because you’re so flustered. It isn’t just papers though, it’s our visualizations that we make. He will ask us to go in and change things as they are being shown. This has happened to me several times already and more often than not I’m ready for it. So today I figured I would go over some of the things I do to make sure that I don’t spend the entire time sweating over edits to my code.


New computer issues…

I took this photo right when I got the new laptop.

Well if I’m not a magnet for computer issues I don’t know who is. If it’s not one computer it’s the other. In this case, I had problems a while back with my desktop (here) where the watercooler went bad and my CPU decided it wanted to scream at me anytime I ran the computer, like just turned it on, not doing anything with it. This time it’s my laptop that I’m having trouble with and unlike my desktop, the laptop is my daily use computer so I’m not too happy.


Fun with Rstudio

Okay, not really. Having to use R is a pain. I’m not a fan and the structure they use is very confusing to me as someone who uses MATLAB on a regular basis. I understand matrices, I regularly make and successfully work with higher dimensional matrices ( > 3, which hurts your brain to think about a 20+ dimensional matrix, but hey whatever gets the job done). R on the other hand feels foreign and the commands feel clunky.


EEG cleaning progress

Yesterday’s coding work went better than expected! That may or may not bode will for the rest of the week, but hey at least I’m sort of ahead of schedule. Today I figure we can take a quick look at what I’ve been doing with the data and why. This will be part informative and part me complaining about how everything has to be so damned hard (basically the usual around here). Mostly it will just be some visuals of the things I’ve had to change to get everything looking like my main-PI wants, he’s got a particular style he likes so a lot of large text, bolded labels, etc.


To code is divine, to err is human

Yesterday we had a problem. My data was not playing nice. It decided that I didn’t really have what I thought I should be seeing and that left me… anxious to say the least. Since this is all so new, one misstep could ruin everything. To make things worse, there was one of three choices and none of them were good news.


Computer rebuild

Okay, lots of work and not a lot of time to do it in, but today I thought I would show off the internals of my computer since I had to swap out the watercooler for one that wasn’t garbage. This is a follow up to this post, so with the background out of the way, let’s go!


Time to work

So this post is coming a lot later than I would normally do this, but it’s been a day (already) and it’s going to get busier. I’ve had one experiment, one class, and now I need to repair my computer so I can perform the analysis of the data I have to get done before Thursday. Fun times ahead!


Computer troubles

It’s my baby! The case is unique, but I wanted something that could grow with my needs and this case is not just fun to look at, it’s huge! Unfortunately that makes the computer super heavy.

I had a feeling this may happen, I just didn’t expect it to happen when I was so against the wire to get this project done. I’m having computer troubles. Not my laptop thankfully, but my desktop computer is feeling a little… warm. I’ll explain and then get into what I’m doing to fix it, so today let’s talk about my computer!


Day 131: My laptop is ALIVE!

poor laptop

The poor thing has been through a lot, notice my c key is completely worn down. I didn’t know I hit c so hard!

Well after a few days of curing time, my laptop is alive again! In fact I’m writing this on it now. YAY!! I honestly don’t have the money to replace the thing and I already have much needed car repairs to attend to, so this cannot break on me yet.


Day 129: Everything is breaking!!!

Day 129 - repairs

Well it’s post Christmas day and I have to say my stealth wrapping was a hit. Of course, after the first gift (or even the second gift) people catch on, but overall it was a lot of fun and I even got a few apologies for some of the ill will based on my apparent lack of wrapping abilities. I HIGHLY recommend giving it a shot. So let’s talk about the image above for a minute.


Day 98: Laptop troubles

Well it finally happened. My laptop looks pretty dead. Right now I have it in pieces while I try to figure out what went wrong with it. Thankfully I have a desktop computer that I use for all my heavy computing as a back up. Just one more expense I guess, I should be grateful that it wasn’t something more serious like the hard drive going out.

