We're a little crazy, about science!

Posts tagged “graduate school

In need of a break

Well that’s the post. Okay fine I’ll elaborate. It’s been a busy couple of weeks, if I’m honest it’s been a busy couple of months! Between all the writing, data collection, surgery, data analysis, code writing, etc, I haven’t had a chance to breathe! Maybe that’s why I feel dead, I haven’t had a moment to collect my thoughts.

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How to process EEG data

This is what Raw EEG data looks like. That big spike in the middle of the screen across most of the channels, that’s (probably) eye movement.

For those just tuning in, I’ve been busy! I made my deadline, barely. Unfortunately that was one of two. The second requires me to have all the work done, not just part of it. I managed to finish one of ten (yes ten) of the datasets I had, so now I have less than two weeks to finish the rest of it Let’s take it from the top and discuss how we process EEG data!

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More data!

Today marks another day that I got to collect data for my project. The good news is we got a LOT of it, the bad news is I got a LOT of it! Okay, only semi-kidding about that last part. I’m happy I have more data than less data, but it’s also a busy time so I don’t get to process it until I finish all this other work.

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That time I angered my PI

king's roads from Jonathan Strange and Mr. Norell
Navigating the right path isn’t always so easy.

I met my deadline, so now I’m going to take a short(ish) break and tell a quick story. I have been debating about telling it since it’s embarrassing and talking about failures (or really mistakes) is uncomfortable. I had enough uncomfortableness just trying to hit my deadline, but now that I’ve made it I figure I can at least tell the story for posterity’s sake.

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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!

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The stress of an education

Art by: DestinyBlue (you should read their story too if you have time)

I’ve got a lot on my plate at the moment. I’m sure that’s probably true for most people, but in academia it’s somehow considered normal that you balance the tightrope of sanity while more and more pressure is added to you. It’s a toxic environment for sure, more so now that COVID and current affairs are gumming everything up.

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More on mentorship

I’m not sure I would enjoy being a teacher. With the typical size of the class you teach I don’t feel like I could give each student the personal attention that I would want to give them. Thankfully, one of my jobs is mentoring, which is like teaching, but with just a handful of people. I absolutely love it and today I’m going to share a very funny (or maybe just fun) story.

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The abyss of uncertainty

It’s been a day. Meetings, planning, the usual stuff, just a whole lot of it. There is a few things that have been left unresolved unfortunately, namely I’m not sure what my main PI is going to do or how to be ready for it. I get the feeling that he’s trying to move on to the next phase in his career and I’m not the only one.

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A storm ahead

I’m not sure how to even start. Maybe I’m just being overanxious. I’m an anxious person and this happens! Frankly, I think I’m just overreacting, I mean I have to be. My main-PI wouldn’t do something to hurt my career, it just doesn’t make sense, yet I can’t shake the feeling and the email I got today doesn’t help ease my mind.

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The PhD proposal

This horror story from phdcomics.com

Well I was somewhat caught by surprise yesterday when we had our weekly lab meeting and my PI reminded me specifically that I should be working on my PhD proposal. It’s yet another milestone that I need to accomplish on my journey to a PhD. I’m not exactly sure why the reminder caught me off guard, I’ve been planning it for a while now. So today I guess we should talk about what a PhD proposal really is and why I need to do one before I can continue my research.

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A whole pile of work

Pretty much a live shot of my life right now…

Why does everything happen at once? I mean you’re minding your own business and bam, suddenly you have a million things to get done. One minute you’re on top of things, the next you don’t know how you’re going to get it all done. I’m somewhere in the middle of all that right now. I’ve managed to get most/all the things I needed to get done, but not without some new things popping up.

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Behind schedule

Well it’s Thursday and by looking at my list of things I need to get done, I wish it was still Monday. There’s been a few setbacks the past couple of days. My data processing is going well, but not much else has been accomplished because of an incident that happened a few days ago. It’s not a fun time…

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Dominoes

It’s going to be a busy week for me. Seems to be a theme in my quest for that PhD to be honest. I’ve got data to process, papers to write, experiments to run, appointments to keep. It’s a lot of moving pieces that all need to be aligned at just the right moment. Dominoes, if I can get everything lined up nicely, the tasks will all fall just as easy.

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Day 267: The problem with exams

test anxiety

I like to take my anti anxiety medication with a light snack thirty minutes before the exam. That way I get the full effect from the meds at about 30 minutes into the exam. The effects don’t last long enough to make it the entire exam, so I split the difference and this gives me the best result since I can’t stop half way and take more. Unfortunately, they don’t help, they never really do. I feel jittery, like I had too much coffee. I can’t remember the things I need to know and screw up even the simplest parts of the exam because I’m more focused on keeping my heart from exploding out of my chest!

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Day 266: Pandemic research pressure

Pandemic

Think of research like the post office, nor rain, nor sleet, nor snow, nor pandemic, we will be there working. My dumbass had to make the transition from design to human experimenting the year before a pandemic. I could be safely at home designing cool robots in solidworks, but no we need to collect human subject data and despite the pandemic, I’m feeling the pressure.

