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Posts tagged “college

Technical difficulties

This is my current cooling setup, which I picked because I needed a replacement ASAP and I thought this would last me until after I graduated and not less than a year.

Well if it isn’t the consequences of my own actions. Or maybe not, maybe I’m just unlucky. I am once again having desktop computer troubles. It’s the return of the heat issue, thankfully this time I caught it somewhat early (I think). Since this seems to be a reoccurring issue I think we’ll try to fix it with a slightly more permanent solution. The problem? The cost, this couldn’t have happened at a worse time, but not all is lost, at least not yet.

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PhD proposal prep

Well I’ve finally made it to the next milestone in my PhD. I’m now at the point where I can do my proposal defense. It shouldn’t be too bad, but there’s a lot involved between now and then that needs to happen including coming to some sort of an agreement between my two PI’s about what exactly the project will consist of. Since I had no idea what getting a PhD entailed when I started, I’m assuming at least some of you have no idea what’s going on so let’s go over how we got here and what I’m getting ready to do.

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Success! Journal paper 1 of 4

Psst, hey you! I got good news! I’ve officially had my first journal paper accepted for publication! I’m literally crying I’m so happy right now. My inbox has been flooded by emails from my collaborators congratulating everyone on this. It’s been a long, hard, and often painful journey, but I’ve finally, FINALLY, gotten something finished once and for all. Since this is the end of the story, let’s tell it from the beginning, one last time, so you know how we got here.

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The week ahead

Well the next two weeks are shaping up to be interesting. I’ve got a lot of the onboarding stuff to get out of the way for my new job (yay!) and I’m still juggling two different papers basically full-time. Considering those two things are really the only stuff on my plate at the moment things feel pretty good, sort of anyway. There’s still a lot of mental health stuff going on and I’m just feeling overwhelmed with the choices I’ve made so far. So what’s the game plan for the week look like? Let’s talk about it.

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The resubmission!

Well we’ve crossed that milestone… yet again. I’ve submitted the third version of a paper I’ve been working on… for years now. Yeah, they can take a while and with COVID, things took even longer. So what happens now and what the heck is going on? Since it’s it’s already been an incredibly busy day, let’s recap the journey this paper has been on and how we got to the latest and (hopefully) last submission of my paper!

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The uncertain future

old door in middle of field, which opens to a whole different world.
old door in middle of field, which opens to a whole different world.

My Co-PI is leaving! Or maybe he’s not? But he could be?! I don’t even know. It doesn’t help that he has no idea and there’s no real deadline for him to make a choice, it’s whenever he’s ready. In fact, we currently have a line graph with his daily percentage on staying or leaving. I wish I was joking. It’s not just my future I’m worried about, there are others in the lab, most of us wouldn’t be able to make the journey to his new workspace, even if we wanted to (and trust me when I say if I could, I would).

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A small success

It was a leap of faith. There were no good choices, but it was the best of options in a string of bad options. I could either work full time in my main-PI’s lab, pulling me away from the clinical research I love, or I could take a job in my Co-PI’s lab. The catch was to take the job with my Co-PI I would have to apply, wait, and go through the onboarding process. That would mean I wouldn’t be getting paid, which would be okay for a few weeks, but longer and I could be in trouble. Nothing is finished yet, but I’ve gotten some good news.

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Minor revisions

Ah, just when I thought I didn’t have to worry about one of the multitudes of papers that I’m working on, it comes right back. This is the journal paper I wrote for one of my classes, which looks to be about ready for acceptance. There were some minor revisions that we were asked to make, but as of ten minutes or so ago I’ve addressed all of them. I think… it will probably be another round of edits with our co-authors to make sure everyone is happy with what we’ve done. Maybe? I’m not even sure at this point.

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I’m not okay, but that’s okay.

Still not doing well, but what else is new? The point of this project was to focus on the journey to my PhD. To talk about my education and to share the things I learn along the way so others can survive the journey themselves. This wasn’t a blog so much about me as it was about the things I’ve learned. Well one of the things I’ve learned is that despite my desire to remain anonymous and share purely my education progress, it is difficult, if not impossible, to seperate myself from my education. And right now I’m not okay, but that’s okay.

