We're a little crazy, about science!

Posts tagged “research

The t-test in statistics

mind reading

Welcome fellow mad scientist enthusiasts, the last time we talked statistics, we found ourselves in an interesting situation and we need to figure out if the mind control device that was developed is actually working. We introduced the idea of a two population problem and today we’re going to use something called a t-test to determine if our mad scientist succeeded.

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What is good outreach?

Yet another outreach event in the books! I have two more events this week and I believe that’s the last for my skype a scientist commitment. Since this term I was assigned classes practically all at once, I may re-volunteer to get a few extra classes in this term. Normally requests for my specific field don’t happen, but they’ve become more frequent, which is interesting to see because biomedical engineering, or my subset neuroengineering, isn’t a widely known field, but it is growing. All this recent outreach has gotten me thinking about what makes a good presentation, so let’s talk about it.

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The road to a PhD program

In hindsight this post should’ve happened a long time ago, like year one and day one of my 365 days of academia project. Things have… evolved in ways I didn’t understand when I started this, originally the project was simply going to be a notebook for my classes, then it turned into my journey as a whole, and even what I do in my spare time. Like anything we create it took on a life of its own and I’m reminded I should touch on the process to getting accepted into a PhD program.

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Paper submission!

This morning I woke up to some good news! I got an email letting me know that the journal paper I’ve been working on has been submitted. It’s not the end, it’s only the beginning really. It needs to be reviewed before we know the outcome, but I’ve spent the past ten months or so writing this damned thing, so this is a huge moment for me.

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The tightrope of mental health

My mental health is like walking on a tightrope, one slip and I’m done. Getting back up could take years for someone like me. The truth is, things are hard on the best of days. Getting out of bed, shaving, cutting my hair at regular intervals, things that would come easy to some require sheer force of will to accomplish. All the small choices through the day eat away at what little energy I have until I’m drained before breakfast. Yet here I am, pushing forward. It’s days like today remind me that for all the progress I’ve made, it’s still just a tightrope I walk.

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Back to outreach

Just hanging out with the bots.

Today was the finish line, like it or not the R21 grant had to be finished. My Co-PI seems happy enough about the outcome, so we’ll have to wait and see what the result is, it could be several months before we know anything. It was a marathon of work, data process, experimenting, and now… nothing. I’m finally done so I can actually focus on other projects, which is the topic of the day!

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A clear path!

The easy path to getting your PhD…

That was quick! I have an update regarding yesterday’s funding debacle already… it’s good news, but that’s all the hint you’re getting for now! Things are happening fast and frankly they need to I only have a few more days to finish the grant before its due for internal review and I don’t know how my Co-PI is feeling right now, but I’m stressed out!

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Trouble on the horizon

I did not see this one coming… or maybe I did and just wanted to pretend it wasn’t going to be an issue. There’s been a difference of opinion to put it lightly. I received an email this morning from my main-PI asking if we could meet to discuss my funding options and he also casually mentioned that the R21 might not get submitted.

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Scientific figure design

Well I’ve done it… sort of. I edited the grant for the semi-last time. Now we’ve got a working copy that reads the way we want it to read, so it’s off to the scientific writer to read over it and make sure it sounds good. You would think that means my work is done, but no. I need to do arguably the hardest part and create some of the figures we will use in the paper. Writing well takes practice, but making a good figure, well that’s art.

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R21 Grant update

We’re not even two weeks aways away from the deadline for the grant submission that I’m working on with my Co-PI and things are getting close! It feels like there is still so much to do that I don’t see how we would ever make it to the end, but really a lot of it comes down to polishing everything to make it look pretty. Part of writing a grant is telling a story, that story needs to be backed up by science, but without the story the grant will fall flat.

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End of the month crunch

It’s the end of the month and that means there are a lot of loose ends I need to tie up before the new month begins. Deadlines I need to hit, plots to make, projects due, heck I even have a book chapter due. There’s just a lot going on and not a lot of time to finish it all. It seems to be a common theme that things are “due” at the end of the month for me. This month is no different, but with school having started, it gets a little more hectic than normal.