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Day 265: The lazy goals

prototyping a microcontroller on a breadboard. Random bits of wires can be seen around the black table.

prototyping a microcontroller on a breadboard. Random bits of wires can be seen around the black table.

A “for fun” prototyping project, I thought would be appropriate cover art for the topic at hand.

It’s the end of the term for me. This will be the end of the second year of my PhD program, we have officially started the big countdown to the end of 365 days with (depending on how you want to count) 100 days left, and despite the pandemic, I am making my lazy goals. Mental health is important and my lazy goals help with that, I’ve mentioned lazy goals before, but let’s talk about it in detail.

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Day 264: Summer Research

EEG cap

Pay no attention to my messy desk… instead look at the cool EEG cap I set up.

It’s supposed to be a busy summer for me. With the pandemic going on, I’m not sure how that will play out. Since we don’t know yet, let’s talk about how it was planned and then we can discuss how that changed thanks to the COVID-19 pandemic. This may be bad as far as my research timeline… maybe.

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Day 263: The Reliable Narrator Fallacy

tell tale heart

True! –nervous –very, very dreadfully nervous I had been and am; but why will you say that I am mad? The disease had sharpened my senses –not destroyed –not dulled them. Above all was the sense of hearing acute. I heard all things in the heaven and in the earth. I heard many things in hell. How, then, am I mad? Hearken! and observe how healthily –how calmly I can tell you the whole story.

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Day 262: A Brief Repose

Legion

A project from a few winters ago in my old home. My workshop was so organized!

A friend once described me as, “a maker if there ever was one.” If you ask me, he was being overly kind, but it’s true I enjoy making things. I’m always looking to learn new skills or sharpen old ones. In fact, I’m taking up some “light” woodworking over the summer to do some custom pieces for my home. It will be a fun task, if not a bit tedious and time consuming. I have a list of projects you see, but not a lot of time to do them.

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Day 261: On Being a Mentor

Tree

One of the many hats I wear as a PhD candidate is my mentor hat. It’s probably one of my favorite jobs and I get to work with some truly brilliant people from all types of backgrounds. I’ve had the chance to mentor a small handful of people and I always look forward to learning from them and through our interactions, in that sense, it’s a mutually beneficial relationship.

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Day 260: The thing about endings

The end

…and thus our mighty hero slay the beast and rode off into the sunset to live happily ever after. But why? Have you ever really thought about the way some stories choose their endings? Our hero goes through live altering and extremely daunting challenges only to brush it off like he caught the wrong bus. Pardon me, but what the actual fuck?

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Day 259: The Postscript

Sleep

After awhile you supposedly end up resembling your pet, I think it’s happened. She looks how I feel.

I just want to sleep for fifty years, is that so much to ask for? The deadline is gone whence it came! That does not mean it wasn’t a fight to the end or that there is a weird stillness permeating the house like a calm after a storm. What is it about things ending so abruptly that throws a person into a spiral of confusion?

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Day 258: The deadline

Deadline

It’s here.

If you’re reading this, then it is already too late. It’s here, do you feel it? It’s in the house… the deadline. It’s a sneaky dark and evil thing from a time forgotten, but you can feel its presence long before it arrives. It whispers in your ear as you sleep, or did it? Of course, there isn’t anything there for real, right?

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Day 257: Tomorrow…

Sisyphus

Well we’re up against the wire now. Tomorrow is the due date for my paper and with it the video I am working on. Will I make it? How much work is left to do? Why am I talking in questions? Find out more… now…?

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Day 256: Two days left…

cookie monster

A live shot of me waiting for my data to finish processing

Well here we are and it’s… ♫ the finalllll count dowwwwwn!! ♫ My paper is due sunday at midnight and between the video I need to make, the data that still needs to be processed, and a shitty team mate who has done absolutely nothing to help, well I’ve got my work cut out for me.

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Day 255: The impossibility of complete knowledge

Magic-spells

Have you ever tried to learn something and you just can’t seem to get it to stick in your brain? That would be my life, well most of my adult life since I left the Marines. There is just so much knowledge in the world and wrapping my brain around even a fraction of a fraction of a fraction of that knowledge seems to be an impossible task. So what is one to do?

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Day 253: A race to the finish

finish line

Well still quite a bit of work to do and some of it was frustrating, but here we are. So let’s run through what I’ve got left to do before the end of the term (ALREADY?!) and talk about the next few posts since I have somewhat of a plan… for once.

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Day 252: Dead…line

dead...line

Today is the day, my group presentation is due. Is it done? Well… sort of? Okay not quite, but we’re getting there. My group member still sucks, but since I yelled at him (in a professional manner of course), he’s gotten a little better and has been more responsive, so what’s the hold up? What a great question, let me explain.

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Day 251: Deadline tomorrow

deadline

Well the apocalypse can’t stop the gears of education. Tomorrow is our final presentation for the class I am in, so there is work to be done and expectation maximization will come another day. For now let’s give a quick rundown of what I’m working on.

