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Author Archive

Everything went better than expected!

So yesterday I had my hands full with a bunch of work to do, no motivation what so ever to do it, and a deadline that was today. I didn’t want to burn myself out, especially since I still have a homework assignment due this weekend and yet another round of tasks set out before me, this time before the next week so that’s… umm terrifying. Let’s just dive into what happened today during my meeting.

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When the exhaustion hits

Woke up this morning feeling less than stellar. This happens pretty regularly when I push myself for long periods of time. It’s not ideal, since I still have a bunch of stuff to do, but thankfully after living with my limits for so long I have a few back up strategies to help me get through it all. Ideally the school would offer accommodations to people like me, but to get them there is a lot of hoop jumping, enough that it doesn’t make it worth the effort. I suspect that’s the point.

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New computer issues…

I took this photo right when I got the new laptop.

Well if I’m not a magnet for computer issues I don’t know who is. If it’s not one computer it’s the other. In this case, I had problems a while back with my desktop (here) where the watercooler went bad and my CPU decided it wanted to scream at me anytime I ran the computer, like just turned it on, not doing anything with it. This time it’s my laptop that I’m having trouble with and unlike my desktop, the laptop is my daily use computer so I’m not too happy.

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Mental health in academia

Five years, that’s the average time it takes to finish your PhD. Depending on who you are and how you think, that may be a blink of an eye or forever. I signed away four years of my life early on so five years and frankly the commitments leading up to it didn’t feel like that long at all. In a lot of ways getting a PhD is a lifetime of work and not long at all. I’ve hit the half way point roughly and I can see why so many people drop out of the program. It’s a lot.

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A week in review

I figure it’s a good time for the recap of the week. I mean there was a lot going on and while I want to spend some more time on my “in statistics” series, I also really need a break. So instead of spending a lot of time making sure the information I’m presenting is accurate, concise(ish), and (with luck) well thought out, I figure it would be easier to talk about the things I’ve had to do this week and the things I get to look forward to! Joy, welcome to life as a PhD candidate.

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Defining parametric tests in statistics

We’ve been throwing around the term a lot in this series. I’ve been saying in parametric statistics this, in parametric statistics that, but I kept putting off giving a definition. It’s not because it’s hard to understand, it’s just that typically when you’re doing statistics you already know if you’re using a parametric test, but because we try to make no assumptions in this series, we’re going to put this to bed once and for all. Today we’re talking about parametric statistics!

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Independence in statistics

A while back we introduced the central limit theorem, it was a way to take data and make it normal (gaussian) as if by magic, which is one of the assumptions needed for parametric statistics (the most commonly used kind). Today we’re introducing another assumption, that the data are independent. The idea of independent events is probably straightforward, but it’s yet another bedrock of statistics that we should talk about in depth to help us understand why things are the way they are.

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Variance in statistics

Sometimes you just want to kick a distribution right in the mean.

Variance, it’s one of those concepts that get’s explained briefly then you find yourself using it over and over. Now that I have a free moment, I figure it’s about time to revisit the “simple” concept and just take a minute to apricate why we have to deal with variance so often and why we try so hard to minimize it when we’re doing experiments. Just like the discussion about the mean, there’s some subtilty that goes into the idea of variance and it’s square root cousin standard deviation and we skip over it in favor of getting into more complex topics.

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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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Clinical research in a pandemic

Male and female characters scientists or lab attendants working in science laboratory using microscope, lab glassware, vector flat illustration. Scientific research, experiment, science and education.

One of the more interesting things about the pandemic is that everything at the university level shut down. They still send out emails suggesting that everyone wants to go back to in person classes, but they haven’t followed through with that threat. Human participant research has been halted and even though we’re probably going back to “normal” in the fall, right now nothing is happening. That’s at the university level though, clinical research is a different story.

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Another approaching deadline!

Well it’s going to be down to the wire this week. It’s good to know we’re keeping the theme, if you’ve been following along for awhile you already know it’s always down to the wire. This week is particularly challenging because I have competing interests for the time I have. There’s only 24 hours in a day, so there’s only so much work that can get done. I would prefer to not do it at the last minute, but here we are… again.

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Fun with Rstudio

Okay, not really. Having to use R is a pain. I’m not a fan and the structure they use is very confusing to me as someone who uses MATLAB on a regular basis. I understand matrices, I regularly make and successfully work with higher dimensional matrices ( > 3, which hurts your brain to think about a 20+ dimensional matrix, but hey whatever gets the job done). R on the other hand feels foreign and the commands feel clunky.

