We're a little crazy, about science!

Posts tagged “writing

Return to the OR

Our OR’s aren’t this futuristic… yet.

It’s been a minute since I’ve had an OR experiment. To be fair there’s a lot going on and with the stuff we’ve been doing there hasn’t been time. But there’s also the participant factor. People need to agree to be part of the study and even before then we need to make sure they are a good fit, so there’s a lot of factors for why we haven’t done one for some time. In any case that is quickly about to change!

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The long week ahead

It’s going to be a looooong week. Mostly because we have what I’m calling “long experiments” coming up this week. Which of course has a lot of work attached to them. When I say long, I mean all day, all day experiments are intense and there’s still work to be done. So this week is mostly going to be focusing on the remaining work I have. But it wouldn’t be a long week if there wasn’t other stuff coming, meaning we have experiments, classes, and a whole lot of other stuff to look forward to in the week ahead.

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The long-term effects of COVID

Sometimes things just work out a particular way. Two days ago I got the bivalent COVID vaccine and that same day Nature Medicine released a new paper on the long-term effects of COVID infection. The paper has already been getting a lot of attention and as you would imagine people are quickly trying to downplay the implications, because the facts are not looking good to those who want to minimize COVID. In fact, at this point ignoring the dangers is ignoring reality and sadly people seem to be okay with pushing that ignorance. So let’s talk COVID… again.

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COVID Vaccine: The first bivalent shot update!

Well it’s been roughly 36 hours or so since my latest vaccination, the bivalent COVID shot and since this is still something being rolled out to the general public, I wanted to document my reactions to the vaccine to keep people in the loop. I think the latest vaccine is pretty widely available at this point, so please make your appointment to get it soon! So that being said, let’s talk about how I’m doing now a day and a half later.

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COVID Vaccine: The first bivalent shot!

It’s about time, but the latest COVID vaccine is making its way to the people. Since I work in a hospital, I just got mine! The bivalent version (the newest vaccine and the one I just got) is designed to be effective against some of the newer strains while still protecting against the older ones. To be clear, this doesn’t mean you won’t get COVID, it doesn’t mean you can’t have serious health problems from COVID, and it doesn’t mean you can’t spread COVID. However, it’s incredibly important to keep getting the shot and today I got mine.

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The slow progress

It’s been a very long day, but somehow not a lot got done. Ever have one of those days? The kind where you’re working from sunup to sundown and somehow nothing got accomplished. I guess there was forward progress, but it feels too slow and right now, I really can’t afford to go slow. If I’m lucky, tomorrow will be better, if not, well then I’m not sure.

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The long preparations

As promised, I’m already preparing for the next “long” experiment. This one will be just as long as the previous, if not longer, so we need to be using our time the best way possible. Ideally we’ll be getting all the data, all of it! But to do that we’re going to need a lot of work between now and then. Part of that will be working out some new code to automate a lot of the stuff we’re trying to do, but some of it will involve making things, because of course it will.

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Another big iteration

Well I’ve barely got the second generation of my “big idea” done, in fact it’s not even completely finished yet, but I’ve already got plans for another iteration. There are several parts involved in making this happen and there are always ways to improve upon the design and create something better. So, with the first round done and tested and the second being completed, I’m already thinking about what to do next. Would it be too much to say it’s going to be… big?

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Dissertation data update 2

Yep, we’re still being lazy and just numbering the updates. Maybe I’ll come up with fancy titles, but for now, this works. Plus this makes it easier for me to search back later. So now that I’ve justified my laziness, let’s talk about where we are. We are here. Okay, seriously, currently I’m still in the pre-processing phase, but there’s good reasons for that. Today I may actually finish pre-processing and I’m hopeful I can hammer out at least a rough idea of what we have… maybe.