So short post, I know, but I have to get this fixed or find some sort of resolution since my laptop is an important part of how I get work done. I’ll have a longer post tomorrow, but for now I think that is it.

Until next time, don’t stop learning!

Day 91: Did that really just happen?

windows10 update screen

Screw you auto update

For those of you following along, I’ve been trying to crack a predictive model using some novel (read: super secret PhD work) neural data. It’s been a journey and I’ve trained and tested about a dozen or so models, with varying success. Things have been flying pretty smooth the past few weeks as I try to create the best model I could possibly create. Unfortunately, technology had other plans for me.


Day 22: Parametric vs. NonParametric Statistics

How Mean Meme

Technically we could call this parametric statistics part 2. However, since we are covering nonparametric statistics and more importantly the difference between parametric and nonparametric statistics, it would seem that this title makes more sense. As usual with a continuation, you probably want to start at the beginning where we define parametric statistics. Ready to get started?*


Day 21: Defining Parametric Statistics


It’s halloween time, we are talking about normally distributed data, so this fits, and I don’t want to hear otherwise!

Well my lovely readers, we’ve made it to the three week mark, 5.7% of the way through! Okay maybe that doesn’t seem like a big deal written like that, but hey it’s progress. So last post we had our independence day, or rather defined what it meant to have independent events vs. dependent events. We also said it was an important assumption in parametric statistics that our events are independent, but then we realized we never defined what parametric statistics even is, oops. So let’s stop dragging our feet and talk parametric statistics!*


Day 20: Independent Events


By: xkcd


Because we introduced the central limit theorem last post, it’s time to introduce another important concept. The idea of independent events, while this may seem intuitive, it is one of the assumptions we make in parametric statistics, another concept we will define, but for now let’s jump into independence.*


Day 19: The Central Limit theorem




Well here we are again, if you recall from our last post, we talked Bonferroni Correction. You may also recall that when the post concluded, there was no real topic for today. Well after some ruminating, before we jump into more statistics, we should talk about the central limit theorem. So let’s do a quick dive into what that is and why you should know it!*


Day 18: The Bonferroni Correction

Keep calm and do the Bonferroni corrrection

Keep calm and do the Bonferroni corrrection

By now we are masters of statistics… right? Okay, not really, but we are getting there. So far we’ve covered two types of errors, type 1 which you can read about here, and type 2 which you can read about here. Armed with this new knowledge we can break into a way to correct for type 1 errors that come about from multiple comparisons. Sound confusing? Well, not for long, let’s break it down and talk Bonferroni.*


Day 17: Type 2 errors


cat asleep

Last post we did a quick bit on type 1 errors. As with anything, there is more than one way to make an error. Today we are talking type 2 errors! They are related in the sense and we’ll go over what that means and compare the two right… now!*


Day 16: Type 1 errors

tiny dog yawning

tiny dog yawning

We did it, we cracked the coin conundrum! We managed the money mystery! We checked the change charade! We … well you get the idea. Last post we (finally) determined if our coin was bias or not. Don’t worry, I won’t spoil it for you if you haven’t read it yet. I actually enjoyed working through a completely made up problem, so if you haven’t read it, you really should. Today we’re going to talk dogs, you’ll see what I mean, so let’s dive in.*


Day 15: Significance, Part 3


Where does our observation fall on the probability density function?

It looks like we’ve arrived at part 3 of what is now officially a trilogy of posts on statistical significance. There is so much more to say I don’t want to quite call this the conclusion. Instead, let’s give a quick review of where we left off and we can get back to determining if an observed value is significant.*


Day 14: Significance, Part 2

Bar graph showing z score across trials

Bar graph showing z score across trials

Z-score bar graph that I made just for all of you using some data I had laying around. If you’re new to statistics it may not make sense, but rest assured we will make sense of it all!

