I’ve been thinking about budgets, partially b/c I just went through a protracted experience of getting the school to give me access to the remaining part of my startup (from almost 5 years ago! And while I was repeatedly told the remaining amount was non-expiring, it was just given to me in an account that expires 5 years from now…). Regardless, the goal is to spend down these remaining institutional funds while bolstering my research group, largely through personnel additions and management.

For that reason, I created a simulation of how personnel salary + other operational costs would exhaust my current funding portfolio (currently one R21 that ends in a year, an R35 that ends in 2 years, and the aforementioned remaining startup account). The black line in the plot below shows this happening, with the line terminating around the 3 year mark. This is presumably around when I would expect to run out of money, if zero future action were taken.

Now, keep in mind that there are some MAJOR assumptions going on here:
1. This simulation assumes that I DO NOT receive another grant in the next 5 years. Of course that will not be the case.
2. Aside from Nisha’s intended graduation date, the rest of the end dates are very roughly estimated. In the case of research staff, this is assumed to be indefinite for two of the individuals. Of course, if money ends up getting tight, A) my salary will end up going down some, which will help alleviate costs, and B) I’ll let go of research staff as necessary, and well before there are impacts on students (to which there is a larger commitment).
3. Everything is modeled as a daily recurring expenditure. In real life, I think everything behaves more like discrete sums that are added into the account yearly (like NIH budgets) or monthly / bimonthly (like salaries).

Note: It goes into the negative values since it’s allowing the startup not spent by the end of R35 in two years to subsequently exhaust (that’s when the line ends).

Now, I’m actively trying to recruit more personnel to the lab, at this point largely in the form of PhD students. That’s what the additional colors on the plot are. A singular PhD student would be the orange line, and two new PhD students would be the red line.

Especially in light of the fact that I *have* to spend that startup (or it presumably goes *poof* into the administrative ether), looks like I’m going to be good for at least a couple of years in the worst-case scenario. Regardless, this really does help me frame what I need to be doing at a given time. If financial situations were dire or particularly worrisome, I would be focusing on writing grant applications right now. Based on the above plot, I think it makes a lot more sense for me to devote focus on publishing existing projects and further developing preliminary evidence to increase the success rates of grant applications I could just as well submit in a year.

When I was an early PhD student, I barely knew about the NSF GRFP, and it wouldn’t matter if I did since I felt too overwhelmed / behind on everything to consider applying. Fast forward to my postdoc, where I was in a lab that expected you to write for postdoc fellowships (it’s a good policy, btw), in a department where half the grad students seemed to *win* an NSF GRFP any given year; this experience made me realize just how useful of a training opportunity writing fellowship applications can be, as well as helping me to realize that there can be a bit of a feed-forward effect for success, where being awarded a competitive fellowship early on opens up a small number of additional possibilities, which can compound over time until the final result ends up being a large effect.

Well, simply bringing this ethos with me when starting my own lab seemingly isn’t enough; there are apparently entire institutional administrative systems that can get in the way. I’ve already talked about a previous experience, where the school grants offices wouldn’t allow a student’s application to be sent since they weren’t in the internal grants management system yet, despite the fact that NSF GRFP applications are supposed to be sent in by the student. At least that application got saved at the 11th hour, and was actually successfully submitted and reviewed, even though it went unfunded.

This year, we had two students put together well-prepared, complete applications, only to be disqualified on the same technicality. Turns out, sometime within the last two years, the school started putting a summer class on the transcripts of incoming biomedical PhD students; in short, instead of the first entry of their transcript being the fall quarter, there is a summer quarter listed on the transcript preceding it. In actuality, the only thing that is happening during this time is rotations, which typically start in July or August here. There may be a handful of workshop type things, but nothing that counts as an academic course that is a requisite for eventually graduating. It’s effectively the same situation as most other PhD programs in terms of timing of official instruction.

Well, in the case of 2nd year grad students, NSF considers that summer transcript entry as indication that they have completed 1 year of graduate coursework prior to submission, disqualifying them. Each of the two students got an email from NSF saying so, and each student tried to get a statement from the university administration clarifying the situation. In neither case was the school willing to deviate from whatever legal wording they already had, so the disqualification appeal filed by the student was denied by NSF.

So two applications (and probably more) where, in retrospect, the student was writing the application documents, as well as corralling letter writers, with a 0% chance of success. You’d think the school would want to change their transcript policies to not unnecessarily disqualify their biomedical PhD students from the NSF GRFP, but there was seemingly little indications that the contacted administrators will do anything about it. So essentially, no CWRU School of Medicine PhD student in their second year should submit an NSF GRFP application, unless something changes. Maybe (hopefully), this isn’t the case with other CWRU schools, like those overseeing biology or bioengineering.