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The lonely cultist

Listen closely as I am going to divulge a secret from the universe. It will be so earth shattering that you will forever remember this movement. There will be an irrevocable before and after. It has taken me decades to uncover this secret and as the sole owner and guardian of it, I am trusting part of it to you. You can be a part of something larger than yourself, find secret truths, and if you are ready to receive them, find your own. There are secrets in this life hidden just beyond human sight and they are waiting for you to find them. They are calling out to you in the wind. Do you hear them? Are you ready?

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Cracks in the support system

Family, friends, relationships, these are just a few things that provide people with a safety net. How many people, if they lost their job, would be able to rely on family for support? Surely not everyone, but a good portion of people have others to help them if they were in need. Hell, here in the US we’ve made it almost necessary to rely on the kindness of others to crowd fund for healthcare needs. Like it or not, people need people, well most do anyway…

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Caution: under pressure

For a third week in a row I’ve been instructed by my main-PI to give our lab virtual presentations on the work I’ve been doing. It’s been a point of stress now for almost a full month and doesn’t seem to be letting up any time soon. After every meeting I get a list of things I need to do before the following meeting and this time was no different, so today I guess we’re going to take a look at what exactly is next on my to-do list.

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On failure

Maybe it’s the hangover from yesterday’s news about my fellowship, but I feel like I got backed over repeatedly by a truck. Maybe it’s the uncertainty of the future, or all the work I still need to get done for tomorrow, maybe it’s a lot of things. Somedays I wish I could just pause, but I don’t think I’ve ever been able to stop and don’t really know what I would do with myself if I did. Actually I do know, since I can recall at least one time in my life where I hit the pause button and it didn’t end well.

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NDSEG fellowship result

Applying for a fellowship is sort of like creating a time capsule. The lag between when you submit it and when you hear anything back can be 6 or more months, long enough that you’ve completely forgotten that you applied. Or at the very least it isn’t at the forefront of your brain anymore. I’ve kept an eye on my application sporadically, I know people who check weekly and I’m sure there are plenty who don’t check at all until the results are sent out. It’s a slow motion car crash, you hope for the best, but it’s no longer in your control.

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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 Bonferroni correction in statistics

Well we’re doing it, today we’re talking about the Bonferroni correction, which is just one of many different ways to correct your analysis when you’re doing multiple comparisons. There are a lot of reasons you may want to do multiple comparisons and your privacy is our main concern so we won’t ask why. Instead we’re going to talk about how to adjust your alpha (chances of making a type 1 error) so you don’t end up making a mistake.

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One-tailed vs. two-tailed tests in statistics

Sit right back because we’re telling a troubling tale of tails full of trials, twists, and turns. The real question is, will we run out of words that start with t during this post? It will be tricky, but only time will tell. When do we use a two-tailed test vs. a one-tailed test and what do tails have to do with tests anyway? With a little thought, I think we can tackle the thorny topic. In short, let’s talk tails!

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The p-value in statistics

We’ve been dancing around the p-value for some time and gave it a good definition early on. The p-value is simply the probability that you’ve made a type one error, the lower the p-value the less chance you have of making a type one error, but you increase your probability that you’ll make a type two error (errors in statistics for more). However, just like with the mean, there’s more than meets the eye when it comes to the p-value so let’s go!

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The z-score in statistics

Okay, time to get back to statistics, if only for today! P-value, z-score, f-statistic, there are a lot of ways to get information about the sample of data you have. Of course, they all tell you something slightly different about the data and that information is useful when you know what the heck it is even trying to tell you. For that reason we’re diving into the z-score, it’s actually one of the more intuitive (to me anyway) measurements so let’s talk about it!

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Freedom of speech

I didn’t expect to have to talk this out, but here we are. Freedom of speech applies to the government, not private entities such as (but not limited to) twitter, facebook, schools, work, and basically any private place you congregate. Freedom of speech also does not mean freedom from consequences of that speech, you can’t talk about blowing up a school for example without consequences, even if it was a “joke.” More importantly, the government already ruled that certain hate speech isn’t protected. Why is this important? Well it’s a good reminder for the internet in general, but this time it’s a little closer to home reminder, namely the lab I work in.

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VA healthcare in a pandemic

With the pandemic stretching now over a year, which really feels like twenty, eventually healthcare was going to be an issue for me. I’ve already had to have a surgery during the pandemic, which was nerve wracking not because of the surgery, but because of COVID. Well it’s become a struggle to keep trying to put off getting care when I’m someone who needs pretty regular care. I went from bi-weekly appointments to once every 6 months or more, not ideal.

