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An orphan bioinformatician

Not a post with code or plots today, but some worries. I’m a PhD student with a Masters degree in Biochemistry and biotechnology, and my (bio)informatics training is almost non-existent. And yet, that’s what I do for more than 3/4 of my time in my PhD research.

Mick Watson introduced the concept of a pet bioinformatician, “a single bioinformatician employed within laboratory based group”. However, since I’m not a full-grown bioinformatician I consider myself an orphan bioinformatician. The department and research group in which I work focusses mainly on genetics and (functional) wet lab work, with two central bioinformaticians handling most of the requirements for the researchers with standardised pipelines. As such the average scientist has a limited understanding of the “bioinformatic black box” which happens between handling the samples to the sequencing core and looking at variant tables. RNA-seq goes from samples directly to differentially expressed genes and deregulated pathways. Those two bioinformaticians are great and I can often ask their help, but they obviously lack the time to fully supervise my work. And they like different programming languages.

I started with a “typical genetics” project, but quickly I felt the call of the dark side and started focussing on bioinformatics. I’ve followed some excellent courses from the VIB Bioinformatics Core to get me started with coding, but that’s obviously not sufficient for learning good practices. While the internet is great for finding bits of code and asking questions, I guess having more appropriate supervision would be beneficial for my development. I’m looking for recommendations on how to overcome this issues. And very specifically, if someone would have the time to review my code (mainly Python, rarely R), that would be great.

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2 thoughts on “An orphan bioinformatician

  1. I understand your situation, have similar issues, though I have CompSci background, and I would say it plays crucial role. I think you should polish your pure programming skills, go to some IT conferences (non-biology related), join open source project (but one with active discussion, chatting rooms), commit issues on github when you have smth to say about your favorite tool, it usually triggers the dialog.

    Based on my experience randomly going through tutorials is useless unless you have at least some little task you want to implement. For example, you may want to reproduce plots from the papers you like or from classical tools such as FastQC (though I think it is a trivial comment and you know it better then me). If you want people read your code and comment you can try to implement a small, but useful utility, push to github and post on biostars to attract users, if people like what you do they can eventually give advises or even commit pull requests.

    You may try to look for a collaboration on your own, especially if you can apply for a personal grant and if your supervisor does not restrict you to do so. In my case it was a starting point, I got to know people, they introduced me to another people and so on. It is different from posting your problem on some forum as you said yourself, because asking someone directly is quicker and you can get more detailed answer. But finding your own personal collaboration requires communication skills, and I would say sometimes it is more important than your current portfolio.

    Also, try to look for some challenges (e.g. http://dreamchallenges.org/), you can use past iterations, because they provide answers to the problems, this way you can train yourself in algorithms.

    Hope it helps at least somehow…

    Liked by 1 person

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