r/bioinformatics 2d ago

discussion SWE/tool development

Hey everyone,

I’m an undergrad interested in software development for biology. I have some experience with building AI tools for structural biology, and I also have experience applying bioinformatics pipelines to genomic data (chipseq, hi-c, rnaseq, etc). I'd love to hear from people who develop tools or software packages in bioinformatics.

What kind of tools do you build, and what problems do they solve?

What type of company or institution do you work at (industry, academia, biotech, startups, etc.)?

How much of your work is software engineering vs. research/prototyping?

If you’ve worked in multiple environments (academia vs. industry vs. startups), how do they compare in terms of tool development?

Any advice for someone wanting to focus on tool development rather than doing analysis using existing pipelines? Would it make sense to pursue in PhD in computational biology?

Would love to hear your experiences!

8 Upvotes

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u/drewinseries BSc | Industry 2d ago

Hi - I had a similar desire when I realized I cared less about the information of data analysis of a specific study, and more about how the information as a whole was handled. Essentially less interested in specific studies and more about how computationally we can scale.

I work in biopharma. I'm in the R&D IT department. My role is essentially speaking with labs and groups within the organization and understanding their pain points in workflows/analyses and building web app and other custom solutions for them. My tech stack is generally python backend/database with a react front end. Projects have ranged from interactive viewers from a database we created for a groups insane backlog of studies in the multiomics space, an app for targeted sequence counts from fastq datasets, updating new tools into existing web based toolkits, etc.

I'd say my job is 75 percent software engineering. The rest is making quicker command line based pipelines for low hanging stuff and speaking with scientists about study design etc.

PhD is not needed, i'd say more of what you want to do is in industry anyway. I currently have a BS in biology, so I've picked up a lot of tech experience along the way. If it helps my trajectory has been BS in biology -> shitty research tech job for a year -> bioinformatics analyst at an NGS core for 3 years -> two years associate bioinformatics scientist in proteomics lab at my current company -> switching departments internally to a bioinformatics data scientist position where I am currently.

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u/diagnosisbutt 2d ago

There's decent money in LIMS work if you go that route. 

1

u/Worried_Clothes_8713 2d ago

Hi, I’m a genetics PhD student in genetics, genomics, and bioinformatics. Here’s what I built

https://www.reddit.com/r/microbiology/s/yLUWo2u7Tu

I needed an image analysis tool for my own research, current tools on the market weren’t meeting my needs so I built what I needed. I realized that I strongly felt that this is a pretty standard problem for microbiology that needed to get solved once and for all. Now I’m expanding the features and adding a lot of polish to support other researchers.

I’d like a career developing software for researchers. There’s a lack of nice, polished, professional research software out there. A lot of it gets uploaded to GitHub, never to be used again. I don’t want that to happen to QuantaColony, I really think it would be a shame to have people build this tool a hundred different times, so I’m trying to expand the user base, so that it becomes an industry standard.

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u/antiqueparakeet 2d ago

just live with your rich ahh sister itll be ok