At least in my SOM-based department, one’s general status is supposedly correlated with the amount of indirect costs they bring in. It looks like I’m currently capped at 4 desks for my personnel, and it’s not clear if it’s worth trying to expand here. Regardless, this is apparently the directs / indirects space I’m operating in with my current setup.

What does this come out to in terms of indirect costs generated per month? Here’s the plot based on my budget reports, below:

Ah, the business of SOM-based academic research. Well, I’m nothing if not transparent.

Rather facetiously got a suggestion to keep track of how my workdays are spent, but that did prompt me to start keeping track since I have gotten into the phase of my job where I’m feeling somewhat burdened by non-research responsibilities and I like having data in hand. As I’ve noted on my other website, my workdays are now largely constrained by daycare hours. Thus, I do have pretty limited hours in a day to get everything done, requiring a fair amount prioritization; doing one things often means not doing something else.

I’ll sporadically hit “run” on my analysis script and the below plot will update. The n values are currently pretty small, but I plan to keep doing this indefinitely.

Keys for the above plot:
Red dashes are mean values across all days. Gray dots are values for individual days.
“Research_internal” denotes activities that directly impact my research group (eg. meetings with personnel, data analysis, benchwork).
“Research_external” denotes research activities that don’t have to do with my group (eg. Science-centric meetings with other faculty, emails to people requesting reagents).
“Administrative_internal” denotes general paperwork (eg. Filling out my annual performance reviews)
“Seminar_director” denotes work related to running the immunology portion of the Dept seminar series (eg. More emails…)
“Postdoc_affairs” denotes work related to trying to manage postdoc affairs for the dept (and in some ways, by extension, the SOM).
“Other_service” denotes other service activities for the school (eg. Corresponding with CWRU undergrads not in my group).

But I can break down some of these activities further. For example, for the the “Research_internal” section where I’m handling things directly related to my research lab, it can be further broken down as follows:

And, well, since so much time seems to be spent writing emails nowadays, this how much time I spend writing emails each day (note: I do all internal communication with lab members via Slack, so this is mostly administrative matters):

Kind of an interesting observation, so I figured I’d post it.

Now that I’ve been here a little while and have gotten some research grants funded, I was curious how my research group was faring from the University’s finances perspective. Now of course this is going to be a gross oversimplification, but I figured a simple metric was taking the amount of money the University has gotten as indirects from my research grants (61% indirects rate; you can figure this out through a simple Google search), and subtract that by the amount of startup funds I’ve spent so far (note: this isn’t all the startup funds I have available; just what I’ve spent so far and is thus officially “gone”). Well, here’s what that looks like over the last two years:

My first pass at trying to analyze this data was incorrect, since my budget reports only list the total money spent (which includes directs and indirects), so I had to go back and extrapolate the direct and indirect funds out of that number for each budget number (with there being three classes: startup accounts with no indirects, the K award with 8% indirects, and the R awards with 61% indirects). So in actuality, I have not yet accrued more indirects than startup funds expended, although I do know that for the last 6 months I’ve been funded 100% off my NIH grants (I haven’t been spending my startup at all), so presumably the trend will keep trending toward the positive.

I’m now in charge of running a decent chunk of the departmental seminars. Thus, it’s behooved me to figure out how to handle the A/V in that room as well, since I don’t want seminars ruined by technical problems. So here are my notes for handling them:

Initial lighting: Preset 2 makes sense for people first walking in. That said, if that seems too dark for the stage, then the full “on” position is fine (preset 1 on the elevator-side panel, or just “on” in the main entrance panel).

I’m going to suggest using your own laptop. The computer there is fine (you’ll have to log in using your Case ID and passphrase) but I still think it’s going to go way smoother with your own laptop. I’m going to suggest any time I’m in control, that we use the “MatreyekLab” laptop for this.

Use the touchpad on the right to wake the projector. Then, click on “Laptop” so that it knows to use the external VGA (which, I’m assuming, usually has the HDMI adapter plugged into it). Note: The cord is *very* finnicky. Like, don’t touch the cord at all, or leave it in a position where it may hang a bit. I’ve tried to tighten it as much as possible, and that seems to keep it somewhat resistant to disconnecting, at least for a while).

If you want to have presenter tools, you’ll have to be in “Extended Desktop” mode. For the LCD_VGA projector, make sure it is in 720p mode or else it may look awful. No underscanning necessary. This is all when on a Mac. To get access to those settings, go to “System Preferences” > “Displays”.

The mic electronics should be on by default, but there is a “on / off” switch at the base on the mic. Once that light comes on, you know it’s on. I haven’t been able to find a volume knob for it or anything. Probably makes sense to just turn it away if it is too loud.

What I like to do, is to have my personal laptop log in as my actual Case Zoom account (the one where I’m presumably host or co-host). After the meeting is started / set, using the Meeting ID and Password, I log into Zoom as a “guest” user on the MatreyekLab laptop. Once logged in, don’t forget to rename yourself to be “Speaker” or whoever the actual speaker’s name is, to make it clear which Zoom window is actually the presenter. Then, using the personal laptop with the host account, make the “Speaker” account a co-host (for this session), so they can easily share their screen. I then just share my screen, and use “Desktop 2” as the screen being shared, and it should be more-or-less set.

