Budget Salary Estimations

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 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 at the 5 year mark (when that startup expires). Based on salary alone, I would expect to just about exhaust all funds at that 5 year mark.

Now, keep in mind that there are some MAJOR assumptions going on here:
1. This simulation assumes that the only expenses that matter are for salary and associated fringe benefits only, and doesn’t take into account reagent, equipment, and core facility costs (as well as the more sporadic costs, like travel and publication fees). While personnel costs is definitely going to be the major expenditure at any given time, historically it’s been slightly above 50% of all costs, so this is a major adjustment to incorporate into my simulation in the future.
2. This simulation assumes that I DO NOT receive another grant in the next 5 years. Of course that will not be the case.
3. Aside from Nisha’s intended graduation date, the rest of the end dates are very roughly estimated. In the case of research, this is assumed to be indefinite for two of the individuals.
4. 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, although a potential postdoc is also possible if it’s the right person. That’s what the additional colors on the plot are. A singular PhD student would be the cyan line. A singular postdoc is the red line. A PhD student and a postdoc would be the purple line. Since a postdoc effectively costs double as much as PhD student here, taking two PhD students (unlikely) would effectively be similar to the red postdoc 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 (I’m erring on the shorter side, considering that I am not accounting for reagent / equipment / service costs, as mentioned above). 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.

PhD Student Rotations

This post was originally from June 2022, but I’m reposting now ahead of the 2024 incoming PhD class rotations.
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 / medicine 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, synthetic 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, or there is no grant yet but the ideas are straightforward and all of the assays are already in place. These are currently listed on this Google Sheet. 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 avoid potentially problematic or toxic situations.

NSF? More like Not So Fast.

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.

Old Lab Photos

As the lab finishes its 4th year of existence, I’m realizing that the older lab photos are going to eventually overwhelm the “personnel” page, but I still want to save them for posterity. Thus, I’ll start only keeping the most recent lab photos on the personnel page, while transferring older photos to this blog post.

Here’s the history of lab photos for the Matreyek and Bruchez labs, from (almost the) most recent to oldest:

September 2022: Matreyek and Bruchez lab picnic! From left to right: Sarah, Michelle, Nisha, Kenny, Alex, John*, Avery, Anna, Lane*, Nidhi, Olivia, Vidusha*. *[rotation student]
June 2021: Celebrating Drew’s last day, and Vini starting grad school at CWRU.
^ Geeks who (mostly do not) drink at Boss Dog Brewery, July 13, 2021.
“The Cloneheads” got 10th place out of 20 teams; a full 10 places higher than we expected to be!

Landing pad kill curves

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.

A personal clingen vignette

Back in 2017, when I was a postdoc and still first learning the human genetics field, I encountered a clinically relevant situation in my own family’s genetics. In short, my bloodline seemed to harbor a quite rare recessive allele in a gene encoding the “battery pack” for a set of critical hormone (and other small molecule) modifying / metabolizing enzymes. When two dysfunctional copies are harbored in the same individual, there are devastating consequences on the developing child.

Figuring this out ended up being an interesting academic exercise, since it was a case where I could synthesize a lot of the knowledge I had built up, from more recently acquired knowledge in human genetics, clinical genetics, genomic technologies, and genomic databases, to somewhat older knowledge I had on literature searches, molecular biology, cell biology, and protein structure-function. Here’s a report I had provided a family member upon embarking on my quest to understand the situation. Aside from my family, I had directly shared it with various friends / colleagues / trainees over the years, but a recent conversation with people in the lab made me realize that I may as well share it more broadly at this point (any lingering minor concerns about publicly sharing “private” health-related information – for both me and at least some of my family members – is offset by what I think is a nice case-study of the importance of science and genetics on understanding human disease.

Note: In the process of having Avery, we did get Anna tested, and she was not a carrier for any variants in POR thus making Avery’s risk of ABS essentially zero (rather than the number I had calculated at the end of the above document). That said, I remember that getting Anna tested was somewhat of a struggle, between it not being fully covered under insurance and there being some miscommunication between our hospital system and the external genetic testing lab, such that the test results were pretty delayed. Such is the US health care system…

LP publications

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).

Manuscript acceptance timing

I’ve now been an author on enough papers to have a reasonable sampling of what the experiences can be like. In short, it minimally takes 2 months to go from initial submission to eventual manuscript acceptance. These experiences typically are those that require little to no experiments for revision. The process, especially when requiring hefty experiments or multiple rounds of revision, can easily stretch to half a year. In some cases it can take *much* longer (in one experience I’ve seen, a journal did the “rejected but amenable to resubmission if sufficient additional impact is added”, which resulted in an informal span of ~ 800 days!!! ). Anyway, at least for the manuscript submissions I was involved with where I had access to an author portal (or received emails when things happened), I noted when the reviews were returned and revisions submitted, to also keep track of how much of that time was technically under one’s control (manuscript with authors; red) or completely out of one’s control (manuscript with journal; blue). See below:

Also, part of the reason it makes sense to post manuscripts to bioRxiv; why have a completed manuscript that is essentially publication-worthy sit in the dark for half a year?

Note: Obviously this data is for manuscripts that eventually got accepted. Rather pleasantly, I’ve never been first or corresponding author for a paper that got rejected, so I don’t have nearly as good a sampling of that experience. But sitting on the sideline as a middle-author for a handful of such occasions, it would seem to take anywhere between a week (eg. immediate desk rejection) to a couple of months (eg. rejected upon peer review) per submission; when sequentially shopping across multiple journals to find a taker, this would seem to add up.

Network drive for file storage

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/

NIH grant expenditures

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:

So, essentially at my steady state (which I’ll probably be at for at least the next 2.5 years), the lab is generating ~ $20k a month in indirects for the department, amounting to about ~ $5k per desk per month.

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