Wednesday, December 18, 2013

State of the lab, year 1 – setting up

I have used this blog in the past to keep track of my academic life where I can give a less formal perspective on papers I have published or ideas I am working on. Starting a group has made me think a bit about what I blog about. I have more responsibilities towards the people that have decided to work with me, towards the institution that has hired me (EMBL-EBI) and funding sources that support our work. At least for now I have decided to keep on sharing my personal view and in that context I though it could be interesting to write down my path as group leader in academia. This might become a yearly “thing”.

I started at the EMBL-EBI January 7 and in a blink of an eye one year has gone by. I have just arrived in Portugal for a conference and holidays and I said goodbye to four people that very courageously decided to work with a unknown newbie group leader. I could sum-up what happened in this first year by saying that the group-leader tittle now makes sense – I am coordinating an actual group. Most of this year was spent applying for funding, recruiting and trying to know more about the different groups working on campus.

From an empty room to a research group

EMBL-EBI is really a great place to start a group. For those that don't know the EMBL system, group leaders are given very generous core funding to work for 5 years, plus an additional 4 years after a review process. The chances of failing the review are small but there is essentially no tenure. Core funding and additional “internal” postdoc fellowships are sufficient to run a small group without external grants. We are encouraged to apply for funding but money is not the most immediate source of stress. So for me, since I started recruiting only after arriving in January, facing that empty room where a group should be working was the first thing on my mind. Recruiting postdocs for a unknown and empty group is particularly challenging. I tried to do some of the obvious things like emailing related groups that could have people about to finish the PhD and promoting the vacancies at conferences. It is hard to quantify but I do have the impression that my online presence has been an advantage in this. Once the first couple of people started and group meetings made sense the empty room stress went away. I know people starting experimental labs right now and I have to say that computational people have it way to easy. We can buy a few computers and the “lab” is set up. 
I spent a considerable amount of time applying for funding which is always somewhat frustrating. I don't mind writing grants but I am happier doing actual research. Around 6 months into the job I managed to re-start doing research and I have managed to keep working on fairly constant basis. I hope I will keep having/making time for research for as long as possible.

Meet the gang

This year we got an HFSP CDA and an ESPOD fellowship which together with the core funding allowed me to grow the group fairly quickly. The first to join was David Ochoa (postdoc, @d0choa, webpage) who will be working initially on PTM dynamics under different conditions. He also introduced me to the amazing BlackMirror series, the best fiction I have seen in a long time. Vicky Kostiou (intern) joined after and is doing a great job of improving the PTMfunc website which should be updated late January (stay tuned). The most recent arrivals were Romain Studer (postdoc, @RomainStuder, blog) and Brandon Invergo (postdoc, webpage). Romain will be using his phylogenetic and structural experience to study PTM evolution and Brandon was awarded the ESPOD fellowship to work with Jyoti Choudhary and malaria groups at Sanger on Plasmodium PTMs. Omar Wagih (@omar wagih) will be the fist PhD student joining in January. Finally, although we have still not signed a contract Marco Galardini (@mgalactus, webpage) will likely join in February to work on a collaborative project with Nassos Typas' group at the EMBL-Heidelberg. 

To be, or not to be, an experimental group

One of my concerns when I joined the EMBL-EBI was that, although the Sanger is just next door, EBI is a purely computational institute. Doing computational work is pretty amazing but progress can often be limited by lack of data. High-throughput research is removing somewhat this limitation since there are probably more observations made than we can all analyze. Still, if you are really interested in going in a specific direction then a experimental group simply has more power to make the right observations. My solution for this problem, for now, will be to co-supervise people with experimental groups including Brandon's EIPOD project, Marco's project with Nassos Typas and a future hire with Silvia Santos' lab in London. This is an experiment in itself and I guess in 2 to 3 years I be able to evaluate how practical this is. One alternative is to make use of research services such as the ones listed in Science Exchange. I have discussed with a couple of companies what would be the prices for some of the work I am interested in doing. These are fairly expensive but might be a good complement to the collaborations.


So overall, the group is off to a good start. It is funded for a few years at a reasonable level and we have collaborations with other groups that share some common interests. There were some things I wish could have gone better. I didn't get all the funding I applied to, which is expected. I also didn't manage to submit the two last manuscripts that still contain work from my postdoc. It would have been great to start the second year with that off my back. Still, I am happy with how things look for the next few years. It is a privilege to be able to coordinate this group of people and level of resources around topics that I find so interesting.