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Long experiment aftermath

Well yesterday happened and I can feel it. Everything hurts at the moment, but I knew I was going to be sore today so there is absolutely nothing serious planned today besides maybe cooking something for dinner, maybe. Leftovers are a way of life in research, leftovers and protein bars. I wish I were joking, both hospital-PI and I brought protein bars as a “lunch” yesterday, which may or may not have been eaten as we ran from one part of the hospital to the next.

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The looooong experiment

Ever have one of those nights where you KNOW that tomorrow you have a huge thing going on and for whatever reason, you just CANNOT sleep to save your life? Maybe it was because every few minutes I was reminded of something I needed to do prior to the experiment, or maybe it was just because there was already so many things left undone. Whatever the reason, what should’ve been a day for me to get a full night’s rest turned into what amounts to a power nap.

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The day before tomorrow

It’s basically the big day at this point and I still have a bit of work ahead of me before the official kick off. We have a very strict schedule and I need to make sure that things go smoothly, or as smoothly as possible. I’m not going to lie, we’re already off to a bad start. It’s going to be rocky and we have a whole 12 hours or so for the electrical gremlins to get into the equipment. The pressure is on!

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Experimental prep: part 2

I feel like a broken record at this point, buuuuut… it’s been one hell of a day. It’s been non-stop go, go, go and there’s still one day between now and the big event. There’s still a lot of work to be done and I’m not sure how long it will take, but I have a feeling tomorrow will be a very long day. In fact, these next few weeks will be some of the hardest in recent memory and that’s saying something.

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Experimental prep: part 1

Okay there’s a few days between now and the incredibly complex and labor intensive experiments we have coming up on Friday, so there’s a high chance that this will be a multi-part discussion, hence the title of the post for the day. We’re rapidly approaching the big day and there’s so much work that needs to happen I’m starting to get a little nervous that I have enough time to do it all. To add to the chaos, there are other experiments happening, that require equipment that we’ll be using for Friday, so there’s no way to setup early.

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Dissertation data update 1

I’m being lazy so we’re just going to number my updates with regards to the dissertation data I collected, because I’m tired and I can’t honestly think of a better way to do it at the moment. This is subject to change if I come up with a more creative way. So a while back I collected a bunch of data, then this weekend I had my first chance to teach the people who assisted the first steps to processing it. It turns out there’s a long way to go with them.

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Another 11th

Twenty-one years is a long time. There’s a whole generation of, for all intents and purposes, adults that weren’t even alive when 9/11 happened. The enduring changes that occurred afterwards are really the only thing left from that day. We, humanity in general, have a short memory for things like that. It’s history and we don’t learn from history, much less the present. It’s on odd day and even when it happened we acted in odd ways.

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Dissertation data processing

Today is the day! Well one of many days… wait let’s start over. Today we are processing data for my dissertation and by we I mean myself and two people who have been helping me in the school lab. They will be learning how to process the data, but I’ll be processing all my data solo. It’s my dissertation after all and the old saying, “if you want something done right…” applies here. I can’t afford to trust that they will do it correctly because they’ve never done it, but they are going to learn how today!

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A completed part!

Ideas are perfect, but the first time you realize that idea it’s often a mess. It’s still an amazing thing that didn’t exist, but it’s never as perfect as in your imagination. You have all the parts, everything fits just the way you want, and it works exactly how you expect it to work, until it becomes a reality. Then it just becomes painful.

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Build, then rebuild

Any good idea really begins life as an okay idea. No matter how brilliant the idea, it’s not fully formed, so it’s imperfect. It’s that imperfect nature that makes it seem perfect. You don’t have to look close at the details. It’s what comes later, the taking a blob of an idea and shaping it into something physical, something real, that the idea goes from being okay to being great. Any realized idea in my opinion is a great idea, because you put the work into making it exist and that alone is worth something.

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Adventures in equipment modding

I have it! I finally (as of yesterday) got all the parts needed to build the stuff I wanted to finish for the studies we have coming up. This will be months of thinking through how to improve our setup and improve the noise rejection capabilities of the equipment. A LOT of planning went into the design and now that I have all the parts for assembly it’s time to earn my keep. But it’s not all smooth sailing.

