Follow up on “Proper upbringing vs negligence of computational students in biomedical research environments”

So it turns out my previous post struck a cord with quite a few readers. Some of them contacted me directly to comment and share their stories. I decided to include three. The first is an update I previously posted quickly after a senior PI misinterpreted my post. The other two came later and reflect personal experiences which I thought are important to share both for the PIs out there that think there is no problem and of course for the aspiring compbio students/postdocs who read this. I think those stories speak for themselves and it’s interesting to see the comments and feedback coming from basically all over the world, so this seems to be somewhat of a universal problem in our field. Of note, those stories are not about evil PI exploiting students (the wrong impression the senior PI from the first update was worried about), but rather various forms of negligence and nonsupportive environments, which is what I was actually describing. For obvious reasons, I removed all details that may identify the people involved (and got prior authorization to post those here).


It seems this post got a lot of views but was also misinterpreted by some who got back to me with legitimate concerns and criticism. Specifically,  a senior PI wrote me they read this as “data generation labs are exploiting the students”. That was never my intention. Let me clarify, and I’ll use Penn’s GCB graduate group to make the point. GCB stands for “Genomics and Computational Biology”. I think the creators of GCB were wise to define it as such. It means GCB caters to a wide range of students who want to get exposed to “real life data/problems”. Some are more into methods development to derive hypotheses (hence “Computational Biology”), others are more into actually generating the data and analyzing it themselves (hence “Genomics”). These are crude distinctions of course but the point is not every student is interested in methods development, not every student requires co-advising. And Sometimes a student may need co-advising/collaboration for a specific project/problem and that’s all. As the PI rightfully wrote me “there is no one size fits all”. Indeed. And students that are becoming experts in a certain field while using/producing Genomic data are not “exploited.” As that PI wrote me: “I’d be better off hiring a good bioinformatician then taking on an untrained grad student who typically needs close supervision and mentorship.” That’s a fair point. My worry, and what sparked this blog in the first place, is with students who want to do more “methods development” at some level and do not get to do that because (a) they haven’t realized that’s what they actually want to do (b) they did not articulate it (see my suggestions above) (c) the system/lab they are in does not support it.


Your recent blog post strikes a deep personal chord with me because, during grad school, I was one of the “computationally oriented students [that were] basically used as in-house bioinformaticians to solve the bioinformatics needs of a data generating lab”.
Before we go on, I should say that my grad advisor is a very nice person, excellent scientist, absolutely looks out for me, and we have a great ongoing relationship. So, this is definitely a classic case of asking the student (me) to “go explore and tell me what you may want to do” “[w]ith all the good intentions.”
I joined a genetics lab with a lot of interest in computational biology but, being a naive undergrad, I did not realize that, although the science was really cool, my advisor will not be able to advise me on the computational aspects of my work. After I started my work this slowly dawned on me when problems were being posed to me and I was being asked to “solve” them without being given any starting point or subsequent guidance. This was still my first year and I found it very hard to cope with.
I struggled day and night to find relevant papers & reviews, read them end-to-end, read online tutorials, improve both my programming and analysis skills, and started working on the given problems. Then, I started seeking out other bioinformatics/computational-biology faculty on campus to interact with and attend journal clubs with, and I was also doing my best to identify one of them to be my co-advisor.
But, the latter – engaging with other computational faculty – was not easy at all due to complicated politics from all parties involved: my advisor only wanted to ‘collaborate’ and did not want me to be partially subsumed into another faculty’s group, distracting me from my main work; he also did not have good experience/relationship with a few bioinformatics faculty whom he wanted to work with, and so, he decided to “grow the expertise” in his own lab and liked to tout that he had in-house bioinformatics capabilities.
I survived by working very hard, making hundreds of mistakes, interacting with folks far and wide across the campus, and finding a couple of “shadow” mentors whom I could go to for general guidance when things really were not looking well. Along the way (just like you pointed out), I also managed to mildly enjoy the part of being in a lab that was generating data and interacting closely with experimental biologists, both helping me tremendously in my scientific development.
So, in spite of my survival and subsequent success, I couldn’t agree more with your post. Now as a faculty myself, I cannot emphasize enough the value of “advice”, “training”, “guidance”, and “well-rounded professional growth” of my students and I’m committed to “improving the upbringing of our future generation of scientists”.
Thank you for your post. This is a super-important issue and I’m glad you brought it up.
Your recent post on computational training has touched me deeply.
I have read this almost 50 times and this completely echoes my sentiments.
We all acknowledge the misuse of computational trainees as in-house bioinformaticians, but your post also talks about the “benign form of negligence”, i.e. not knowing what to do with a computational trainee.
I am currently in the same situation, figuring out what to do next. Unfortunately, most people never realize this problem until it is too late.
Thank you again for this post.

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