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The voracity for exploration

Humans have set foot on the moon, multiple times in fact. We didn’t go once, we went six different times. Six times. That feels both like an incredibly large number and an incredibly tiny number all at the same time. For you and me it probably doesn’t feel like anything special, but for the people who’ve done it, they KNOW it was life altering. They told us so and it’s a shame that in my lifetime I will probably never set foot on another planet and have the chance to feel so… insignificant.

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Education in a pandemic

Well the term is officially underway and with it comes in person classes! Because if there’s one thing a life is worth, it’s money and there’s money to be made by forcing you into the classroom. Yes the world has changed and we adapted with it, somewhat, but even with hospitals on the verge of collapse (again) we’re given the unequivocal message, “We’re going back to normal!” from schools. There’s nothing normal about it, but the economy is built on the backs of the people, so I guess, in a way, we are returning to normal.

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Multi-paper madness!

HELLLP! I’m doing way too much writing and it’s the scientific kind, which is to say soul sucking! Okay, it’s not that bad, but for the past month it’s been a mad rush to get several different papers written. Today I plan to go over all the papers I’m working on, the progress I’ve made, and why I really hope I’ll never have this happen again. Far too much writing! It has to end eventually though, right?

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A small job update

It’s not a straight line to the finish, that’s for sure.

A week ago almost exactly I did something incredibly stupid. Okay, I did it because I really want it, but there’s a chance it could blow up in my face, I’m going into research full-time to help pay for my PhD. Now, I’m not paying for my PhD, that is never a good option. Instead the hospital I will be working at will be paying for my PhD now and I will get paid better while I wrap up the last two years or so of my degree (more here).

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Analysis fails

I’m an idiot. So for the past few weeks I’ve been working with our super fun new dataset! Like a big kid, I did the statistics, made the checks to ensure that the assumptions held, then got my result. Everything was going well until I realized there was a typo (here) in my code. Well it turns out that wasn’t my only problem, but everything should be fixed now… should.

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A new school year

Well today marks the start of year three for the 365 days of academia project! It also means I’m now a fourth year PhD candidate. Since we’re going into another year I think today I’ll revisit why I started this project in the first place and basically just give everyone a reminder about what keeps me going. That way I can talk about all the anxious feelings I have heading into the new year and how I feel like I’m nowhere near where I should be.

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The stress of change

When I think of change, I think of fall. Maybe it’s an apt time for a change in my life then.

I’m used to things changing. In fact, when things are static it’s actually slightly scary because I never had a stable life growing up. Things were always in flux, from what state I lived in to what school I went to, every few years it was time for a huge change. But things are different now and I prefer consistency, I try to live a structured life. Even if the only reason I do is to keep things simple because I feel like I’m constantly rushing around trying to get stuff done for my degree.

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A leap of faith

Well I did something today that I will not be able to undo. Since I have a policy of honesty with this blog, I will admit that I’m scared. I don’t like taking risks, but I didn’t have a choice so now I’m going through the grieving process wondering if I’ve made the right call and how quickly I will end up regretting it. I had a choice, I made a choice, and now we wait. It’s a leap of faith, one I’m not sure I am ready to take.

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The R21 Result

Well I’ve been meaning to write this for a bit now, but the R21 I helped write back at the beginning of the year was not funded. It was a longshot and my Co-PI who helped write and submit the proposal was not surprised as to the result. Worse, it was not discussed. Since I’ve spent the past year learning the hard way how grant writing works, I figure today I can pass on that knowledge and we can who knows, maybe it will help others who are grant writing.

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Countdown to the grant submission

We’re just days away from the deadline for the grant I’m writing. We’ve got an awesome team of people that have agreed to be a part of this project and the funding will go towards the big idea I had several years back (what I’m calling my “super secret technique”) so I’m excited! My main-PI thinks the proposal has a good chance of being funded and I trust his judgement since he’s been doing this for a long time. So today I figure I can brag about the team and what will happen in the next few days.

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An unfortunate typoo

Yes, the title was on purpose. No, I’m not thrilled at the moment. Sometimes you just need things to go smoothly, but life has other plans and yesterday I hit one hell of a stumbling block. The good news is I’ve caught it, but the bad news is there is now about 104833423x more work for me to do to fix the issue. No matter how careful you are, something is always going to get missed, yesterday was just a reminder that you can miss things even when you’re paying close attention. I may go as far as to say, especially when you’re paying close attention.

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Why is it always a rush?