Well here we are two weeks into 365DoA, I was excited until I realized that puts us at 3.8356% of the way done. So if you remember from last post we’ve started our significance talk, as in what does it mean to have a value that is significant, what does that mean exactly, and how to do we find out? Today is the day I finally break, we’re going to have to do some math. Despite my best efforts I don’t think we can finish the significance discussion without it and still manage to make sense. With that, let’s just dive in.*


Day 13: Significance, Part 1

Normally distributed data shown using a histogram plot

Normally distributed data shown using a histogram plot

Histogram of normally distributed data. It looks very… nomal. No it really is normally distributed, read on to find out what that means and how we can use it.

If you’ve read my last post I hinted that today we would discuss filtering. Instead I think I want to take this a different direction. That isn’t to say we won’t go over filtering, we most definitely will. Today I want to cover something else though, significance. So you’ve recorded your signal, took an ensemble average, and now how do we tell if it actually means something, or if you are looking at an artificial or arbitrary separation in your data (IE two separate conditions lead to no difference in your data). Let’s look at significance.*


Day 12: Signal, cutting through the noise

example data

45 separate trials of very noisy data with the average of those trials (black). Believe it or not, this is actually very useful and very real data from something I am currently working on.

Noise, it can be troublesome. Whether you are studying and someone is being loud or you are trying to record something, noise is everywhere <stern look at people who talk during movies>. Interestingly enough the concept of noise in a signal recording sense isn’t all too different from dealing with talkative movie goers, so let’s talk noise!*


Day 11: Why even use the spectrogram?

rotated spectrogram showing all three dimensions

rotated spectrogram showing all three dimensions

A spectrogram plot rotated so we can see all three dimensions.

So you wanna use a spectrogram… but why? What does a spectrogram do that we can’t do using some other methods for signal processing? As it turns out, there is a lot of reasons you may want to use the spectrogram and today we are going to cover some of those reasons and number four may shock you! (okay not really, what do you think this is a clickbait website?)*


Day 10: Spectrogram vs. the banana of uncertainty


The banana of uncertainty (okay, it’s not a real banana)

Well ten days in and we’ve just introduced the idea of the spectrogram. While a lot of this information is just the broad strokes, I like to think that we’ve covered enough to give you a good idea about how to use these tools and what they are used for. However, we do need to discuss a limitation to the spectrogram, something called the banana of uncertainty, okay not quite the name, but you’ll see why I keep calling it that.*


Day 9: Reading a Spectrogram

rotated spectrogram showing all three dimensions

other example

Definitely not the same spectrogram as yesterday, no really look. Now for the part where I tell you how to read this thing…

Last post we introduced a new tool in our arsenal of signal processing analysis, the spectrogram. Without knowing how to read it, it just looks sort of like a colored mess. Don’t get me wrong, it is an interesting looking colored mess, but a mess nonetheless. Well today we are going to talk about how to interpret the plot and why exactly we would ever use this seeming monstrosity.*


Day 8: The Spectrogram Function


Example spectrogram from some data I had recently processed

To (somewhat) continue with our signal processing theme that we have going on at the moment, over the next few days, let’s look at something called the spectrogram. It’s three dimensions of fun!*


Day 7: Small waves, or wavelets!

Meyer Mother wavelet

This is the Meyer wave, a representation of a so-called mother wavelet function to use for the wavelet transform. Notice that it is finite!

Waves! We’re officially one week through 365 Days of Academia! Woo! 1 week down, 51(.142…) weeks left! Let’s wrap up this weeks theme (there wasn’t originally a theme, but it kind of ended up that way) by talking about other ways we can get to the frequency domain. Specifically, let’s stop the wave puns and let’s talk wavelets!*


Day 6: The fast and the Fourier


A good example of how the Fourier transform can approximate signals. The red signal is our input signal and the blue shows how the output of the Fourier transform.

