Three days ago I began a new job as a Research Assistant. I have a bachelor's and master's degree in Biology, and have a very small experience with coding, database management, and bioinformatics in general that comes from younger years when I toyed with turning my computer into a Linux system and attempting to learn code.
With that being said, I am not scared of a terminal window and I'm confident in my ability to "complete" tasks using online resources. Notice I said 'complete' and not entirely 'understand'. I mean I can probably download a tool (for instance, bedtools) and then find a command line prompt entry from another user and then use it to complete a task I have been assigned.
Now the reason I'm here: I have background in academic research, and when applying for this position I was told that I'd have to manage a MySQL database, and potentially work with python script pipeline that has already been written by someone else. Now I have some experience in MySQL databases, I can run commands (
count(*), create a DB, create a table, etc.) and I have a little bit of experience with Python scripting (I could potentially write very short, basic scripts if required). After having interviewed, I was offered the position.
My first two days I was tasked with recreating images (boxplots, heatmaps, annotation of peaks) from a paper that a lab member had generated. This was extremely easy ... The python scripts were already written, I literally just had to open up a command line and follow some very broad documentation that was provided to me by the graduate student on how to generate all these images and type in a command and poof these images were generated for me.
Now however, I am the ONLY computer-enabled person in my lab, and I have officially taken on the role of "lead Bioinformaticist" or "computer guy" as they call me. The PI has told me that my first few weeks are going to be dedicated to taking care of our current MySQL database, and python script pipeline and helping other members of the lab generate computational analysis data before I start "lab research" which is what I am trained in. This scares me, because I have Ph.D and Post Doc students asking me to help them generate either images or databases of peaks, or information that I just don't know how to begin generating. Being only my fourth day into this type of work I am very afraid that I will be un-able to complete these projects or help these students get the information they require to finish their dissertations.
I've spent hours researching online how to try and get the information they require, but I'm often met with technical answers that I only understand at literal value (for example, if I am attempting to research how to analyze ChIP-Seq data to find peak overlaps within four different BED files, I will usually find some sort of
run multiintersectBED -a -b FILENAME FILENAME > OUTPUTNAME and if I happen to be unable to get this command to run ... then I'm pretty much shit out of luck and have to find another command that will hopefully work.
I guess the question I'm asking here is: is this type of work something I can learn with no previous experience on the job? If I have absolutely no idea how to generate bioinformatic data that someone asks for and I can not find or comprehend the information online then how would I ever start learning how to generate this data? (please keep in mind, no one in my lab would be of any use, even the PI) ... How do I practice common practices such as DNA alignment, gene and protein peak annotation, creation of bigwig files, bedgraph files and many other tasks I have completed over the last few days without access to the scripts already designed in the computer? How did the old lab member (who was a computer science guy) even begin to create these scripts? (I don't have access to his e-mail, and even if I did I am not sure he would take the time to teach me how he built these scripts from the ground up).
I know the questions are broad, but I'm panicking.
Thank you for any help.
"The imposter syndrome is strong in this one." - Yoda (during his post-doc years)
Don't worry, its extremely common in Biologists who switch to Bioinformatics - all of us go through it, but you will get there in the end :)
Only two bits of advice I can think of are:
Find a mentor. Ideally someone in the building you can go to for support. In Bioinformatics it's often the case that when you're totally stuck, you're doing something wrong. If you have someone to talk to, a seemingly inconsequential "have you tried X?" will save you weeks of work (happened to me just the other day actually). If there is literally no one where you work, you can try making friends on IRC and people there will reassure you.
When your usual support group fails - use Biostars! Just remember that questions here have a very wide audience, so you'll do yourself and everyone else a favour if you keep your questions succinct, use screen shots/sample data where you can, and try very hard not to XY-problem people. It's obviously difficult to know when you're XY'ing, so get in the habit of stating the problem first, and then concluding with the reason you want to solve the problem in the first place.
All the best :)
I didn't know Yoda did a Post-doc! ;-)
In the netherlands we have a saying: In the land of the blind people, the one-eyed is the king. You work in a lab where no one knows what to do with bioinformatics so everything you do will be very helpful to them. Don't worry, be inquisitive, ask questions and you will learn yourself.
Being the only one with expertise also brings enormous responsibility. If nobody questions your work, errors will easily remain undetected and you will have to do a lot of literature work to keep up with developments and methods as well as to understand existing approaches. I doubt that you will find the time to do that being the one-eyed king of Bioinformatics ;-)
But even if nobody in your lab is into Bioinformatics, you will likely find other Bioinformatician at your campus. I urge you to contact them and probably participate in their seminars etc.
PS: I generally think that everybody has the ability to learn everything (besides some might learn particular things faster), so you can learn also how to program etc. But, if you are not willing to or are really afraid of it, you are probably not the right person for that job. This may sound hard, but you might be much more happy with a different position and if this is the case: quit and look for something that makes you happy!! ;-)
PPS: But at least give it a month or so and start simple and with small tasks. Feeling overwhelmed in the first few weeks at a new position is totally normal - as I experienced recently too when I changed my position. Heads up!
We believe that this post does not fit the main topic of this site.
“Fear is the mind-killer.” -- Frank Herbert
For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.
If you disagree please tell us why in a reply below, we'll be happy to talk about it.
Not sure this question should be closed. Should we help this bioinformatician in trouble? I know other people in this situation.
Let's re-open it as a Forum question for a few days, and in case people feel it is not appropriate, we will close it again.
I think people are getting a little too happy with the close-hammer these days. This is a legit request for help, even if broad, and a snarky close reason doesn't help anyone.
I agree closing questions should be reserved solely for topics that have nothing to do with bioinformatics.
I think reclassifying it as a Forum question is the best thing to do. We should probably improve the description of the post categories here in Biostar, because they are not clear and new users can be confused.