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Day 250: Maximum Likelihood Estimation

probability

If we are going to talk about expectation maximization (now that I’m done complaining for a bit), we are going to have to introduce the idea of maximum likelihood. It’s going to be very easy to introduce, but it is a very powerful tool in estimating the state of something. Of course, it takes understanding a little bit of statistics, but trust me, if I can understand it, so can you.

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Day 249: A stern email later…

angry

Photo of me responding to his email …

I don’t want to jinx it, I really don’t, but I have an update on my group member situation and it isn’t completely awful! I mean, I’m still doing all the work and blah, blah, blah, but I’ve got an interesting story and I hope that things will be better now.

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Day 248: A Virtual Conference

background

Every zoom meeting I try to break my PI and get him to laugh, this was my last attempt, still nothing… my work continues.

This will be my first conference since the pandemic and it will be a virtual one. To be completely honest, it wasn’t until yesterday that I was reminded we had one today. It’s a little bit different from our normal routine and I think that is what is throwing me off.
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Day 247: The Kalman filter – Part 2

Kalman filter estimate

The Kalman filter converges on the optimal state estimate using noisy measurements and a model that we create.

Okay I lied, I think we can do a better job explaining the Kalman filter, more importantly I have a fun little demo I can share with everyone. It’s not mine, but I like it a lot and it will give you a feel for what the kalman filter does. So let’s get started!
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Day 246: The Kalman filter

We have 3-dimensions here even though it is a 2 dimensional problem. the third dimension is time, this way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.

We have 3-dimensions here even though it is a 2 dimensional problem. the third dimension is time, this way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.

This is just one application for the Kalman filter, I estimated a two dimensional position using a random walk model. We have 3-dimensions here even though it is a 2 dimensional problem, the third dimension is time. This way we can see the path over the course of the recorded time. Notice there are no units, becuase in this case we were working with synthetic data so the units were meaningless and I did not include them.

Since we’ve been talking a lot about it, I thought it might be a good idea to formally introduce the Kalman filter. This will be a semi-high level introduction (like my knowing your spinal cord series), but at the end of it you should have a relatively good feel for what a Kalman filter is.
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Day 245: Fine, I’ll do it myself.

Thanos - I'll do it myself

I will not fail this class becuase of a shitty team member. I will not allow it, I’ve put too much effort and time into this class to do poorly at the last minute because my team member can’t be bothered to do the job he agreed to do. I suppose, this was… inevitable

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Day 244: The end of the term!?

end of term

Okay, where the hell did that come from?! It’s almost the end of the school term. WHAT THE HELL!? It feels like we just got started, but my instructor just sent out the final assignment, which is due the last week of school… next week. I’m sort of freaking out right now.

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Day 243: Deadlines approaching!

deadlines

It seems like it’s been non-stop for me left and right. I have experiments to do, papers to write, and classes to work on. With the pandemic I was hoping to get a chance to take a break, but nope it seems like I’m even busier than normal. I HAD thought that I was caught up finally when I finished processing some of the experimental data I had laying around, but nope I was reminded yesterday that I had not one, but two major deadlines coming.

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Day 242: Experimenting in the time of a pandemic

Experiment-blur

Another day forward in our new normal. I’ve left the house exactly once in the last two weeks and while it’s nice not having to commute to school, I do miss living in a world without the constant fear of catching the virus. What day is it? Who knows, it doesn’t matter anymore. I do have some things coming up though, so let’s talk about experimenting in the age of COVID-19.

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Day 241: Modeling the COVID-19 Pandemic

COVID-19

COVID-19

Today is the day. I submitted my super high level explainer video on how I modeled the COVID-19 about  a week ago and I got an email from my professor telling me that it was great (yay) and that she had uploaded it to her labs youtube channel. That means I finally get to share it with all of you!

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Day 240: Conferencing at a distance!

video conferencing

video conferencing

Not everyone has access to such luxurious setups.

It’s that time of the year again, well one of two times of the year really (for us anyway). Unfortunately with the coronavirus conferences are better held virtually than in person. While I have mixed feelings about the usefulness of meeting virtually to share our work, I am grateful that there are workarounds, don’t get me wrong, but there are some logistics that make it, well painful and some things that make this worthwhile.

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Day 147: First day in the lab

lab

A semi good photo of our lab!

Today is the first day in the lab since break. It was nice to have some time off, I got some housework done, got to spend the bulk of my time sick (not my idea of fun), and best of all I got to see some of the city. It’s been good and now that I’m ready to get back to it, the week is looking to be busy.
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Day 146: Back to school!

Back2School

My photo, but not my school, just one I visited.

Tomorrow is the big day, back to school, back to classes. This means that any and all house projects will inevitably come to a screeching halt until spring break (most likely) and it marks the shift in blog posts from life outside the lab to life in the lab. There are a few things I like to do to get ready for classes the day before, so let’s talk school.

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