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Posts tagged “neuroengineering

Learning can be painful

Well today was the final lab meeting of the term. While the weekly meetings will (probably) be continuing, it’s still a big deal and could (hopefully) mean the end of my six weeks or so of torment. Normally I give it a few days before I talk about just how badly the meeting went, but this time was different and I’m thankful for it. The difference? My main-PI was out for medical reasons, so we got to talk about the project a little more freely.

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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.

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Apparently I’m close?!

We’re talking about it again, the fact that every week for the past 5 weeks now I’ve been given tasks to do and then presenting on them the following week. It’s been… hard. However, my main-PI gave me hope that the end of all this is close, at least that’s the hope. He said I was close, so today we’re going to talk (as usual vaguely) about what I have left to do before this weeks meeting and why I cannot wait to be done with this.

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When you don’t want to say no

In undergrad I had a discussion with my advisor, or rather he was more of a mentor, he wasn’t technically an advisor. It went something like this, I don’t know what to do next because it all seems so interesting. He argued that it was a good problem to have and while I have generally narrowed down my focus (I am doing a PhD after all), I still have an issue with focusing my excitement. It’s like being at Disneyland and trying to force yourself to go on just a single ride your entire trip. I don’t wanna, I want all the knowledge!

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Journal club

Okay, get this I completely skipped over the fact that my Co-PI started a “journal club” for our little lab. I say little because for the longest time it was just the two of us and the research coordinator (who is amazing by the way!), but now we have not one, but two others in the lab. It’s nice not having to do a lot of extra work, but different topic for another time. We formed a journal club a short 8 weeks ago and every other week one of us sends out a research paper they find interesting about a week prior to our biweekly meetings and then that person presents on it. This week it’s my turn and of course, the universe is against me.

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Fun with coding!

Yesterday I worked and worked, then I worked some more. By the time I called it quits it was well past my normal stopping time. The problem was that nothing was going right yesterday. When I finally gave up I had gotten exactly nothing done. It was one of those days as a collogue said sometimes you just have to power through it. The problem is I don’t have the time to just power through. Which reminded me of how I normally deal with stress, which is funny and I recommend others do this too.

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Another week in review

A week ago exactly I gave a review of the week I had and a look at the week coming up. I thought it was so much fun I’m doing it again, because that’s what passes for fun around here. Who knows maybe I’ll do this regularly! Basically a lot has happened this week and now is a good time to catch everyone up on some of the oddball things I’ve done and things I may have missed in favor of freaking out about the work I’m doing. So let’s just jump into my semi-traditional introduction, then we can look back and ahead. It’s fun for everyone!

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I’m giving a talk!

Well I slipped through the cracks yet again! It hurts me to admit that I’ve probably earned this one. The 7th annual BRAIN initiative investigators meeting is coming (in June) and I was selected for a Trainee Highlight Award. Is it a big deal? Probably not, but I’ll take a win when I can get it. Today we’re going to dive into what exactly this means for me and why even little victories should be celebrated. Is it a little victory? I mean they did pick me, so what does that say about them?

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Scientific figures are hard!

Well now, part of the work I needed to get done this week involved making some new figures. Actually I had added work dumped on me yesterday that I got done just as quickly thankfully. However, there’s a bunch of other figures I need to make that are due… tomorrow! Ah! So of course instead of actually making them I’m here to talk about how big a pain figures are and why we (the scientific community) stress out about them so much.

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The long data processing road

Okay I’m taking another break from the “in statistics” posts, at least for today since the next topic is going to be a long multi-day post worth of stuff and I need an easier post for today. I have way too much stuff going on at the moment to organize a long post! In any case, I figure I could give an update to the data I’ve been working with and how that whole mess is going. It’s mind numbing and exhausting work, but not in the way you would think.

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The new to-do list

It’s been busy! So busy I was trying to find time to write while working on the million other things I have going on. Since I have a moment, I thought now would be as good a time as any to go over the big list my main-PI gave me to do before next week. It’s a long, long, long list and as you may expect, he’s pretty far removed from the situation, so I don’t think he realizes how difficult it is to do what he’s asking, but we’re doing any anyway! Thankfully I’ve gotten pretty good at coding, the bad side is that it’s not my code I’m working with, so that’s the start of my struggles.

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Twice the work, half the… fun?

I work with… Braiiiiins!! Well yesterday I touched on an experiment I did waaaay back in October-ish of last year! With the way things are going it feels like five years not 5 months, but what can you do? My main-PI has started to not so gently or subtly push me to process the data to his satisfaction and start working on the publication of the results. There’s been a lot going on that has pulled me away from the project, from the end of December to the middle of February I was working on grants, but now there isn’t a whole lot stopping me from working on this project almost exclusively… if you don’t include the other grant I’m writing and the fellowship I’m supposed to apply for.

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A roadblock

I haven’t spoken with my Co-PI about this yet because I’m angry. Like fist balled, white knuckled, want to scream into some endless void angry. This was not the post for today, but I’ve learned a long time ago that I should get things out instead of bottling it up and letting it eat me alive. It’s the reason I’m still here today and one minor step to my success in not falling into the abyss that is depression. I am angry and I need to chose my next words carefully, because as you’ll see, I have no power here.

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A meeting with my two PI’s

Yeah it feels pretty dangerous…

If I could make a comedy TV show about my life, I would call it my two PI’s and I would get into hilarious situations while trying to make both of them happy. Mostly you would see me get a lack of sleep and sort of feel like I’m running on a treadmill, going as fast as I can, but getting nowhere. It’s not all bad and I respect my two PI’s, but there’s a saying about having too many hands in the cookie jar and sometimes it feels like that’s what is happening. It’s a lot like the old game “telephone” where I’m given information to pass along between the two, so we’re all going to meet… *cue dramatic music*

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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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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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Make a SciComm video, the hardest way possible!