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The week ahead

It’s been busy around here. Between data collections, experiments, papers, and making things, I don’t know how I manage to find time to sleep. This week promises to be slightly slower than the few previous, but that can always change and it looks like it may be changing as I’m writing this. Because of course it is, so let’s just dive in and talk about what’s coming before it all changes around again.

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A few new skills

Not working on anything serious today. Nope, not doing it. I took yesterday for myself and I’m taking today for myself. So instead of working on something strictly productive, I’m going to spend some of the day, maybe just a few hours, looking over some of the skills I’ve been meaning to pick up that I haven’t had time to learn/read about. Will this help my work? Yeah, of course, but it’s also something fun I wanted to learn. I’m a sucker for learning something new and that’s exactly what the plan is for the day.

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Dissertation – The first aim

Okay, with my data firmly in hand (so to speak), I’m ready to start tackling my first aim. Despite having all my data collected however, I’m incredibly behind schedule, by about four months if I check my handy proposed timeline. So it’s a race to catch up if I want to graduate on time and oh do I want to graduate on time! Then there’s the other issue, I have the DARPA Risers conference coming so it would be nice to show something new, that’s only a few months away so the race is on…

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Success! 10 of 10 dissertation experiments

It has been a struggle and I really, really don’t want to ever have to do something like that again, but after a few short weeks (well what feels like short), I now have 10 out of 10 of the datasets needed for my first aim. Will there be an aim 2 data collection? Maybe, if what I’m proposing turns out to actually work. In any case, this is now done and I can focus on the next step.

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Success! 8 of 10 dissertation experiments

Well today was the day that would never end. I only had one experiment today, but it took the whole day. To be fair, we didn’t start until the afternoon, but it was well into the evening when we wrapped up and that was exhausting. Since it’s been such a long day, I’ll recap how things went. For everyone who’s interested, but also for myself since I hope this will help with my dissertation writing sooner or later.

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Equipment modding time

Well today was a long day, but something good came out of all the running around. Some of my new equipment showed up, which will improve how I do the experiments that I want to do, but also make my life so much easier, like way easier. Unfortunately, the usual applies,I can’t talk about it directly, but it’s a good time to discuss how ideas evolve and how you find ways to improve things as you go!

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More coding adventures

It’s another day and another chance to make progress with data processing. Since it’s been a busy few weeks since hospital-PI has returned to the lab, I haven’t had a ton of time to work on the dataset that we collected, the first of hopefully many. However, the initial analysis is done, so it’s time to move forward and start thinking about what comes next. That is, how can we refine what we’ve done? There’s a lot of steps I can take, but I think today we’ll sum it up and narrow it down to the steps I’m most excited about.

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The last participants

Well I had other topics in mind for the day, but I’m so excited that I wanted to make a little post about it. I’ve finally confirmed the last three participants for my dissertation project. I have 7 out of 10 datasets collected and needed three more for this first aim. For the past few days I was nervous that I wasn’t going to get it done this week. Sometimes that happens, things don’t work out how you plan, but that isn’t the case! I’ve confirmed all three participants for my project.

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The helping hands

So granted it’s my blog, my journey, and basically all about me, so maybe I think too highly of myself. I’m trying to not read too much into the implications and what that says about me, but I’ve always thought of the blog as more of a tracker for myself than anyone else. Not that I’m not happy to have the company! Today though, I thought it would be nice to talk about why it takes a village to make a dissertation, despite what it may sound like sometimes.

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The presentation work

It’s still the weekend… right? Well since it’s dissertation data collection season (is that a thing? I feel like that should be a thing) my weekends have been condensed to the point of getting a short break, but it’s temporary, at least that’s what I keep telling myself. Since there will be virtually no time between now and the hospital lab meeting, today is the day I need to get my presentation ready. Am I ready, not exactly, but that’s the way these things go. Maybe I’ll manage to make progress today though.

