My first year as a PhD student: short summary

In November last year I got accepted into a PhD program in Bioinformatics at the Department of Biochemistry and Biophysics, Stockholm University. Becoming the next Sonja Kovalevsky*  was my long aspiring goal ever since…

Ok, I don’t actually remember when the idea to become a researcher got into my head. Perhaps when I was sitting at my first math lecture at the Bauman University or when I learned about Rosetta (a computer program that is predicting 3D structures of proteins using machine learning algorithms) or when I realized that I need a greater challenge in life than just writing PHP code 9-5.

For some reason I thought less about my ability to actually do science or the exact way I will accomplish a great life of daily contributing to the common knowledge, but someone told me that a PhD degree is what you need first…

So long story short, here I am, finishing my first year of a PhD program.

Some numbers:

Times I changed my main supervisor  1
Times I considered quitting  100?
Times I thought it’s the most awesome job ever  100?
Times I rejected a job in the industry with a much higher salary   5
Papers published  1
Papers in review 1
Credits earned  18.8 (~4 months of studying full time)
Programming languages learned 1 (R)
Programming languages improved 1 (Python)
Papers I read about my research topic(s): ~100-200 


Lessons learned or  “I wish a year ago I knew that…”

  • Most bioinformaticians can’t program and don’t even now that
  • No one cares about well written code in academia
  • Software is not the center of my life anymore. Results are.
  • I will be working alone 99% of the time
  • I’ll feel stupid and useless 99% of the time
  • Research project is 60% trying to figure out what to do and how, 10% actually doing it, 30% trying to interpret your results
  • Academia is really reluctant to change, even in progressive Sweden
  • Many PhD students are very unhappy human beings (been one of them for a while)
  • After graduation ~80% of PhDs don’t find their experience related to the jobs outside academia
  • The most important choice you make isn’t even your research topic, it’s the supervisor
  • Ok, picking your research topic is important as well. Make sure you believe in the direction you are going and enjoy working with it.
  • It’s important to learn to let go: let go of the useless results you produce, of the code you’ve written for 3 months to obtain them and of countless meaningless things you need to do just to get through the PhD studies.
  • It’s really important to stay healthy: exercise and eat well. Stressed and depressed brain(at least mine) is not productive at all.
  • Effective time management is the key: prioritize and do one thing at a time.
  • Learn to write well, starting now.

The above being said, it has been one of the most interesting and challenging experiences of my life and when I actually manage to keep the big picture in mind, I feel like I’m on the right track. Whatever the next step might be.


*  did you know that Sonja, or in Russian actually, – Sofia Kovalevskaya
became a professor at SU, because in Russia she wasn’t allowed to work as a lecturer, being a woman and all.


  1. Hi Oxana, kudos for having the insight to take such a summary of your life as a PhD student after one year already. I wish I’d have thought of that when I was one year into my PhD.
    While my personal experience differs in the details, I think I’d agree with the general assessment you take in the “lessons learned” section, I pretty much felt the same way when starting out. After playing this game for a while now, I’ve found a couple of things that help to keep me going. Maybe one of them might help you and other people as well.

    On the “most bioinformaticians can’t program” part, I’m not sure how many programmers in out in industry can. I’ve found that Michael Feather’s book “Working effectively with legacy code” was a help with dealing with other people’s code when I had to, or at least made me feel better because obviously enough people had these problems that a publisher felt like printing a book about this. 🙂

    I agree that very few people care about well-written code in academia, because novelty trumps maintainability, and most code is probably written by PhD students with no experience in code maintenance whatsoever.

    I’ve had the luck to be working with a collaborator for one of my larger projects, but in my lab I was the only bioinformatics person, so I can relate to the “working alone” part a bit. I’ve found it very helpful to network with other bioinformaticians. Twitter is very useful for that.

    I think the “feeling stupid and useless” sadly is common when doing your PhD, and in my experience mostly a case of imposter syndrome and very unjustified. I’ve tried to work around this by setting small iterative goals I could reach every day/week, and keeping track of my success there. That at least helps with the “feeling useless” part. I think feeling stupid comes with the territory of doing science, otherwise it’d be engineering. 🙂

    1. Thank you for your comment, Kai.

      I do try to interact with other bioinformaticians and initiate group projects to avoid being stuck and feeling isolated.

      Setting small iterative goals is very important and reviving the interest in the subject after an unsuccessful period is another key to thriving in academia I think.

  2. A good post, the point about the supervisor is excellent. A good supervisor and lab group are critical.

    Also when deciding on if a supervisor is good or not don’t necessarily rely on other peoples opinions. Instead you need to make sure they’re a good supervisor by your own definition.

    I’ve known some people who thought there supervisor was great because he’d ring them up if they were 15mins late to the lab in the morning and ask where they were, and would constantly check up on them to make sure they were working…
    Another friend would bike to work with his supervisor, have morning & afternoon tea breaks with them each day etc
    And then other supervisors who’d organize a meeting once a month or so and otherwise just left their students to get on with the research, but was happy to take the time to go over papers or aspects of the research when the student got stuck.

    Each is a very different style and each suits a different type of student, so it’s critical to make sure the style of the supervisor is one that suits you…

  3. Sounds like students really need to do their research before deciding to pursue a PhD in order to make sure that it’s right for them. However, it is definitely worthwhile if you are passionate about it and willing to put your all into it. Great point about picking the right supervisor; it will make the process so much smoother.

  4. For instance, losing confidence that the novel will be read makes me stop writing, and when I can. It isn’t hard
    to increase motivation for this type of individual,
    because generally all that’s required is the creation of more responsibility for
    them. Another important by product of goal setting is that you will find yourself doing more than you normally would to achieve your goals, because you’ve programmed yourself to achieve success.

  5. Today is the start of the second year as a PhD students. What I learn is the importance of efficient, because I thought too much but did a litter and no output last year.

Leave a Comment

Your email address will not be published. Required fields are marked *