A day in the life of... a core facility bioinformatician

A day in the life of... a core facility bioinformatician

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Introduction: After a degree in chemistry from the University of Patras in Greece, including a biochemistry-related project, I pursued a PhD from the Demokritos National Centre of Scientific Research Institute in Athens, Greece on silkworm oogenesis. I then joined the lab of Dr D. Thanos at the Biomedical Research Foundation of the Academy of Athens, Greece, as a post-doc, where my interest in bioinformatics developed: I had always had a “natural” inclination towards computers (e.g. I was familiar with Linux/Ubuntu and carried out some self-taught programming as a PhD student), but during my postdoc I was introduced to Next-Generation Sequencing (NGS) technology and methods that rely on NGS, such as RNA-seq and ChIP-seq. As a next step in my academic career, I joined the group of Dr A. Papantonis at the Center for Molecular Medicine in Cologne, Germany. There, my increasing interest in epigenetics and transcription regulation slowly but steadily pushed me towards a more bioinformatics-based role, and in 2019 I was employed as a staff member at the Cologne Center for Genomics (CCG) in Cologne, working as a bioinformatician for the NGS core facility. 

I start my day by…

Making a coffee, while organising the day’s tasks. During this time I usually go through all unfinished jobs and check on their status, check my email to see if there are any new incoming jobs, verify that all finished tasks have been properly forwarded to the facility’s collaborators or clients, and if needed inquire about the delivered analyses and resolutions of previous assistance. In the meantime, I am always in contact with the lab about possible pitfalls from new sequencing kits and chemistry so that I can be prepared for any adjustments or updates that need to be made to the pipelines.

Most likely by the end of the day I will need to adjust the existing code to accommodate newer library preparations, track errors and find their source, and probably prepare new pipelines. My work is coupled to the wet lab workflow, and so we are in constant communication when necessary.

My primary role is…

To make all automated analyses work like clockwork; the keywords are speed and accuracy. I always strive to find a delicate balance between speed and my main focus, which is accuracy and reproducibility. In my “spare” time, I tend to read the release logs of any updated software, about interesting available new methods both for wet lab and in silico, and I am always testing something new that could be incorporated into our pipelines.

I work alongside…

I work together with the whole NGS facility at CCG. However, I am mostly in contact with the head of the wet lab team Dr Janine Altmüller, who keeps me informed about all the new projects that are starting, about deadlines, and the possible introduction of new methodologies or kits. The whole team is one of the best teams I have ever worked with, and this is mainly due to Janine’s supervision. Special mention goes to my fellow bioinformaticians, Dr Susanne Motameny and Dr Holger Thiele. Without their initial guidance, I would not have been able to get on board so quickly. And of course, I am working alongside our collaborators/clients for any type of assistance or clarifications.

My most visited websites are…

While I was active as a researcher, my most visited sites were mainly academic journals, such as Nature, Cell, Genome Biology and Nucleic Acids Research among others, and one important database, PubMed. I visited sites to learn and to get the latest advances in my field, in order to use the gained knowledge in my daily work – from planning an experiment to data interpretation. Since I started working as a core facility bioinformatician, there has been a substantial shift towards code deposit websites (such as GitHub), and forums discussing problems and solutions on programming, with Stack Overflow and Biostars being at the top of my list.
I still visit PubMed and bioRxiv to stay informed on the latest tools being used, but learning about the advances in basic science is not my bread and butter anymore.

There is a balance between working on my own and as part of a team…

In my field of work, I mostly work on my own. Meetings are scheduled on demand, in contrast to the weekly lab meetings. When there is a need for clarification or assistance, I usually ask my colleagues for a short meeting. I get in touch with other bioinformaticians to ask for advice, but most of the time the internet is where I will look for answers. This has not changed during the pandemic, but it has become a bit more difficult to get in touch with any collaborator for “quick and immediate” troubleshooting, since I am only working from home. Each of us has specific tasks related to our personal experience, but with regards to mundane duties relating to the general operation of the centre, we are always in touch and are informed of any changes or optimizations taking place in order to avoid any downtime.

