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.(more…)
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.(more…)
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.(more…)
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.(more…)
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.(more…)
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?(more…)
Well today is the day! I’m just hours away from collecting my first dataset for my summer project. I’m excited, it’s a cool project and I get to be first author on the paper. The topic is impressive to me so I think it will be a good way to get my name out there in the field since this will be my first paper in my Co-PI’s lab (well first, first author paper). It’s a lot of responsibility and of course I don’t have any time to prep. The first experiment is always the hardest…(more…)
After meeting with my Co-PI and discussing the super cool experiment he wants me to do (here) it sounds like I’m in control here. Scary thought, right? This is that whole working WITH my Co-PI and not FOR my Co-PI, he trusts me to make good choices. I mean either way he’s going to need to sign off on it when I finish the design, but it’s kind of interesting to be the one who gets the say in how we do this.(more…)
*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*(more…)
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.(more…)
Every sunday without fail I make my list of tasks for the week ahead. Some of them are automated and repeat as needed, but most are specific to that week so I need to go in manually and add them. It’s nice to have everything written down in one place, in order, with times and reminders. I don’t have to stress out about remembering everything when I have a nice app on my phone that keeps me informed. Unfortunately there is a downside…(more…)
Another long day for me. Back to back experiments (with a short break in between thankfully). It’s a lot, but I’m hopeful that after it’s all done things will slow down at least for a moment, hint they won’t. In any case, I just need to make it to tomorrow then I get a break for a few days.(more…)
Well today my midday experiment was cancelled so now I have some time to relax. Just kidding, now I have time to work on the million other things I need to get done this week! That’s the problem with writing daily, a lot of it is the same stuff, but there are some minor differences with today’s list of things to do.(more…)
Most times work can be a trickle, we get one or two subjects a week and that’s all. 6-8 hours in the entire week dedicated to collecting data and the rest of the time I’m free to process data, work on other things I need to do, basically live day to day like I didn’t live in a lab. Most of the time. Sometimes it’s a flood, like this week and next, then I’m reminded that I definitely need to work.(more…)
Sunday means getting ready for the rest of the week and what a week it will be. In my Co-PI’s lab we typically have a steady stream of people coming and going for experiments, this week (and probably next) it will be a flood. We’re trying to make my main-PI happy.(more…)
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.(more…)
Well that was a …flop. Today I had an experiment, had. There are a lot of moving parts when it comes to an experiment, especially in my line of research. Technology, can’t live with it, can’t live without it. Still, somedays I wish I was living in the future, one where I didn’t need to reset my router randomly. Then I would know for sure the singularity was close.(more…)
Everyone go back to what you were doing, nothing to see here! Yesterday I had an existential crisis, one that could’ve derailed my technique and any hopes I had at introducing something new into the world. With it, my PhD dissertation topic, meaning I would be over two years in and I would need to reevaluate my goals. Let’s talk about what happened!(more…)
You know… that’s how it goes sometimes. You’re cruising along and everything looks great then, BAM! Totally derailed. What happened? Turns out I have a problem with my data. Not a problem persay, more like an anomaly, one that throws a rather large wrench into what WAS a perfectly running operation. Things were looking good, but now… I have a doubt.(more…)
Well I’ve processed (poorly) about half of my data. Now, when I say poorly I just mean the visuals for it are garbage and I need to tweek the sizes and things to make it look nicer, but the idea is that I’m more interested in finding something than I am in making it look pretty. I’ve processed two of four of my subjects and well I’m excited!(more…)
I’m trying to remain calm. I am an objective observer in the world of science and whatever the result, I will NOT let it cloud my emotions. I am neutral and I will remain that way… oh who am I kidding, I DID IT! Two years of planning and convincing people this would work. Then last night I had my first result, and it was a relief. It was a small step, but one I was afraid the data wouldn’t let me make.(more…)
Well I didn’t plan for it, but today is a busy day! I’ve got a lot going on at the moment so not a lot of time to write. Let’s just talk about what I’ve done and have left to do so I can get back to it.(more…)
It’s a process… that’s for sure. So you’re a scientist and you collect a ton of data, well now what? We’re talking about me of course. I did it, I collected a ton of data and now I need to do something useful with it. This is the part I wish I could skip over and get to the part where I get all the cool results, but I guess we’ve all got to start somewhere.(more…)
Well today is going to be a quick recap of my experiment yesterday. This will be just as much for me as it is for all of you. While I can’t go into the experiment details (since I’m working to publish this) I can give a pretty good overview like I did the last time around.(more…)
Yesterday I told the story of how we got to this point, a long two year journey and next week I finally get to take the next step. It’s exciting, but it also means because of my flare-up, I’m behind on what I need to do to be ready. Not to worry though, I’m taking it slow so I don’t make whatever I have worse. What goes into an experiment like this? I’m glad you asked!
Okay I’ve got an experiment update today and I’m really excited to share because it feels real finally. I know I already wrote about some of this, but when I reread my previous post, it felt disjointed so let’s go over how we got here and what’s coming. I’m excited, are you excited? I’m excited!
Well today despite feeling like refried dog poop I have to go do experiments. It’s part of the job and to be honest I want to do it even though I feel like dried monkey vomit. I could go on, but you get the picture. I do have some more good news not related to yesterday’s news. So that is the conversation for the day.
It was bound to happen eventually. We all knew it would, but we didn’t expect it to fail in such a spectacular manner. That is to say, all at once. One of the people I’m mentoring checked out some lab equipment since we had come up with a way to do experiments from the comfort (see: safety) of her home. That was the plan anyway…
Well it finally happened. We’re doing experiments again. It’s kind of scary to be honest to be working in a hospital again when the pandemic is going on and we have protests still happening. While I could do without the pandemic, I hope with all my heart that the protests don’t end until the corrupt system that caused them ends first.
