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Doing All the Things [enzyme assays]

You can probably ascertain, by relative quiet, that I've been busy.

I've been working on some enzyme assays with our Chinese Visiting Scholar, B. Mostly, he's the one who's working on the assay logistics, while I'm the one who knows where the equipment and samples are, and how to work the equipment. This leads to a lot of back-and-forth and a bit of babysitting on my part, but it is important work.

Wednesday morning, he ran some preliminary experiments. At around 3 pm, we needed to make a decision: forge ahead with the actual assay, or wait? For forty logistical reasons, we decided to forge ahead. It took me around an hour to dissect out and prep the tissue samples. Due to some miscommunication, I then wound up having to wait for a very long time before I could set up protein assays, which have to be completed on the same samples as the enzyme assays. If I'd known in advance, I would have brought in dinner. Unfortunately, I get really grumpy when I miss dinner. But it was satisfying to get that batch of work out of the way, and we should be able to make good progress next week.

Meanwhile, I'm working with three different undergrads these days. One is learning the ropes for analyzing cricket activity across the day and night, and on Thursday we finally hit the stage where he commented that things finally feel like real science. Working out that pipeline became something of an ordeal because the open-source software we're using isn't being maintained anymore, so we had to figure out a machine where we could install Ubuntu 12.04. By itself, that wouldn't be a big deal, but there's something weird about the Dell we were trying to work with, where we couldn't simply boot Ubuntu from a flash drive or DVD. Finally, we installed Ubuntu on a separate hard drive and stuck it in the Dell, and it works. So C got to do his first test-tracking on Thursday, which worked well, all things considered.

The second undergrad is new to the lab, but not new to research. I'm teaching her how to do various basic biochemical assays, so we can assay the composition of cricket hemolymph in the California species we work with. The early stages of mentoring a new student take the most time and effort, but she's a quick study, so that's good.

The third undergrad is cooking along on her honors thesis project, which involves feeding different diets to crickets and then tethering them and flying them in front of a fan. One day, she had a conflict and wasn't able to fly her cricket, so I got to do it instead:

Tethered cricket flying

I'm generally excited about her project, which could turn into a nice publication.

But I'm feeling antsy about making progress on academic writing, because working with a lot of people sucks up a lot of time and mental energy. Time to get more strategic about scheduling.



( 6 remarks — Remark )
Feb. 19th, 2017 09:34 pm (UTC)
What's the package that isn't being maintained anymore? I know people who take on projects like that, if it's primarily porting existing stuff to newer distros.
Feb. 21st, 2017 06:38 pm (UTC)
Well well well...
I haven't dug in deep enough to determine what's involved, but here's the GitHub repo with the current state of affairs:


If you know people who are interested and enthusiastic about this kind of thing, you know some really awesome folks. :^)

I should reach a point fairly soon where I will do another write-up of the workflow for this project, because we're getting close to having a defined workflow again, and it's a cool project.
Feb. 22nd, 2017 02:32 am (UTC)
Re: Well well well...
Yow, that's a big project. I'll poke at some people and see if anyone thinks that would be fun.
Feb. 24th, 2017 11:05 pm (UTC)
Re: Well well well...
Yeah, I won't be surprised if nobody bites.

One of the tracking options I originally explored involved using Ethovision, a software program published by N*****. At one point, I contacted them for a quote. $20,000. But when I tried using Ethovision, it froze and crashed repeatedly because it hated my video file format, and there wasn't a good way to change anything to deal with the problem. By now, there are a couple other competitor programs out there, but I personally hope the open-source options can be kept alive because I feel like this is an area of technological innovation that should be made widely available.
Feb. 24th, 2017 11:05 pm (UTC)
Re: Well well well...
I should add: I had access to a copy of Ethovision that another lab had purchased.
Feb. 25th, 2017 02:23 am (UTC)
Re: Well well well...
I figured. I'm in a similar situation at work right now, running off a friend's machine to see if software will do what we need.
( 6 remarks — Remark )

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