Well my latest grant is due at the end of the week, so I am now just a few short days away from the deadline and rushing to meet it. There has been plenty of time between when the proposal for funding went out and now, so why does it always feel like things are last minute? It probably has to do with the iterative approach to writing and the edits that go on forever. Since I need a break from scientific writing I figure now would be a good time to talk about the process and why a far off deadline is never enough.

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The other funding options

I think I would describe my life as controlled chaos. It’s a delicate balancing act of stuff I need to do, mental health, physical health, and just my horrible luck in general. For the past few years my level of panic has been steadily increasing as the end of my funding was getting closer and closer. Try as I might, I have had no luck getting further funding for my PhD and in less than four weeks that dreaded deadline will be here. Which for those who are not students, means I will not be getting paid, my school will not be paid for, and the house of cards I’ve built will come crashing down around me. But there’s still some hope…

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Yet another grant…

The search for funding continues! We’re less than a week away before I need to submit my latest attempt at securing funding for my PhD to the end of my degree. Right now we’re running out of time and in just a few weeks I could be without pay, without tuition reimbursement, and basically on the verge of being homeless again… my how the tides turn. Not to fear though, I’m not doing this alone and I have options. Today we’re going to talk about the grant I’m writing, why it won’t help my current situation, and why I’m still going to do it.

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The final day of summer internship

Today marks the last day of the summer internship for our early career undergrad researchers. On paper, it’s been a long, sometimes bumpy road that wasn’t always the easiest thing to work through. In reality, it was all too short and it feels like we just got to know our interns and now it’s time to say goodbye. Through the experience I’ve got to watch the intern I was mentoring grow as a person, and grow more confident in herself. It’s been a privilege that I got to be a part of this.

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A small celebration

Salted caramel apple empanadas covered in cinnamon and brown sugar, the result of my labor of love (and frustration)

It’s my Co-PI’s birthday and to celebrate I’ve been busy. The rest of the lab took care of getting a cake and hanging the decorations. Since I split my time between two labs at the moment, I wasn’t around to help and I felt slightly guilty about it. I like my Co-PI and even though he’s (probably) leaving soon I at least wanted to do something nice for him. So in spite of all the work I had to do I got to baking.

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A surprising request

Basically the same face I made when he asked…

Well yesterday was unexpected. I got a phone call from someone I wasn’t expecting to ever hear from again. My former classmate who I wrote the journal paper we just finished reviewing and resubmitting. It was unexpected because after we submitted it the first time he sort of dropped off from contact (despite the back and fourths with the other people on the paper). He was asking for a reference for a research position and I said I would do it, but I was a little surprised given our history.

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So you want to email a PI

It’s that time of the year again, people are gearing up to apply for graduate school and with it a flurry of things to get done. Graduate school isn’t for everyone, but if you’re planning on making the jump, now is the time to lock in the schools you want to attend. More important than the school is the lab you want to work, you have looked into the labs at your dream school… right? Finding a good PI (primary investigator or the boss of the lab) is, in my opinion, even more important than getting into that dream school of yours. So buckle up and we’re going to talk about how we find the perfect lab.

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The end of summer internship

Well today wasn’t the official day, but we had our first presentations for the summer internship program. Friday will be the last day for the interns and we will bid them farewell and good luck with whatever they do in life. The presentations today were meant to be fun and just a way to celebrate everything the interns learned while they were with us. We got to see work done in all the labs and the experiences were varied, so that made for an interesting time. Basically summer is near the end and it’s a little hard to process to be honest.

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The hunt for knowledge

Sometimes science is like digital archeology. Thanks to the internet I have the sum of our collective knowledge at the tips of my fingers. I just need to ask the right question and I can find the answer. Unfortunately, the right question isn’t always the question you come up with. The right question may not be worded the exact way you think it should. The right question may not even be the right question at all, it’s just the first in a long list of questions you need to work through. In a digital world, we’re still stuck looking for ways to get the answers to questions the system may not understand. I’m on a hunt and so far I’ve been fairly lucky.

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Juggling papers

It finally happened, it’s the big deadline, or at least most of the stuff I have due is due pretty much right now. I’ve been working on three different papers, and now I have a fourth added to the mix that I sort of forgot about until my Co-PI asked me to review the work we did in that paper, so yeah a lot going on at the moment and it’s all basically writing. So of course I’m working hard on writing… this. The truth is I need a break so I figure blogging would be a good distraction while still feeling like I’ve accomplished something. It beats doom scrolling twitter until the entire day has passed me by.