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Success! 7 of 10 dissertation experiments

One more time. Well technically it’s two days, but whatever. Today marks the completion of 7 of the 10 dissertation experiments I need to get done! Wow, things are moving quick, but maybe not quick enough considering I still need, you know, process the data and make sense of it all. But that’s tomorrow’s problem and I don’t have to worry about that today. Let’s talk a bit about how today went though!

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The first DARPA meeting

Not too long ago, I was nominated for the DARPA Risers program and shortly after I was selected as a DARPA Riser. It’s a big deal for me and DARPA has always been a dream of mine. With the conference coming, I still have a lot of work ahead of me to prepare. None of the new data has been processed or analyzed. I don’t know if the technique (my “super secret technique” or SST) works, or if what I found was something erroneous. I have data, I just need time and as of yesterday time is not on my side.

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A timeline revisited

Balance, it’s all about balance. Right now I have school on one side, the hospital on the other. So far things have been good and in order to keep the balance, hospital-PI and I had a long discussion about the big idea I had almost a year ago and we agreed that the pace is going too slow. So it’s time to hit the turbo button. But what does that look like and where do we go? This is a tale of collaboration, combining different studies, and me, stuck in the middle of it all.

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The internal scars

Not all trauma leaves a visible mark. Just like not everyone who is disabled “looks” disabled, not everyone who has had a traumatic event, even a very physical one, will have scars that show. That doesn’t mean they aren’t there, or that if you look hard enough you can’t find evidence of them, it’s just not a big flashing neon sign saying, “here I am!” It also doesn’t make them hurt any less, or make them any less real. Sometimes the trauma you can’t see is the trauma that hurts the most to carry.

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A big presentation

Ah I’m not ready! Or at least that’s what I wanted to say, but it’s not like I get a whole lot of choice in the matter. But alas, I do not! Instead, next week I’m going to be presenting some of the data I recently collected, from the “big idea” experiment. It’s n of 1, but the results have so far been very promising. There’s a catch though, because isn’t there always? Anyway where to start…

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Experiment juggling

We’re off to a busy week, not that the previous few weeks haven’t been busy mind you! Since I started my dissertation data collection it’s been non-stop, but there’s a lot of other things going on too. In fact, I’ve got experiments on both ends, the hospital side and the school side, so the next few weeks will be just a touch busy! I just got word today that we’re starting another set of experiments and we now have additional experiments later on next month, and by next month I mean next week.

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Journal paper updates

With everything going on lately (my dissertation) I have completely ignored the updates regarding more papers I’m working on. Now that I don’t have a ton of papers in backlog, things have been seemingly moving at a pretty constant pace. So it’s time to talk about where I am on those and what’s coming next. Oh and of course, plans for my dissertation paper(s). So many papers.

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The halfway point

It’s official! As of today I have 5 of 10 datasets collected for my dissertation. There’s still a lot of work going forward for sure, this is just the first step, but it’s a big one. Between the last two days I’ve performed three experiments and I’ve found a few other people to help with the next round. If all goes well, I’ll have all the data for the first aim collected in the next few weeks. So what now?

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The final year

Well today kicks off the final year of 365 days of academia, this will be year four of my little project and year five of my PhD. There is a chance we may have to extend slightly, but for now I’m keeping my eye on the prize and until the deadline comes and goes, I am planning to do whatever I can to make sure I graduate on time. It’s going to be a challenging year, but since it’s a new beginning let’s talk about how we got here. Three years is a long time after all!

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Music to kill myself to

This time of the year is always hard for me. It’s close to the anniversary of my last suicide attempt and while a lot has changed, there’s always some things that stay the same. Today marks the end of year three of my 365 days of academia and today we’re talking about suicide and music. What is it about a song that when you hear it you remember things so clearly? This post wouldn’t have happened if it weren’t for something very special that occurred this year and there’s been a wide range of emotions leading up to it.

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Big idea progress!