There are occasional other tasks in this role…

A few variations spice-up the job. Occasionally, people will ask me for advice on wet lab best practices based on my previous wet lab experience, in conjunction to my bioinformatics role, so that they get the best possible outcome after an analysis. This part, which I actually enjoy the most, is where my previous experience in the wet lab comes into play. There have been occasions where I have been also asked to help, or even perform, a full analysis by interpreting the data or making figures.

I’m finding the skills and experience I draw on most in this role are…

The basic skills for this role are knowledge of programming languages, and more importantly, knowledge of NGS methods. Regarding programming, such as bash scripting and R that are necessary for my role, practice and constant engagement are important for improving my skills. Having been a wet lab researcher provided me with a great advantage. Since I am familiar with wet lab protocols I am able to be comprehensive with my wet lab colleagues.

I decided to move away from basic research into a more streamlined work as in a core facility because…

Most people who are interested in science but chose to move away and be employed in jobs unrelated to science, or work in science-related projects in industry, or even in positions between academic research and service provision, will argue that their choice derived from the fact that working as a researcher in academia is by far a demanding job. I would even, based on my experiences, describe it as unforgiving.

Things that made me feel uncomfortable were, for example, the modern publishing experience, the constant dedication to writing grants, the striving for funding to sustain one's research or one's lab, the constant struggle to be relevant and known, the time spent reading numerous publications (sometimes unworthy of one’s time), the extreme working hours and time dedicated in the lab, and so on. Some years ago, I would have added the argument of “lack of job security” as one of the major points, but it turns out that in light of current global developments every job is insecure.

I therefore looked for job opportunities where I could still be involved in research without working directly in basic science, and without having the pressure of the “publish-or-perish” ideology. Working as a bioinformatician for the core facility was one of those choices that also provided me with peace of mind. The work is still as stressful and tedious as any other job, and there are still timelines and deadlines, but everything is on a manageable level. I do not miss working in the lab and I still have plenty of opportunities to get involved with scientific projects.

I end my working day by…

Closing the monitor and just going home, but frequently the computer is kept on overnight since there may be analyses running in the background or I may want to return to my previous working environment in a snap. There are also occasions where I return home with some unfinished work.

Most of the time I tend to re-check what I accomplished throughout the day. I double-check that all urgent analyses are completed or ongoing, or I may dedicate some time to finish up. I sort out the tasks that have been successfully completed, taking notes on the ones that failed and need to be resolved, and try to be proactive for the newer ones. Sometimes, in the case of an urgent analysis, I also need to continue working from home.

What I like about my work is…

To make things clear, I do love my current position. Although it may appear as a dull, trivial and repetitive job, constant stimulations and updates, as mentioned before, contribute to a continued workflow variability. The main pipeline provides a constant source of work in the form of errors that need to be resolved immediately, or small fixes that need to be applied to the code to keep up with the updated sequencing or analysis options. It is also necessary to understand both code and wet lab protocols to be able to best communicate with all layers of the core facility. That leads to the communication aspect of the job; there is a demand for clear and transparent communication throughout all parts of the core facility. I need to be familiar with all the colleagues working or run the lab so that we can promptly resolve any issues that may arise.

Another thing that I like is that this occupation provides me with the option to leave work in the office and enjoy other activities, such as meeting with friends for dinner, going to the movies, enjoying a new album I purchased, and many other things that lighten up my day. This is a luxury that I did not have as an active researcher.

My advice to early-career researchers interested in a career in bioinformatics in a core facility…

To forget about projects of your own and think more about using your acquired skills as a service, “for the benefit of others”. In addition, the time spent on reading academic publications is minimized, in contrast to the time spent updating your pipelines, troubleshooting errors, and interpreting results for collaborators/customers. So, in a way, less science and more technicalities.
Bottom line, if you like to code, to dig into manuscripts, to be able to connect lab work and bioinformatics, and code a lot, then you are already halfway there. Working as a bioinformatician in a core facility group feels more like being in the middle of the lab work and the bioinformatics analysis. But if you want to excel, you also need to bring in previous scientific experience.

Top image of post: by liyuanalison from Pixabay. 

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