Wednesday, January 19, 2022

State of the lab 9 - an informal report on the 9 years of EMBL-EBI

This blog post is part of a yearly series (or close to yearly) on running a research lab in academia. 2021 was the last of 9 years as a group leader at EMBL-EBI, which is the standard time given to group leaders to establish and run their labs at EMBL. For this year's blog post I thought it was a good time to look back at the full 9 years and I am going to (briefly) cover the time at EMBL with some numbers including giving an approximate account of the finances. This is something that I do with the group at the start of every year but it still feels strange to make financial numbers public. 

The scientists

A lot has happened during 9 years. Starting with the people, we have had 7 PhD students, 1 of which co-supervised, 13 postdocs and 10 interns/visiting lab members. The total group size was around 10 for the majority of the time which, as a manager, feels about right in what I can do as a direct line manager. It is fair to say that science is a very social activity and working with different people with different personalities, through the good and bad, is really enriching. Not to get all corny but the personal interactions are some of the things that stick with me the most over the time. It is always in those extremes - the "unfairly" rejected paper or unexpected positive response, individual personal and work difficulties that are overcome or sometimes not. Mental well being is an example of such difficulties that across the broader society we are not good at dealing with and that have also not always been easy as a manager. 

From these 30 lab members there are 7 that will continue with the group over the next few years: Cristina (senior scientist), Jurgen (postdoc) and Miguel (postdoc) have joined me at ETH and Eirini (PhD student), David (postdoc), Inigo (postdoc) and Danish (postdoc) will remain at EMBL-EBI with funding that cannot be moved. From the PhD students and postdocs that have left all but 2 have left with published papers as first or co-first authors. One PhD student decided not to continue the PhD and one postdoc left after several years without a first author paper. In both cases I feel some blame as the project ended up being difficult and the results were just not very positive.  

The publications and science

In total we published 45 original research papers, 3 review articles and 2 news&views over the course of 9 years. This includes only research that was really done after starting the group and also includes 8 preprints that have not yet been published in a journal after peer-review. This is split into 27 papers where I am listed as co-corresponding author and I also think our group played an important role in the final outcome, plus 18 on which our group had some input into. I am showing on the figure the distribution of these papers along the 9 years. The first paper from our group only came at year 3 with the first real significant set of publications coming at year 4 and 5. In regards to the non-tenure track system, even by this crude metric it is easy to see how different it would be if I had to apply to the job market at year 6-7 vs year 8-9. Of course, note that the numbers for 2021 in particular are inflated by preprints that will ultimately be published in a journal most likely in 2022. Another clear trend that feels true to me is the increase of small collaboration efforts where our group just helped out in some modest way. I think this is a reflection of just being more integrated into the local and broader academic networks.

I am not going to go into the scientific outcomes of the 9 years in any detail. I think some of the strongest work we did was on the evolution and functional importance of protein phosphorylation with multiple publications that have built on each other and where I think our contributions move this field forward. There was also a smaller line of research on the genetics of trait variation that I wouldn't consider to be at the cutting edge but it has been fun to work on. In particular it has been interesting to step closer to the fields of human genetics and genetics of human disease where making advances requires the interactions between people with such different ways of viewing science. Just the language barriers between human genetics, cell biology, biochemistry and chemical biology have been fascinating to get into. 

The funding

So now something that feels less comfortable or at least less common to discuss - the funding. Before going into any numbers, I should caveat this by saying that these are very rough approximations that of course should not be considered an actual financial statement. These numbers also don't take into account the money spent on the whole infrastructure (administration, grants, IT, etc) but are just the funding spent on research lab members, including my salary, and consumables. With that out of the way, over 9 years we spent approximately 5.7 million euros as broken down per year on the figure. Although we have had a small wet lab running in the last 6 years, I would say that 90% of this was on salaries. Of these around 2.7 million were from external grant funding, plus ~450k from competitive internal postdoc fellowships. This of course just shows how amazing it is to work in a place with core funding. I ended up being very successful early on with 2 million funded in years 2 a 3 and this made me too careless about applying for grants later on which I now consider a real error on my part. I applied in total to 13 external grants with 6 being successful. 

So a number that immediately is easy to get but that is probably quite meaningless is the money spent per research paper. We spent a total of ~127k euros per paper or 210k if we only count those where I am listed as co-corresponding. Of course this varies so much per paper really with my very rough estimates on bounds to be something like between 25k to 1 million.  Given that we mostly spend the budget on salaries this simply reflects the amount of people time spent on a project. 

To new beginnings 

This is a somewhat dry recap of the 9 years of EMBL but I thought it would be interesting, at least to me, to have these things written down. Even if these are just numbers, I am curious to see what the next 9-10 years look like. I am sitting in my new office at ETH, just close to two weeks after arriving in Zurich. There is a lot to adapt to, including teaching material that I should be preparing right now. I am curious to see how long it will take me to get into the local academic network and how much the move will impact on our capacity to do work. The lab work is really the part that will take the longest as I don't think we will run any experiment before middle of the year and although we have the budget for an MS instrument that will take even longer to get going. In any case, I am excited about the new beginning here.