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The complexity of biology

Why couldn’t things be simple? Maybe you would take a measurement and have the correct value every time. Or you would perform an experiment and get the same result no matter what. The human body is an amazing feat of engineering by evolution. It’s layer upon layer of stuff that all work together to do the thing that needs to happen. The fact that it works at all is amazing, it’s like throwing a bunch of computers into a room, shaking it, and out comes a fully working robot that’s more advanced than anything you’ve seen.

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The big presentation

It has been a day friends. Yesterday I got an email from my main-PI asking me about a funding proposal I’ve been working on and when I responded I asked if we were having our lab meeting this week since the last two have been cancelled. He said yes and he mentioned that today would be the day I presented the work I’ve been doing with my project. Thankfully I was ready for it, but it was pretty stressful and there are some changes that need to be made. Overall the lab seemed pretty impressed by the presentation and the work I’ve been doing.

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Programming overreach

This is what happens when I try to get fancy with the work I’m doing. I end up attempting to do things that aren’t done easily or if they are done easily, I figure out the hardest way possible for me to get them done. A week or so ago (here) I was excited because I came up with a super cool way to do something and I thought that the hardest part was behind me. Oh how wrong I was… but I’m close to figuring this out, I just need to do a lot of work to dig out of this hole I threw myself into. This is why you should never do anything fancy!

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A five dimensional pain

This is what it’s like working in higher dimensions. Oh is it moving? It shouldn’t be, this is a still image. Welcome to the mountain of madness!

We’re back and this time working in five dimensions! But wait, we’re not done, we’re going higher and I’m not thrilled about this at all. Working in higher dimensions is a pain especially when we’re stuck in a three dimensional world. So what am I doing in a five dimensional space? Well besides pulling my hair out, I’ve been trying to do some not so basic math to find some significance, in life, but mostly in my data.

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Sometimes the progress is slow

Today has been incredibly busy, but incredibly frustrating. So far next to nothing has been accomplished towards the work I have to do, but I did help a few people out and we discovered some interesting issues with some software the lab uses. Okay not issues exactly, it just doesn’t work the way we thought it did. In any case, there has been a lot of running around and doing things, just nothing productive for myself. Some days are like that though, hopefully I will have better luck tomorrow or maybe even later tonight.

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More competing projects

Were does the time go?! I have no time left to get my projects done and yet there’s still a lot that needs to happen. Today is one of my semi-famous lists of stuff I need to get done in an outrageously short amount of time. Didn’t we just do this a month or so ago? I think so, but here we are counting down yet again to the newest set of deadlines and as with all my deadlines they clumped together and fall at what amounts to the same time. Don’t believe me? Well let’s take a closer look.

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A unique figure design

Over the past few weeks I’ve been hard a work making a new visualization for some of the data I’d recently processed. This again is for the project I won an award for (here), and while I’m not trying to brag, I’m super proud of how it came together. It was the first time I tried to do something like this and not only did my main-PI give me his approval it sounds like a lot of people from the lab were impressed with this as well. Unfortunately, I can’t quite give away what I did or how I did it, but I can share some of this.

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Initial results!

Okay I’m excited! I had a project my Co-PI offered me for the summer that I really, REALLY wanted to do (this one). We’ve been slowly collecting data and haven’t had a chance to do a detailed analysis of the result yet. It looked like we had something cool, but we weren’t sure what it was. Our data had a lot of noise in it (which is a given when working with EEG) and we needed to clean it to give us a better “view” of what was going on, so yesterday I sat down to do just that…

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Finishing a project… maybe

Today is the day! Well, maybe today is the day, I’m hopeful though so let’s go with that. Today is the day I finish the analysis of the data I collected a while back for the experiment I wasn’t super thrilled about doing. The one I got an award for doing, funny enough (more). This project was a huge headache from the start, but I’m finally about to do the last bit of the work on the analysis and then all I have to do is write the paper. So let’s talk about what’s going on.

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Experimental limits

Well this is turning into a drama, but we keep having issues with the experiment. There are once again changes that need to be made, we’re four out of ten planned experiments into the project and while we’ve done the first four the same way, we keep trying to adjust our testing to a slightly different version of the protocol and it’s running into… issues to say the least. There are some things we just can’t accomplish using our testing paradigm and we have to accept that, but we still try to push those limits, even if it hurts.