Okay, if you’ve been keeping up with these posts, we know about Welch’s method, Thomson’s method, the things that make them different, and the things that make them similar. The thing that both of these transforms rely on is the Fourier transform. What is the Fourier transform? Well, something I probably should have covered first, but whatever this is my blog we do it in whatever order we feel like, so let’s dive in!*


Day 5: Whose window function is it anyway?

Window function - funny

This is not how we use a window function on the computer…

One day someone looked at the windowed fourier transform and said, “Don’t be such a square!” and thus window functions were invented. If you believe that, then I have an island for sale, real cheap. But seriously, let’s do a dive into what a window function is and why the heck there are so many of them, because there ARE a LOT! So let’s get started!*


Lots of selfies may suggest you’re a narcissist

This awesomeness is from The Oatmeal, check out his website for the rest of the comic!

This awesomeness is from The Oatmeal, check out his website for the rest of the comic!

Well I’ve got some bad news to all you selfie fanatics out there, a new study showed that men who posted more online photos of themselves than others scored higher on measures of narcissism and psychopathy. The study looked exclusively at men, however the men out there should have no fear, there is a follow up study being done with women as well.


A new type of memory storage on the horizon

memory storage

For those of us old enough to remember the days of the Apple II, you know that storage has exponentially increased. Even just 10 years ago 20+ gigs of data seemed huge, now my cellphone has 64 gigs. Yet we still need more data storage and we are looking for new ways to get it. Now a way to use weak molecular bonding interactions to create well-ordered and stable metal–organic monolayers with optoelectronic properties has been found. The development could form the basis for the scalable fabrication of molecular optoelectronic devices.


Carbon’s Place in a Silicon World


Everything is silicon based, well mainly your computer, your TV, your ipad, and pretty much every piece of electronics in existence. Still the world turns and so does technology; at a similarly fast pace no less. Even as the 2014 Nobel Prize in Physics has enshrined light emitting diodes (LEDs) as the single most significant and disruptive energy-efficient lighting solution of today, scientists around the world continue unabated to search for the even-better-bulbs of tomorrow. In this search we are now ditching silicon for new carbon-based electronics.


Optical Cables, from Thin Air!


It’s a project that would make Tesla proud. Just imagine being able to instantaneously run an optical cable or fiber to any point on earth, or even into space. That’s what researchers are trying to do. Did I mention it was instantaneous and involved no connection other than the air around us? Well if you are as excited as I am, then you should read on! If not, two words, laser weapons!!


Silicon Brains: Not as Cuddly as the Real Thing.

Well played brain, well played.

Well played brain, well played.

Are you real? What is ‘real’, more of a philosophy question than a scientific one, but what if a computer worked like your brain? What if, one day the line between computer and human were blurred? That day might be coming sooner than you think.

Currently there are two major problems with designing a robotic brain. The first is hardware, the brain is an incredibly complex thing that we don’t even fully understand, even if we could theoretically produce something close to that work of art there is that second problem– The software, designing software to take advantage of that type of power would take something short of genius to do, especially if it were going to be something easy enough that you or I could use.


DNA nanobots perform in living cockroach


Cockroaches, not the cutest thing on the planet.

The six million dollar man has nothing on these cockroaches. We can rebuild them, better than they were before. We have the technology, and as it turns out, we do! While DNA robots may not, in itself be a new thing,a study published in Nature Nanotechnology is definitely not only new, but it’s something to talk about.


It’s a swarm… of robots?!


The rather cute TERMES robots doing their thing. Photo credit goes to Eliza Grinnell, Harvard SEAS

You’ve seen a swarm of bees, you’ve seen a swarm of ants. But now, a research group at the Harvard School of Engineering and Applied Sciences have introduced us to a new kind of swarm, a swarm of robots.

The idea stems from, of all things, termites.

Normally, when you have any sort of large scale building operation, like a home for example, you have someone in charge telling each individual what to do. There are specialized functions for each person, a electrician, a carpenter, etc and if one of them walks out on the project, the project is stalled until they are replaced.