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Experiment Results

It’s been a crazy week, more so than usual! The R21 grant I’m writing is due to my Co-PI today, it’s our self imposed deadline. It’s not THE deadline, but it might as well be in my mind. I’ve processed most of the data from the experiments and yesterday I said we would talk about the result from finding an error in my code. Well let’s talk about it!

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The last experiment!

Today’s the day! It’s the last experiment for our R21 grant, we had our first set of experiments last week and today we’re completing the final experiment today. Hopefully we’ll have some good results for our grant, I got done processing some data last night and if I didn’t make an error the results were slightly underwhelming, but we’ll have to see I guess. There’s still a lot of things I need to check so I’m not too worried, okay slightly (very) worried…

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Overloading in education

Get your PhD they said! It will be worth it they said. You’ll have a good time they said! They certainly say a lot don’t they? Well I say things shouldn’t be so freaking hard. I get that getting your PhD requires work and frankly, it should require work, I mean it’s a freaking PhD! That said, it shouldn’t be a four to six year gauntlet of torture to see how many times you break down mentally and physically. It doesn’t build character, or better PhD’s, but it is the system we work in.

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Experiments update!

Yes the data always look like a bunch of random squiggles, that’s why it takes forever to make sense of it.

Well a lot has happened this week, maybe not the most interesting of things for my readers, but this week has definitely kept me on my toes. Today we’re going to have to talk in circles because I can’t give away my “super secret” technique I’m researching, but I also have news about that technique. It’s all very hush, hush, top secret, would have to kill you if I told you type stuff for now, but that doesn’t mean we can’t talk about how the experiments I’m doing went!

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Second grant experiment

Data processing…. now in parallel!

Ever have one of those days that is so packed full of stuff to do you don’t think you’ll get a chance to eat? Well today is one of those days for me, I’ll be busy from morning to evening today between my experiment and class I don’t get a break! Since that’s the case, I think we should look at what’s on the agenda for the day in a bit more detail and how I plan on managing my time so that (hopefully) I won’t be late for anything.

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More on grant writing

Got the first round of edits back from my Co-PI on the R21 grant I’m writing. At first they didn’t look too bad, but it turns out he reworded quite a bit. Not that big of a deal honestly, but he did suggest that it was close to perfect, so I would hate to see what “not close” looks like. Today I figure we can discuss what I have left, why there’s a rush to get all this done, and why the heck I’m doing soooooo much writing!

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The first week of classes

When you start a PhD program, or a Masters program (I have a BS and MS so I can speak to this) things aren’t as structured as they are in undergrad. Not that undergrad programs aren’t hard or not hectic, it’s just that there are scheduled times for everything so you know when and where you will have work. It’s a lot like highschool in that respect, you get homework, but there’s a clear end to it. Not so much in grad school, your homework takes a year or even years (for a PhD) to finish. Still, it’s the first week of school, so things change, if only slightly.

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A day of meetings and emails

Okay, my inbox isn’t that bad, but if I didn’t keep up with it, it could easily get there.

It’s a new day with a new and long list of things I need to get done. I’ve already got a ton of bad news about my car issues and the rather large bill that is coming with that, but I’ve also got meeting after meeting scheduled for today on top of a long, long list of emails that need responses from me. Basically today is going to be exhausting and all I will have done is sit in front of a computer, how the hell does that even work?!

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First grant meeting

Time to put the fun in funding?

Well it’s been a weird couple of days and by weird I mean, WTF?! For that reason let’s shift slightly back into the school aspect of things. I had my first meeting with my Co-PI to discuss the grant writing I’m going to be doing and what we want to focus on. Turns out there’s a lot going on and not all of it had to do with the grant, but it was a good meeting and I’m excited to get started.

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New year, new grant

It’s all connected somehow… I just know it.

