Experimental prep: part 1

Okay there’s a few days between now and the incredibly complex and labor intensive experiments we have coming up on Friday, so there’s a high chance that this will be a multi-part discussion, hence the title of the post for the day. We’re rapidly approaching the big day and there’s so much work that needs to happen I’m starting to get a little nervous that I have enough time to do it all. To add to the chaos, there are other experiments happening, that require equipment that we’ll be using for Friday, so there’s no way to setup early.

A lot has been happening. Mostly we’ve been trying to hammer out the protocol for the next experiments. There are two so far and probably a few more in the works, but really right now I’m mostly worried about the one we’re doing in the next few days because I really don’t want to think that far ahead right now. Currently I’m juggling several experiments on the hospital side. That’s not an uncommon occurrence, it would be more odd if I were only focusing on one frankly. So I need to find time in between all my other duties to make some new equipment, write some new code, and arrange the equipment in ways that make sense for the experiment. Because above all, time is a factor.

So where to start with the discussion… let’s talk about the protocol prep.

Every experiment you do has a protocol. No matter what type of experiment, there are certain steps that need to be carried out. Ideally your protocol will help you answer certain questions (or on occasion just a single question). The trick is to account for everything else, or as much as you can anyway, so you do the thing you need to do to get the answer to the question you have. This is easier said than done, there are a lot of factors to take into consideration and sometimes the experiment you do doesn’t actually answer the question you have. It’s a common occurrence, believe it or not! So the first thing we did was to hammer out the details of the protocol we wanted to use. This was done using the experience we got from our first two experiments, which were serious experiments, but also sort of a trial for us.

Even though we’ve worked out the details of the experiment, we still need to make sure those things we want to do are organized in a way that makes sense. We’re on a serious time crunch to get everything done we want in the time we have allotted to us. In order to maximize our chances of success, part of my job is to organize each of the experiments we’re doing in a way that minimizes the time between each experiment. This too is easier said than done (a theme for sure). Mostly it involves thinking about how we can reuse the setup for multiple experiments or how to minimize the differences in setup between experiments. I’m still trying to work out the details, but I’m hoping to have that figured out by tomorrow.

Of course, what good is an experiment without the proper equipment? Now technically speaking I have all the equipment we need to pull of the experiment built and tested from the previous uses. However, I’m not content with just doing it with the equipment we have because I want to do better. To do that I’m fabricating a whole new set of equipment for the experiment. To be fair, some of it won’t be used this time around (or for any of these experiments it sounds like), because we need some other equipment we don’t have to use the stuff I’m making, but it will be there for when we do get the equipment (optimistically by the end of the year). This new equipment I’m building should be much improved over the last version and I’m excited with how it’s taking shape. I’ve already figured out ways to improve it for the next set of modifications, because we can always do better, so I’m going to keep trying to make equipment that will let us get better data.

Then there’s automating everything. The less you have to think and/or do the less chance you have of making a mistake. So a lot of the stuff we test I try to automate. This is a semi-new thing for our lab, but I’ve been slowly trying to automate basically everything we do and hospital-PI has been very grateful for the changes I’ve made already. They’ve helped speed experiments up and reduced our chances of making mistakes. For this experiment I’m still writing the code we need to run the experiments. I’m hoping to have the last of it written out tomorrow.

Tomorrow there will be a meeting with the entire crew helping us do this experiment, there’s a lot of moving parts and it’s an incredibly ambitious experiment, so we need to have the entire team (literally like a dozen people or so) meeting to discuss their roles in the experiment and make sure we’re all on the same page. Once we have everyone on the same page, we need to get our small group together and test out the equipment.

That will happen the day before the big event. We’ll have the entire equipment wired up and ready to go. We are collecting so much data that we’re using three different systems from two different labs. It’s a lot of equipment, a lot of data, and so, so many wires. A ton of wires, like hundreds and each of those wires will need to find the correct home. Some of them won’t get plugged in until the experiment itself is underway, but most of it can be setup in advance and checked to make sure it’s connected correctly. It’s probably the most stressful part of the entire thing and it will be the difference between getting the data we want and getting absolutely nothing. Or worse, getting something, but it not being useful. The very worst case is that we get something, we think it’s something amazing, only to find out that the equipment wasn’t connected correctly.

Yeah, no pressure or anything, we only have a few days to hammer all the details out and I still have some equipment I need to make before we can, you know, plug it all in. But hey, that’s the job I signed up for. I’m really looking forward to doing the experiment, don’t get me wrong this is all very, VERY, exciting and I wouldn’t want to be anywhere else. We’re doing some very cool stuff that I’m excited to get to be a part of the project. It’s made a lot more work for me, but it’s going to be so worth it.

So this is the big countdown to the first official experiment using the “big idea” equipment. Not exactly for the use I intended, but it’s a funded project, it’s going to help the project I’ve designed, and it’s one step closer to the big nature paper that I really want.