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Changing the experiment

For the past few days I’ve talked about the importance of experimental design. Well sometimes midway through you realize a better way to do things. That was yesterday when I realized the thing we were looking for in our experiment could be found a better way. I’m not thrilled about this, but sometimes it needs to happen and I think we will have a better chance of finding what we’re after if we do it this way.

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We meet again, figure 1

If you’re new around here, I’m working on a handful of papers all at the same time. Five in total, all first author journal papers. For those not in academia, that’s a lot. I don’t know how this happened or why it happened, but here we are. Two of them are basically finished, two are just starting, and one will (hopefully) be started soon. Which brings me to the topic of the day, figure 1. Figure 1 is arguably one of the most important figures in the type of work I do, so let’s dive into why and what I’m trying to accomplish.

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Sometimes you’re too close to the problem

I’ve had a breakthrough! I’ve been working for months on a problem and I probably could’ve come up with the solution sooner if I hadn’t been trying to force it. Maybe I’m weird, but I find the easiest way to come up with a solution to a problem is to just walk away from it. I don’t always do it, but I always end up regretting that I didn’t just step away from the thing long enough to get the full picture.

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On the research I do

My 3D printed spine (as in my own spine made from my CT scans, make your own body part here!).

“They are changing the world and I want to help,” one of our regular volunteers told the guy who runs the hospital department. It was a glowing review from someone who had spent the better part of the last decade paralyzed after a high level (cervical) spinal cord injury. We’ve seen him regularly for the better part of a year now and you would’ve thought we coached him if you could hear the review he gave the man who came to see our little lab. I feel stuck a lot, but yesterday I was reminded of why I do what I do.

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The connections we make

Networking. It’s all we ever hear about. It’s not what you know, it’s who you know. Maybe it’s not even so much about who you know, but how you approach people. I know if it were not for the people I’ve reached out to, I would not be where I am today. In fact, I can think of at least a handful of people whom I’ve reached out to only to have them change the course of my life for the better. Yesterday I got the chance to do the same for someone else.

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Two wild days!

If you’re reading this then it’s too late for me. Or rather it’s too early for me since I need to be up super early tomorrow, which is today (when you are reading this). Confused? Well it’s supposed to be a daily blog of my progress, but I’m cheating and writing today’s post last night. That’s because really, if you’re reading this I’m in an experiment. No, it doesn’t matter when you read this as long as it’s the day I posted because I’m definitely in an experiment. Don’t worry, I’ll explain.

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When you need to say no

Awhile back I wrote a post called “When you don’t want to say no” about some cool experiments that I was going to do and how the heck could I say no to cool experiments?! Well today is the other side of the coin. Sometimes you need to say no. You may not want to say no. You may not feel comfortable saying no. Nevertheless, you need to say no. Today is that story, the story of how I said no.

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Experiment result preview

This summer I am performing an experiment that could change our understanding of what a certain type of stimulation is doing. It’s all incredibly exciting (as always when I’m in my Co-PI’s lab) and I get to be the first author on the result. If we can show that this thing we are looking for is true then it will be a big shift in our understanding, but more importantly it will open the door to new types of non-invasive treatments. While I cannot talk about the details (as always) I can share that I’m excited about what may be coming.

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The week ahead

For a few weeks I was trying something new and doing a “week in review” well this week is exciting for a lot of reasons so I wanted to look at the week ahead! As usual I cannot give details about what is going to happen or why, but at least I can share my excitement and maybe one day soon I’ll be able to share what we did and point back to this post. So instead of looking back, today we’re looking forward. It’s going to be busy, but hey what else is new?

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Intro to MATLAB – Part 4

computer programming
computer programming
As a reminder, always have your coding cactus nearby in case you need some motivation (slap to activate super motivation powers).

We made it! This is the last post (for now anyway) in my four part Intro to MATLAB series. I reserve the right to go back and write more on the topic, but at the moment this is the end. If you’re just finding this and want to read the other posts in the series, I’ve made a super helpful Intro to MATLAB category where they are listed. Today we’re going to take a dive into editing code, finding ways to make your life easier, and just some bits of magic I’ve learned over the years that makes my life so much easier now. Let’s goooooo!

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