Nope, still on vacation… I tell myself as I make arrangements to meet with my Co-PI. This is important though and unlike some of the other projects it has a firm deadline. That’s right, I’m writing a grant. No this isn’t an update to the last one I wrote, this is a whole new one. How did I end up in this position? Who knows, but I’ve been trying to figure it out since it happened. Let’s discuss, shall we?

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A year in review

So long 2020, while the calendar is a human construct, I hope that the significance means something for mankind as a whole. Who knows maybe we will finally take the pandemic seriously, or global warming, maybe even gun violence. Yeah, I don’t think so either, but one can hope. In lieu of stating my hopes for humanity, let’s just take a quick look back at the year I’ve had and what this new year holds. This is my year in review.

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I’m getting my COVID vaccine today!

Today is the day! About a week ago I got an email letting me know that I could be vaccinated. While I’m a researcher in a hospital, my work involves a high risk population (people with spinal cord injury) so I’m front facing with patients on a regular basis. I’m also disabled which may have factored into my group placement. Whatever the case, I got a spot in line and now it’s my turn. My Co-PI who’s lab I work out of already got his, but he was in a higher group than I was. As usual I have some thoughts on all this…

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The perils of publishing

So you want to publish some science. I don’t blame you, as a scientist we’re driven by the “publish or perish” mindset. The further along you get the more you’re stuck having weird nightmares about h-index and impact factor. Or maybe that’s just me, who knows? In any case, any publication is a labor of love, one that typically turns into a labor of spite. Because publishing isn’t easy, or maybe that’s just me.

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Outreach

I just finished with my Skype a Scientist session! You can do it too if you want, just sign up. I had a lot of fun and while today was going to be on a slightly more depressing topic, I figure we can talk about how it went instead. I love doing outreach, it’s probably one of my favorite things about being a scientist and I got to show a whole bunch of interesting things I get to do as a scientist. This was an interesting group, so that’s also a good reason to talk about it.

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On the importance of vaccines

Once upon a time polio was more feared than the atomic bomb. Thanks to the vaccine we’ve practically (not completely mind you!) eliminated polio from the planet. We successfully eliminated smallpox, the only existing strains live in special labs now. Vaccines are a triumph of science and are so successful that people have forgotten they are necessary for a reason. In short, vaccine fear is a byproduct of vaccine success.

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And finally something good…

I don’t know why my mind went with hidden treasure, but that’s what we’re going with today.

It was bound to happen eventually, some good news for today! I had a meeting with my Co-PI and we went over the latest findings in the dataset I’m processing for my “super secret” technique and I have to say it went much better than was expected! He’s excited, I’m excited, we’re excited. The issue is we don’t know what any of it means, but I think that’s why it’s so exciting!!!!

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Outreach in a pandemic

I’ve been matched! No, not with a dating service, with an outreach program called Skype a Scientist. If you are a scientist (any type will do) you can get involved too! I’ve talked about some of my outreach activities in the past, but heck let’s run through why I think outreach is so awesome and how the pandemic has actually made it easier to do!

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A change in my timing

The meeting with my PI is done and it’s not all bad news. It went better than expected in some aspects and not so great in others. That’s how these things work out, it’s not a linear progression, it’s a lot of going back and forth and sometimes side to side too. Thankfully we met before I made any firm plans! Anywho, let’s just dive in and talk about what happened.

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A meeting with my PI

It’s a treacherous path, but one I need to take

Well I may have overestimated how fast I could get the data processed from yesterday. I have it basically done, but I was up until almost 2am getting it to that point and I didn’t have the energy to start the analysis so that’s going to happen today. Instead of sharing my excitement for a second day in a row I thought I would share some news. I got an email back from my PI and tomorrow we are meeting.

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An early present

Since my deadline has come and gone I can look around for a moment, but more importantly I don’t feel the pressure to hyperfocus on a single project. So today instead of working on that dataset I’m switching to a dataset I need to get done before my PhD proposal defense. It’s data that will (assuming I find something) further help make my case for studying my new “super secret” technique for the next 2-3 years depending on how long everything takes.