Writing, and filming, and edits… OH MY! I’ve done it, I’ve committed to making this science communication video (SciComm for short, if anyone was wondering about the title). Yesterday I went into the lab to do some filming and realized that I was about to make a great video, or at least I like to think so. But more importantly I was going to do it the hardest and most convoluted way possible. Why? Well, why the heck not?

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A new science outreach project

Today we’re making a movie! Okay, it’s not a movie persay, it’s a virtual outreach project I’ve been tasked with by my main-PI. Unlike most outreach I do, this is going to take some planning, a bit of script writing, a easy to do exercise that can be followed at home, and lastly a little write up on everything going on. So when I say some planning, I mean a LOT of planning!

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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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More experiments!

*Cue mad scientist laugh* It’s alive!!! ALLLLIIIIVVVEEE!! No, I’m not reanimating corpses, I just work with human participants so if they weren’t alive it would be awkward. I mean really, really awkward. Thankfully since they are non-invasive experiments the risk of serious injury is almost zero. All this build up to say I’ve got some new experiments starting today, as in MY experiments! *Cue second mad scientist laugh*

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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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My first surgical shadow

With all the COVID excitement going on around here, I haven’t had the chance to share my experience about one of the coolest things I’ve had the chance to do thus far in my career! Since starting my PhD I feel like I’ve had all sorts of interesting experiences and while they haven’t helped me publish anything, I’ve learned a lot. Making a jump across fields like I did (design engineering to neural engineering) has had a steep learning curve from the start, but almost three years in and I’m feeling good about the decision.

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I’m going into surgery… sort of!

Okay well this came out of left field, or rather happened faster than I thought it would. My Co-PI and I had discussed just last week seeing some of how the more clinical stuff gets done in terms of electrophysiology and invasive monitoring. He suggested I shadow some of the doctors while they are performing surgery to see how they do the things they do and now I’m about to get the chance to do just that. Yeah, that’s a lot of doing.

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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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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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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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The coding hole

Help, I’ve fallen into a coding hole and I can’t get out! Okay, to be fair I actually DID get out, but at the time it felt like there was no hope and I would be trapped banging my head against a wall trying to figure out what I was doing. Today I figure we can discuss how I code and what my idea of a coding hole is, it will be a fun break for me.

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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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The art of coding

Well I did it. I got all the code written for the next two (of three) steps for processing my data. I can’t do the third until the second step is done for at least one dataset, but I’m almost there and the last bit of code is to visualize the data, which is substantially easier. So let’s talk about what I did and why I won’t have to do it again now.

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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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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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The due data

It’s time, my data and the results from the experiment are due today. Okay, if we want to get technical the due date is tomorrow. HOWEVER, and that’s a big however, I need to get it to my PI today to review before I submit it. Which means he needs to see it today so I can send it off to the center for review.

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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!

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A race to the deadline

Yet another day closer to my deadline for this EEG project and I’m still trying to pre-process my data so that I can make sense of it. We’re racing the clock here and my PI is pushing me to get it done, sure I think I can do it, but then again… maybe not?

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Funding and you, a PhD story

New day, yet another topic for me to talk about. Today I’ve decided to spare everyone from hearing about my data processing woes to instead touch on a topic that I haven’t discussed before (at least I don’t think I have!). Today we’re talking about funding your PhD. Specifically why it’s important and what power you have over the funding you recieve.

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The end of the experiment

Well today was a milestone for me, the end of an experiment I wasn’t too excited to do in the first place! Of course, now comes the semi-difficult part. I need to process the data, draw some conclusions, probably publish a few papers, and get a presentation made. Things need to happen quickly too, so while I’m done, I’m not. At least, not yet.

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Fellowship applications

Well looks like we’re switching gears. That’s right, now that I’ve finished (FINALLY!) writing the draft of my grant proposal, I can move on to some other funding opportunities. It’s fellowship season and since it ’tis the season, I need to iron out my CV and best of all I get to do something different!… wait it’s just more writing.

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The Dissertation Committee

Well it’s been a journey… but every person I emailed has responded and they all agreed to be part of my committee. That’s right, we’re making serious progress on the road to my dissertation proposal. It’s been a little surreal and I’m nervous that even though I’m here I’m not quite ready for it. Today, let’s talk about my next steps and what forming my committee actually means.

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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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Committee selection

Old black and white photo of blindfolded man in a suit reaching out in front of him.
It feels exactly like this somedays…

Well here’s a post that I thought I wouldn’t be writing this soon. Or maybe I’m right on track and I just don’t want to admit that I’ve made progress. Either way, even though it is the weekend I’m taking an important step in my goal to my PhD! I’ve formally submitted my list for my dissertation committee to my PI. Not a PhD or don’t know what that means? No worries, that’s why I do this, so let’s talk about my committee!

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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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Technical writing: How to write gooder

Know your audience, it’s the first rule of technical writing. I’ve taken several technical writing courses during my education and they all start off the same way. KNOW YOUR AUDIENCE! In my experience that is usually the end of the advice given. Most technical writing courses assume you know how to write, an odd assumption when you’re supposed to know your audience. Today I’m going to go over what I do BEFORE I write, in the hopes that it will help some of you. Fair warning, this is long and detailed!

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