This is a little late, but for the past few weeks I’ve been taking my time working on some of the “big idea” dataset we collected a while ago. The first of many, I hope. There’s been a lot of work, but it doesn’t feel like much because it’s all behind the scenes stuff. Kind of like you can build a home, but until it’s finished it never really looks more complete. Well at the beginning of the week I finally had some answers, while there are still a lot of questions, so far so good.

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Tuition chaos aftermath

It’s been a long day, but I’ll cut to the chase and say that I’ve figured out all the tuition stuff! That’s good news because this morning I got a email and phone call from the school letting me know that surprise! tution was due today. After I got that call, there was a ton of phone calls and emails, but somehow I got it done just under the wire.

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Tution chaos!

Well the term is about to start and I got a no-so-friendly reminder of that today when I started trying to figure out how to access my theoretical tuition benefits via the hospital. There was a lot I didn’t understand and now that I’ve dug into it there’s a bit of a concern, but hopefully it will work out… maybe? I don’t even know at the moment, but we’ll just have to wait and see what happens because what else can I do?

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The long road to the end of my dissertation

Sometimes you’re so focused on something that when you take a second and look up you realize it’s almost the end of the year and you’re wondering how the hell that happened. It feels like just yesterday summer had started, we had our interns at the hospital and I had just defended my dissertation proposal. Now we’re roughly 8 months to the dissertation defense deadline and there’s work to be done. But there may be more, depending on how things go.

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Success! 2 of 10 dissertation experiments

Well today went better than yesterday and yesterday went pretty good to being with, so I’ll take it. All in all there were some things that I needed to iron out and a few things I still need to figure out, but it was successful and that’s all that matters. Since yesterday I already went over the rough outline of how it went and doing that again would be redundant even for me, I figure we can talk about how even the best laid plans can change once you start experimenting.

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Success! 1 of 10 dissertation experiments

What a day… I’m so exhausted. It’s been such an overwhelming amount of work, but it’s over and that’s one of the ten experiments I need (for the first phase of my dissertation anyway) done. The data collection went smooth, I love the new equipment, and I only ran into what appears to be one problem with the recording, but I’m hoping it wasn’t a real issue. So quick recap of how it went and then I get to remind everyone, and myself, that I get to enjoy doing it all again tomorrow!

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Experimental preparations

Finally. I’ve got not one, but two dissertation experiments lined up one for tomorrow and one on saturday. It’s going to be a busy few days and there’s a lot of prep that needs to happen today and ostensibly tomorrow before and after the first experiment. Since I am in the habit of sharing my process, I figured it would be a good idea to talk about how we set up for experiments. I’ve spoken often about how long it takes, but I can’t find a recent example of going over what that actually entails. This will be… interesting.

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On the design of experiments

Okay, well a lot has happened today and I’m not even sure where to start! I guess the main thing I want to write about today, despite being exhausted, is planning. I plan everything, I probably write more about my plans than anything else now that I’m done taking my required classes. It’s no secret, I love planning because having a plan means knowing what to do when that plan goes sideways. It means knowing what to look for before a plan goes sideways. Most importantly, it lets you know you’re on the right track.

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Race to the deadline

What is it about self-imposed deadlines that feel more important than the ones you hardly have control over? Maybe it’s because I’m competitive or maybe it’s just that I hate failing at something that I set for myself, but whatever the reason tomorrow is my latest deadline and I’m so close to finishing I can taste it. So today I’m hoping to finish my coding work so I can process some more of the “big idea” dataset I collected several weeks ago.

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Attack of the code

Here’s the thing, all code is bad code. Some code is just better than others. For every person who writes a program, there’s someone else who would do it a totally different and, to them, less complicated or confusing way. However, as long as the code you write works, it shouldn’t really matter how badly it’s written, right? To me the difference between bad code and worse code is comments. The frustrating thing about taking apart someone else’s code is that there are rarely enough comments to figure out what the hell is going on.

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