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A mental health day

Today the fatigue of the past few weeks has finally caught up to me. With the adrenaline rush that came to a head from the presentation I did yesterday wearing off, I feel exhausted. So today I am taking some time to recharge and rethink what the next few months will look like. This is me taking a mental health day, but let’s talk about the events leading up to today and what the plan is, at least for today.

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How to fail giving a presentation

Today is the big day! The day where I showcase the stuff I’ve done. It’s a bit anticlimactic to be honest because I haven’t had time to do a full analysis, just a very general overview. It was COVID you see, we shut down for a few months there so I didn’t get any data collected. When we finally got started again I had weeks to do the analysis, not months. Needless to say it’s not good.

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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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The science behind an MRI

Today I had an MRI, don’t worry it was for research purposes. It wasn’t a short MRI either, I was in the bore for almost two hours. Yep, stuck in a tube with nothing but my thoughts, some music, and the sounds of the MRI machine doing its thing. I figure we can discuss what an MRI is, why I had one, and why I don’t mind that it took so long. I may even show off some of the scans, but not today I don’t have them yet.

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A look ahead

Okay the next month or so is going to be busy. Complete and utter chaos levels of things to get done. So today instead of complaining about the data I have to process (since I already did that yesterday!) I figure we can look forward. I have some exciting things happening so might as well give you all a sneak peek at upcoming events.

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Back to EEG processing…

It’s the day after thanksgiving and I made my annual I don’t want to have to cook for the next week or two spread of tasty foods. I don’t do the traditional Thanksgiving foods though, I prefer Mexican dishes (since I’m Mexican). Namely I make a huge batch of tamales, since they are a bit of work I tend to make a comically large amount, think 100 or more. So while I have food to last, I need to get back to my main focus and that’s work!

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EEG Cleaning: ICA and Dipoles

This is (a very, very, small portion) of the data I’m working with for this post!

Let it be known that I’m a person of my word and today we’re going to give a rather broad overview of ICA and dipoles. Don’t know what those words mean? Well start here and that will give you a high level view of the entire process. Today we’re going to do a slightly deeper dive into what the heck a dipole is, why we use it for ICA and why ICA is so helpful in EEG data processing. Sound like a lot? Well it is, but let’s take a crack at it anyway!

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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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EEG, not quite mind reading

Still one of the best photos showing how we set up EEG, that syringe has a blunt tipped needle and we use it to apply gel to the scalp. Don’t worry, we don’t break the skin, so it just looks scary, but it’s really safe.

Well I’m behind schedule and even though I was given an extra week (6 days now) I don’t know that I’m going to meet my deadline. It’s not me, it’s my computer, things take time to run so I’m stuck waiting for it to do its thing. Today let’s talk about what EEG is and how we make sense of it.

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NDSEG Fellowship Tips

I might as well talk about it, this will be my second time applying for NDSEG, so today we’ll go over exactly what that is, why I’m doing it, and why, if you’re working on a PhD, you may want to do it as well. NDSEG is tricky, but if you get it then you should be pretty well set for funding, it’s a great program, but it also means you’re being funded via the DOD.

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A writing realization

I had one of those shower realizations last night. I was thinking about all the writing I’ve done and how much I still have left and suddenly it occurred to me that I was done with all the writing… for now. That’s not the only thing though, I had the realization that I wrote more the second two weeks than I had the first two, by a lot.

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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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Calm before the storm

a painting of a ship at sunset on calm seas
I’m sticking with the sea theme, it’s metaphorical!

Time is a great teacher that eventually kills all of its students. We’re all dying, I mean that in the literal sense. We’re slowly headed to a brick wall that we can’t avoid. I guess the difference between that plodding path forward and what I’m feeling now is just a time-scale difference. You see, I’ve set off a chain of events that are destined to blow up. I just hope I’m not part of the casualties. Am I being dramatic? Well, let’s review and you be the judge.

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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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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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