Well I’m alive, despite the VA’s best efforts. I’m struggling with some serious nausea to the point of vomiting, which has never happened to me before. I’m also in a lot of pain, but that was expected. In any case, start to finish (start as in the operating room and finish as in getting home so +30 minutes or so to the actual finish time) it took ~9 hours total good times for everyone. Anywho, I feel like death so I’ll write more later.
Well we did an experiment. I wish I could talk more about what we did, how we did, and why we did. Alas, I cannot. So instead, let’s talk about the vague how it went metric as in, maybe we found something maybe we didn’t, also this experiment highlights several quarks between the my school lab and the clinical lab.
Today is day one of ten for the time that I have to do some experiments. It’s an awkward time for sure, I mean surgery, school, etc. However, that’s just the way things work in academia, I actually had a break, so I’m ready to go to be honest. Which really means this isn’t horrible timing. I’ve already discussed the million things going on these weeks, but let’s talk about what goes into experiments, really.
Today was an interesting set of events. I had my meeting with my two PI’s (which I still think would make a hilarious television show). The meeting went well, I’m very excited, but I’m also getting ready to be very, VERY busy. Let’s breakdown how it went shall we?
Today’s post was inspired by a conversation I was having yesterday in the comment section (you know who you are and thank you for the questions). I thought I would elaborate on how we record from the brain and why. There are a lot of different ways we can do this, some of them are super invasive and others are non-invasive. In the lab I work in now, we do things non-invasively there are good things about this and bad things about this, so let’s get into it!
Yesterday I mentioned that I had some rat data to go through. It was an old(er) dataset, about five years-old to be exact, but it was one that was going to help me validate some of my findings. Unfortunately there existed no invasive human datasets to compare my human data to, so I needed to find an animal model, in this case a rat model. Let’s discuss the importance.
A few days ago I mentioned I did a thing, well an experimental thing really. It was… fun? It was definitely something. Overall it went well, but I said I would give everyone an update and I try to be a man of my word, so let’s do this.
Today I had my experiment (yay), so now I need to process the data. I also sat in another PhD defense for one of our lab members, so now that I have a free second I wanted to give an update. Expect a longer post tomorrow, but for today, I have sooooo much work to do!
Until next time, don’t stop learning!
Here we are another day another post. Today I will be spending the bulk of my time studying and getting my slides ready for the confrence I’ll be attending next week. That will be … fun? However today is also an important day for one of my fellow students, he’s defending his PhD.
It looks like things are moving a little quicker than I thought for me. As you may or may not know, I’m getting ready to do an experiment. Well, we finally (finally!) finalized the protocol and just in time too. While I won’t make the deadline for my project update, I will have some data to show when we get to the conference, which is a good consolation prize.
I’ve talked about my impending deadlines a lot lately. I also mentioned that I had an experiment that I needed to do to meet a deadline, well it looks like we may or may not meet this goal. Let’s talk about the latest headaches.
Because we introduced the central limit theorem last post, it’s time to introduce another important concept. The idea of independent events, while this may seem intuitive, it is one of the assumptions we make in parametric statistics, another concept we will define, but for now let’s jump into independence.*
Well here we are again, if you recall from our last post, we talked Bonferroni Correction. You may also recall that when the post concluded, there was no real topic for today. Well after some ruminating, before we jump into more statistics, we should talk about the central limit theorem. So let’s do a quick dive into what that is and why you should know it!*
By now we are masters of statistics… right? Okay, not really, but we are getting there. So far we’ve covered two types of errors, type 1 which you can read about here, and type 2 which you can read about here. Armed with this new knowledge we can break into a way to correct for type 1 errors that come about from multiple comparisons. Sound confusing? Well, not for long, let’s break it down and talk Bonferroni.*
Last post we did a quick bit on type 1 errors. As with anything, there is more than one way to make an error. Today we are talking type 2 errors! They are related in the sense and we’ll go over what that means and compare the two right… now!*
We did it, we cracked the coin conundrum! We managed the money mystery! We checked the change charade! We … well you get the idea. Last post we (finally) determined if our coin was bias or not. Don’t worry, I won’t spoil it for you if you haven’t read it yet. I actually enjoyed working through a completely made up problem, so if you haven’t read it, you really should. Today we’re going to talk dogs, you’ll see what I mean, so let’s dive in.*
It looks like we’ve arrived at part 3 of what is now officially a trilogy of posts on statistical significance. There is so much more to say I don’t want to quite call this the conclusion. Instead, let’s give a quick review of where we left off and we can get back to determining if an observed value is significant.*
Well here we are two weeks into 365DoA, I was excited until I realized that puts us at 3.8356% of the way done. So if you remember from last post we’ve started our significance talk, as in what does it mean to have a value that is significant, what does that mean exactly, and how to do we find out? Today is the day I finally break, we’re going to have to do some math. Despite my best efforts I don’t think we can finish the significance discussion without it and still manage to make sense. With that, let’s just dive in.*
If you’ve read my last post I hinted that today we would discuss filtering. Instead I think I want to take this a different direction. That isn’t to say we won’t go over filtering, we most definitely will. Today I want to cover something else though, significance. So you’ve recorded your signal, took an ensemble average, and now how do we tell if it actually means something, or if you are looking at an artificial or arbitrary separation in your data (IE two separate conditions lead to no difference in your data). Let’s look at significance.*
Noise, it can be troublesome. Whether you are studying and someone is being loud or you are trying to record something, noise is everywhere <stern look at people who talk during movies>. Interestingly enough the concept of noise in a signal recording sense isn’t all too different from dealing with talkative movie goers, so let’s talk noise!*