Forum:Would reaching out to local labs and startups help with my career transition?
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8 weeks ago
Mango ▴ 10

I'm a software engineer with 8 years of experience looking to transition into bioinformatics. I've been doing some Coursera coursework recently to get a grasp of the underlying concepts and it's pretty interesting. It's cool to see how different algorithms that one studies for regular coding interviews are used for things like, say, finding optimal alignments of two DNA strands. However, these courses (made by Pavel Pevzner and Philip Compeau) don't seem to go over much of the actual tools that are used. They focus more on the underlying theory and algorithms.

I've also checked out two O'Reilly books from the library about data bioinformatics computer and data skills and I plan on going over those. I've also purchased the BioStar handbook and plan on going over that.

Still, the process of going over all these different sources will take a while and won't really give me real world experience. To be honest, I've found that real world experience tends to be a better way to learn than just taking courses and going over books. So I'm wondering how I can get some of that real world experience.

Would reaching out to local universities, professors, labs, and non-profits help? I live in the Bay Area, so Stanford and Berkeley are right in my backyard. I'd be open to volunteering or being an assistant. Is that something people do? What do people normally do when they want to transition into bioinformatics and need real world experience?

Also, how exactly would I reach out to these institutions/people? Would I just cold e-mail them? What would I say?

career volunteering • 542 views
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What sort of position do you envision long-term? So ideally, what would your work be?

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8 weeks ago
dsull ★ 5.8k

Went to Stanford for college -- I'd reach out to professors there and ask them if you can be in their lab. They're generally more hesitant if you ask to get paid (but I don't think working for free after being a software engineer for 8 years is really that wise) -- though with your background, you might be able to find a paid position. I would just cold email them and CC the lab admin (if you don't get a response, reach out to a postdoc or grad student in the lab). Attach your CV.

It seems like you care about using tools rather than developing those tools and their underlying algorithms. I think a way of getting that experience is just to take a paper, reproduce it, and then extend the analysis.

But yes, reaching out to professors to get real-world experience helps -- Stanford professors have access to rich datasets and there are a ton of analyses you can do for them depending on what the PI is interested in. I worked in the school of medicine as a wet lab biologist, then, one day, we received FASTQ files, and then I picked up analyzing those haha. It was that experience where I acquired skills as a bioinformatician, not any course I took nor any book I read.

Edit: Also consider UCSF. Some of the best computational biologists are there.

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8 weeks ago

If you want to develop tools:

As a software engineer you can make a big difference to many open source projects. Browse github, contact the dev to check their interest, and see if you can contribute. Most devs are more than happy to have input.

If you want to use tools:

Also, pick a couple of small projects, eg bacteria.

  • Get reads from https://sra-explorer.info/
  • de novo assemble the reads with the spades tool
  • annotate genes, eg with prokka
  • use blast or interproscan to annotate output sequences

You'd learn a lot and face a lot of challenges in a small project like that.

Learn to read papers, eg on bacterial genome assembly and annotation, and especially the methods section

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8 weeks ago
GenoMax 141k

This is a two way street. People will need to put in a significant amount of effort/time to bring you up to speed. So simply reaching out to people may not bring immediate results. You may need to see if you could get a 30 minute meeting so you can convince the person of your genuine interest. Try to see if there are any local user group meetings that you could go to and network with others.

I will link your prior related question here to give people some additional information : I’m considering a career transition from software engineering to bioinformatics. Is it a good fit for me?

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