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EEG cleaning progress

Yesterday’s coding work went better than expected! That may or may not bode will for the rest of the week, but hey at least I’m sort of ahead of schedule. Today I figure we can take a quick look at what I’ve been doing with the data and why. This will be part informative and part me complaining about how everything has to be so damned hard (basically the usual around here). Mostly it will just be some visuals of the things I’ve had to change to get everything looking like my main-PI wants, he’s got a particular style he likes so a lot of large text, bolded labels, etc.

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The juggling act

The middle colorful plot, it’s called a spectrogram and if you notice the colorbar to the right has values ranging up to 25,000, that’s not right…

Blogging and coding and writing, oh my! There’s a lot to get done, seems like a running theme around here doesn’t it? If it were possible to clear some of it off my plate it wouldn’t be so bad, but the sad truth is deadlines seem to like to group together and there are quite a few coming up. Most of them are for my class so I can’t really miss those even if I wanted to. My research deadlines I can’t really miss either, not without some consequences anyway. So we’re back to juggling everything, but as we’ve seen in the past, I’m pretty good at this.

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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 PhD proposal defense

Not mine, at least not yet. A colleague of mine is defending his PhD proposal today and while I was going to wait until I did mine to go over the details about how that works and why we do it, I figured today was as good a time as any to do it. Besides I probably (definitely) repeat myself a lot around here, but that’s the catch with blogging daily. So let’s get into what a proposal defense is and why it’s important, shall we?

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COVID variants and our future

Awhile back I wrote a post on everything you needed to know about the COVID vaccine (here), I talked about the science, my experience with it (as someone who got vaccinated very early on), and more importantly why you should feel safe getting your shots too. Very ominously I mentioned that the target for the vaccine was the spike protein because it would (ideally, but not for sure) be conserved across mutations, well it’s time for an update and the news isn’t great.

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The mean in statistics

Yeah it seems simple, I mean (no pun intended) the mean is just the average! Yet as with so many different things in statistics there’s more to the mean than meets the eye! We’re going to go into why the mean is important, why it’s our best guess, why it may not always be your best option, and why we work so hard to find the mean sometimes! It seems simple, but I promise today we’re answering a lot of the big “why’s” in statistics, so let’s go!

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The Tukey test in statistics

No, not turkey, Tukey, although they are pronounced very similar (depending on who you ask I guess? I’ve seen people pronounce it “two-key”). Any way, today we’re saving our job and the wrath that comes with failure. The mad scientist boss of ours tasked us with testing mind control devices and determining statistically which one (if any) worked. After the last failure, we now had four new devices to test, so we couldn’t use the same method as before. However, an assistant’s work is never done, we didn’t finish the job! That’s what we’re going to do today.

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The ANOVA in statistics

Image from: Listening a great sci-fi movie (in my opinion)

Our mad scientist is back and this time they are not taking any chances! After statistical failure in the last example, they created not just one, but four mind control prototypes! We’ve been tasked with determining if they are working or face certain DOOOOOOOM! Sure, working for a mad scientist can be stressful, but we can do this… right? I’ve been dreading this post and you’ll see why, there’s a lot to cover before we solve the mystery, so let’s dive into it!

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Significance in statistics

That feeling when your p-value is lower than your alpha, aww yeah! But what does it really mean? It’s one thing to say there is significance and on the surface it means the two things are different “enough” to be considered two things, but I think there’s a simpler way to explain it. So today we’re going to talk about what significance actually means in the practical sense. Maybe it’s super obvious, but it never hurts to state it anyway.

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The f-test in statistics

Yep, we’re getting right back into it. I’m still working out things from yesterday, so we can just talk more statistics. This will be an interesting one and hopefully it will be pretty straightforward. The f-test, which in this case is really the f-test to compare two variances. You may have guessed, but the t-test uses the t-distribution (sort of like the normal), well the f-test uses the f-distribution, which is nothing like the normal! Let’s dive in, shall we?

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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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First project deadline!

I didn’t have anything particularly lined up for today to add to the “in statistics” posts I’ve been doing, so today I thought it may be better to outline what I’m doing in the statistics course I’m taking. At the very least it may help me get it done, because as usual around here, the project is due… today. Yep, it’s yet another mad dash to the finish. Will I make it? Will I ever figure out what statistics is? Will I learn to stop asking questions in this format? Find out all this and more!

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Confidence intervals in statistics

Wait… this is the wrong kind of confidence!