I have found that while the built in mic can be OK for this, a cheap $30 mic off Amazon may give you better sound for the speaker’s voice, and help pick up on the sound from audience questions as well. Probably makes sense to at least move the Zoom bar on the presenting computer away from the top, since it’s going to obscure the slide titles. Even better if you change the settings in Zoom (on the presenter computer, not on the personal laptop) to get rid of the floating Zoom bar, so that it doesn’t start taking up a bunch of slide space when people start asking questions

I can monitor how things look and sound from my main laptop, although there is a half-second lag between the real-life voice and the captured voice transmitted through Zoom, so it’s only possible to check in on the sound periodically for short amounts of time.

When ready to start, I find this to be easiest order of events.
1. Go up to the podium. On Zoom, turn the speaker laptop off mute. Go to more > “Hide floating meeting controls”.
2. Turn on the microphone for the seminar room so people in the back can hear.
3. Go to the control panel on the stage and set the lighting to 4, which will dim the lights in the room.
4. Start talking!

Finishing up: Probably makes sense to go back to Lighting preset #2 during Q&A, so people can see each other talking easier.

It’s PhD student rotation season again at CWRU, so I figured I may as well put this post on the lab website to 1) inform any prospective PhD students that may be perusing through the lab website, and 2) remind me of the things I like to bring up before people rotate.

1. If you’re interested in rotating, we should definitely schedule a meeting so I can get a sense of your background and interests, so I can tailor the rotation appropriately (and screen out people who are likely to be really poor fits; see point 3 below). It will also give me the opportunity to talk through some of the other points listed below.
2. Rotations are suuuuper short here (Generally 4 to 6 weeks). Thus, there is ZERO expectation on my end to get any “publication quality” experiments done. My main goal is to make sure you’re familiar with some of the bread-and-butter methods in the lab (eg. molecular cloning, landing-pad -centric tissue culture, script-based data analysis). Failed experiments are fine, since it gives us the opportunity to talk about the data and troubleshoot together. The main thing I’ll be looking for is how well we’re able to communicate and work together, since that’s arguably the most important thing we can learn from that rotation that could be extrapolated to predict how good of a dissertation work environment it would be for the specific individual.
3. There isn’t really any prerequisite experience for rotation students. Yea, it would be helpful if you know how to pipet, have done some basic tissue culture work of any kind, and have designed and interpreted some experiments before. Being housed in a wet-lab department, I have very little expectation of computational experience. That said, wet-lab people that have zero interest in learning computational biology and data analysis are probably not great fits, since all projects in the lab will always have hefty data analysis components. Conversely, computation-only people with zero interest (and maybe even experience) in wet-lab research is also likely a bad fit, since all projects in the lab will also always have hefty wet-lab components.
4. The lab is pretty interdisciplinary. Like, some people work on virology, while other people work on proteins related to clinical genetics. Thus, you’ll have to be generally interested in science / biology to enjoy your time here. In contrast, if you only care about subject XXXX or subject YYYY and nothing else, then lab meetings are going to be really boring to you. There’s always talk about (practical) statistics, molecular biology, cell engineering, assay development, and high throughput sequencing; thus, if you’re into those things at some level, then you’re probably fine!
5. There are three very different options in terms of dissertation projects. There are some “ready-to-go” project ideas, where I’ve already crafted a grant application very clearly explaining the project scope. There are also some projects where I’ve played around a bit with some ideas / preliminary data, but it’s not really clearly written out anywhere and things will need to be hashed out. Both of these types of projects should be listed in this “Research Directions” network graph. Then again, there are probably some really great projects that I haven’t thought of yet, that A) are in line with the student’s interests, and B) can be tackled with the techniques / perspectives that the lab is good at. If it’s a decent idea that has links between cell culture assays, cell engineering, genetics, proteins, cell biology, and pathological consequences, I’m sure I’ll find it interesting and get on board. Highest potential risk, but also highest possible reward for the student (at least from a training for independent thinking perspective).
6. Rotation projects don’t have to be on the same topic as potential thesis projects. In my opinion, it’s oftentimes best to separate them, since potential thesis projects likely don’t have any DNA constructs made for it already, so working on it means only doing (likely failed) cloning during the rotation, which is no fun and not particularly informative.
7. I’ll only ever take one student any given year. So while it’s not a competition, some people who may want to join may not be able to. Something to keep in mind!
8. I expect every student to give an “end of rotation” presentation during lab meeting. The main reasons are A) So I can get a sense of where you’re starting in terms of presentation skills, and B) so we can go through the process of giving feedback on a presentation, since that’s an important part of doing a PhD in the lab (giving and receiving critiques / constructive feedback). It’s OK if you didn’t really generate any real data during the rotation; pretty hard to generate data in such a short rotation, and as I note in point 2 above, it’s not really the goal of the rotation anyway. Instead, what I would be looking more for would be signs of understanding the concepts behind the project and the techniques, and thoughtfulness in organizing the presentation for clarity.
9. While I suppose I’ll have the final word into who is potentially offered a spot in the lab, I will still be soliciting opinions on rotating students from existing lab members. The idea isn’t that it’s a “popularity contest” in any sense; it’s more, I want to make sure that all full-time personnel that join the lab are able to get along with the people already there, to curtail potentially problematic or toxic situations.