I am biomedical scientist considering a switch to computational biology (specially computational immunology). I would love to get to a point that I can get a job in it in the next 6 months. Any tips will be much appreciated.
Ask HN: Best way to learn computational biology/immunology?
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Re: Ask HN: Best way to learn computational biology/immunology?
#2[deleted]
Re: Ask HN: Best way to learn computational biology/immunology?
#3Are you specifically interested in immunology? Computational biology is a pretty broad umbrella. My personal experience was learning bioinformatics, which was heavy on Python and genomics/proteomics.
A brief search for comp immunology turns up things like data mining and mathematical modeling, I would assume Python and R would be a good place to start. You may even be able to find some lectures that cover some of the basics online.
Re: Ask HN: Best way to learn computational biology/immunology?
#4The vignettes for Seurat are the place to start.
Also, I'm a founder at Immunai and this is literally what we do. Please dm if you have further questions. Happy to help however I can.
Re: Ask HN: Best way to learn computational biology/immunology?
#5I think one of the easiest ways to get into it is by knowing how to use a software called MaxQuant Perseus (https://maxquant.net/perseus/). It's like advanced Excel that was designed so scientists don't have to learn R but still get the job done. Good luck with your journey!
Re: Ask HN: Best way to learn computational biology/immunology?
#6Knowing how to do programming is a must: Python, R(both are quite popular). Being hands-on with Linux helps as well, as many real-world datasets won’t fit your laptop, so you’ve got to use high-performance computing infrastructure. But it’s mostly about being able to make inferences from data. You need a solid stats background for that.
There’s a ton of courses online and https://www.edx.org/bio/rafael-irizarry is a good start.
Re: Ask HN: Best way to learn computational biology/immunology?
#7I think one of the easiest ways to get into it is by knowing how to use a software called MaxQuant Perseus ( https://maxquant.net/perseus/ ). It's like advanced Excel that was designed so scientists don't have to learn R but still get the job done. Good luck with your journey!
You probably won’t go far by just looking at MaxQuant. But here’s a good introduction to proteomics https://statomics.github.io/pda/pages/techVideos
Re: Ask HN: Best way to learn computational biology/immunology?
#8The vignettes for Seurat are the place to start. Also, I'm a founder at Immunai and this is literally what we do. Please dm if you have further questions. Happy to help however I can.
>>> vignettes for Seurat are the place to start
Wow, incredible resource! Thanks for linking it up. Looks like the raw dataset is compact enough to run experimental inference right on your laptop ;)
A somewhat related, but certainly left-field question: is there a similar tutorial / library for exploring the frontiers of quantum computing and neuroscience?
Quantum Computing at the Frontiers of Biological Sciences
Re: Ask HN: Best way to learn computational biology/immunology?
#9I think one of the easiest ways to get into it is by knowing how to use a software called MaxQuant Perseus ( https://maxquant.net/perseus/ ). It's like advanced Excel that was designed so scientists don't have to learn R but still get the job done. Good luck with your journey!
You probably won’t go far by just looking at MaxQuant. But here’s a good introduction to proteomics https://statomics.github.io/pda/pages/techVideos
A biomedical scientist probably has a good base in proteomics already, learning the ins and outs of the tools used for research would be the best option for a bio scientist wanting to get into the computational side of things.
Re: Ask HN: Best way to learn computational biology/immunology?
#10Computational biology is a pretty broad term. Usually things that have to do with computers & biology are bioinformatics or computational biology. Briefly, for bioinformatics you’d need things like C++ under your belt and interest to come up with ways to make things work really fast and optimal on huge sequencing datasets.
Comp bio is a super fun field to be in. For me it's mostly using computers to do biology. But it’s a mixture of domain knowledge in bio, a good grasp of stats, and a whole lot of programming (usually not terribly difficult tasks, though).
Basic python and R are what you absolutely need to know (I started with intermediate python, no R). To do comp bio well, you need to learn computational statistics. I can’t stress enough how much knowing statistics matters in this case because there are so many assumptions that all sorts of libraries make about sequencing data and you need to decide for yourself how you’ll go about things and produce good science.
On a practical level for comp bio, I suggest: 1. Learning python & R 2. Basic knowledge 3. Knowing what your fave labs use for techniques (eg NGS? What kind of NGS?) and learning how it works, 4. Learning probability & statistics (lin alg always helps too) 5. If you got bored, learn clustering methods... Because, good god people in this field love seeing pretty tSNE figures and 98% of them have no idea how they just produced what they did but make biological assumptions based on it. You’ll probably have to learn them anyway