Well since our mad scientist from yesterday’s post is on a short break, today we’re going to fill in some of the gaps that post brought into view. First up is the confidence interval. There are some subtle points here, so this should help clarify a few things that may not have been clear yesterday. We’re going to do a somewhat deep dive into what the heck we’re doing when we talk confidence interval and why the standard deviation of our data is important in determining the values.

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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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We interrupt your regularly scheduled programing…

This is not the post you are looking for. Error, please try again. Okay, seriously I need to get some work done today and I don’t have time to solve our mysterious mind control device problem that I posed yesterday, so today I’m going to give some quick thoughts on something totally unrelated because there isn’t time for anything else and while trying to figure out a header for this post (where I was originally going to say hey can’t talk today) I was reminded of max headroom. I genuinely don’t know that I’ve ever said that before, but here we are…

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Two populations in statistics

As a mad scientist, or maybe just a grumpy scientist, you want to test a new mind control technique! To do this you decide that you want to test this works by having people select one of two objects set in front of them. *Insert evil laugh* Using your mind control technique you want your unwitting participants pick the object on the left. You don’t get 100% success, but suspect it’s working, how do we know for sure?

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A fair coin in statistics

It has been a busy day, but the show must go on so to speak and I’m here today to tell you I have a nice shiny new coin for us to flip! The catch you may ask? Well it could be a fair coin or I may have just swapped it out for a coin that was not fair! Our goal is to see if I’m being sneaky and to do that we’re going to need some statistics!

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The central limit theorem in statistics

Today we’re gonna push it to the limit! The central limit theorem that is. It’s a cornerstone in statistics and the short and dry version is that it lets us turn any distribution we have into a normal distribution. If it wasn’t for the central limit theorem statistics would hurt far worse than it does now (speaking as someone taking a stats class now). For the longer version we need to discuss why a normal distribution is needed, why we prefer to work with them!

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Effect size in statistics

Imagine our population data is the red curve and our sample data is the blue and the post will help you make sense of it.

We’ve been talking statistics for the past few days and today we’re talking effect size. The short explanation is effect size is the difference between two conditions! The bigger the effect size, the easier it is to tell the two conditions apart, easy… right? There’s a lot that goes into determining effect size, after all it’s hard to know what your effect size is without having some prior knowledge about what you’re groups look like, so let’s go into some detail.

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Errors in statistics

type 1 erro
type 1 erro

Everyone makes mistakes, that’s okay! In day to day life there are a lot of different ways you and I could make mistakes. In statistics however, there are just two ways for you to make a mistake. That may sound like a good deal, but trust me when I say two ways to make a mistake is two too many. To think, you spent all that time picking the right statistical test, did the experiment, analyzed the data, just to make an error in the end. Don’t worry, it happens to the best of us, but knowing what they are will help you prevent them!

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The hypothesis in statistics

As promised today we’re talking statistics for experiments! It’s more interesting than it sounds… okay it’s exactly as exciting as it sounds. Depending on who you are that’s a lot or not at all. No matter where on the spectrum you fall, knowing how it works is useful. So we’re starting at the beginning and discussing what a hypothesis is and how we test it.

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The last PhD requirement

Real photo of me determining significance between two samples. It’s scarier than it looks.

We’re already at the end of the month, how the hell did that happen? It’s been close to a month and a half since the term started and it feels like it’s flying by. I realized that when I first started this project I covered a lot of the stuff I was learning at the time. In fact one of my previous class notes posts was in my top 10 highest viewed blog posts for 2020. Somewhere along the line I stopped doing that, so today we’re going to talk about what I’m taking this term, why I’m taking it, and why I’ll probably be adding a few step by step instructions for how you can do what I’m learning too in some of my upcoming posts.

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Great expectations

What did you want to be when you grew up? Sometimes the question ends in hilarity, a dinosaur, a unicorn, or maybe some other type of animal. Sometimes it leads to dreams of a sci-fi future, deep space traveller, Mars colonist, maybe a superhero. Whatever the answer is, they all have something in common. No one dreams of being average, but the average exists because so many people fall into it. Most of us have our dreams die as the reality of our existence becomes clear. I say fuck that, dream big until your last breath, why not?

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A look ahead

With the weather trying to kill everyone, the pandemic trying to kill everyone, and just life in general I feel like things are moving…. slooooow. I have a weekly meeting with my main-PI who reminded me that I’m behind and while he agreed it was probably due in part to the pandemic, it’s time to try and catch up. There is a lot going externally and internally, but I’m hoping that by covering a few things here I will have a nice little list I can refer back on and keep me on track. That’s the idea anyway.

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