Well, the biomedical PhD students can still apply in their first year, right? I suppose so, although if they’re new to the campus, they probably aren’t writing their application based on a 4 to 6 week rotation (the expected rotation duration in our school). Only those that were in the know and had strong, supportive research environments prior to grad school would be in the running, and I suspect that isn’t a large fraction of our incoming student populations.

So a school that simultaneously bemoans a lack of student fellowships, yet through lack of experience and rigid / misguided administration, manifests the same situations it bemoans, with little indication that this will ever change even when notified of the problem. Institutions, man.

I previously did some recombined cell enrichment curves using flow cytometry of mixed cells populations (containing both recombined and unrecombined cells) upon treatment with various selections (Blast, Puro, Hygro, Zeo), but my recent experience testing out the various plate readers got me in the mode of doing serial dilutions with various cell viability / (relative) cell counting assays, so I did that for our mostly commonly used Single Landing Pad HEK cells (LLP-Int-BFP-IRES-iCasp9-Blast) as well as our still unpublished Double Landing Pad HEK cells. Here are what those curves generally look like.

Note: The Double Landing Pad cells encode hygromycin resistance within the second landing pad, so the difference in hygromycin IC90’s in the SLP and DLP cells is expected. Once we have the plate reader purchased and back in the lab, I’ll probably do some other conditions (eg. unmodified 293Ts, recombined SLP cells, recombined DLP cells) for some of those common cell culture antibiotics.

Note 2: Also, now that I know the general effective concentrations of some of these chemotherapeutics (eg. cyclophosphamide, gemcitibine, vincristine; although I did completely overshoot the concentrations for gemcitibine), I’m somewhat set up to see how the IC90 changes when I overexpress various transgenes that should increase resistance to those drugs.

For my own curiosity (as well as for some data in case I want to show to granting agencies that I’m not hoarding the research tools / materials that I make), I keep track of the papers that have used the landing pad cells / materials in their work. Here’s a chart of publications using some version of the LP cells over time.

The first few papers were mine, but from there, there have been roughly 10 or more papers per year. It’s seemingly been a little higher in the most recent couple of years, although the 2023 date has a dotted line projection for the end of year number (in the instance of my originally writing this paragraph, it was early June).

I’m so tired of being jerked around by various cloud storage services. Institutional Google Drive was unlimited storage, but now the University has capped it at 100GB (how uselessly small…). I believe the institutional Box account was also unlimited, but apparently it is now 1 TB. Which, I mean, is better than 100GB, but also the Box interface is painfully awful and IMO is not useful for anything other than “cold storage” of files, where 1 TB isn’t going to cut it. Regardless, I solved this problem for actively used shared file storage for my lab by purchasing 2TB of GoogleDrive cloud storage for $100 a year (out of my personal bank account). Still doesn’t solve the “cold storage” problem for microscopy data, which can easily run much more than a terabyte.

Well, I have an iMac at work that is hooked up to a landline, and I have plenty of external hard drives, so I’m going to try to allow one of those external hard drives be discoverable on the network, and see if that works as a way to store our microscopy data. To access this network (on a mac, at least), follow these instructions:

1. If you’re not directly hooked up to the landline on campus, you’ll need to VPN in. This is done through FortiClient. This will require DUO authentication (so check your phone to accept).
2. If you’re now connected to the VPN, you can now try to load that external network drive. to do this, hit Command + K while in the MacOS Finder (or go to the top menu and hit Go > Connect to Server…) and then enter the following:
   smb://[See the IP address the Matreyeklab_Overview_Googledoc]/MLab_5TB
3. You might have to put in a username and password. This will be the standard lab username and password (refer to the Matreyeklab_Overview_Googledoc if you’ve forgotten, but you must have memorized this by now…)
4. Voila! You should now have a Finder window for the external hard drive, which will (at the least) have a folder called “Microscopy”.
5. Now what if you want to do things on the Terminal, since you’re a power user (perhaps aspiring power user?). In that case, load up a new Terminal instance, back out of your own account directory into one of the root directories of your computer (ie. do “cd ../..) and then go into the “Volumes” directory, and if you’ve accessed the network drive like described above, you should now be able to go into the external hard drive directory off the network (ie. do “cd MLab_5TB), and start doing what you need to do there.

Yay, problem solved. Obviously the above instructions are only for lab members. If you run into problems, LMK, and I’ll try to help troubleshoot.

Various links / references, mostly for my own use:
https://support.apple.com/guide/mac-help/set-up-file-sharing-on-mac-mh17131/13.0/mac/13.0
https://support.apple.com/guide/mac-help/servers-shared-computers-connect-mac-mchlp3015/13.0/mac/13.0
https://support.apple.com/guide/mac-help/connect-mac-shared-computers-servers-mchlp1140/mac
https://www.makeuseof.com/how-to-set-up-access-network-drive-mac/