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So I'm a rising sophomore in my university and have been doing research for a year now. I joined my first lab in my first semester as a part of a program but didn't like the topic that much and joined a different lab that does research on topics I am interested in at the beginning of my second semester. Since the program I was in with the first lab required me to do research for at least a year, I couldn't quit that lab. Now I can quit it and focus on my other research but I may publish a paper with my first PI this year.

I am not really interested in the topic but I don't want to waste all the effort I've put into this research and lose the opportunity to get a publication out of it. I want to apply to grad school as well and professors I want to work with are in really top universities so I don't want this to hurt me in my grad school application. I will also continue on with my other research this year so I am a bit scared that I won't be able to handle both and higher level classes.(I think I handled them both with my classes well last year but this year's classes will be harder than last year's probably.) What should I do? Should I quit it considering my grad school ambitions?

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Since you are planning to do research in the long term let me break something to you: writing always takes time from something else. Of course, your clases are going to be more manageable if you don't have another 'distraction'. As researchers, we are doing many things on different fronts at the same time: grant applications, publications, teaching, seating in a committee, reviewing a book (my field is book-based), delivering a talk, putting a panel together, etc. 

Considering your grad school ambitions, as you put it, it seems to me you have more to benefit from a publication with this PI than to hurt. First, he can be a potential LOR writer. Second, you'd have a publication in your CV (it doesn't matter the topic, it's a publication). Third, you'll show you can manage your time professionally. Fourth, you'll show you are resilient in your research, ready to collaborate with others. Fifth, the experience will teach you how to navigate the paper-publication world (if you haven't already).*

Now, what you have to do is decide if these benefits are worth your time. I am not familiar with your discipline, so you should evaluate why this move at this time is not in the best of your interest. 

* I say "show" because in our applications we tend to say that we can do X and Y and Z, but with this you'll have evidence that you can do them.  

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