Getting started with bioinformatics 

How old are you ?

you had an interesting story ...tell me which careers do you have?

I'm so glad to hear that! I struggled to find resources when I was starting out too, so now I'm just deciding to make them myself :)

I like this idea, even if I am not sure I am qualified to make any sweeping conclusions. But I am happy to share a few thoughts and predictions based on what I have seen happen in the field so far. Thanks!

Awesome work on the enzyme structure! I think C makes your head explode regardless, so may as well add Python. I found Python pretty easy to learn in comparison coming from C++. Good luck!

I am going to take your advice. Thank you!

I'm so glad to hear that! Thanks for keeping me updated :)

Hi! Can you please add here which courses on Coursera you recommended? I'm a beginner. Thank you! Great work, Maria!

I found them in your HP :)

Rosalind is a good place to start for some basic practice. You can also pick a paper that is using an interesting approach and try to reproduce their bioinformatics results. If you need data, the UCSC table browser has all the same tracks in the genome browser that you can download as bed files, so that gives you something to play with.

Woops; something to add! Glad that you use Argparse. I am the lead on github.com/PMA-2020/argparse-to-web , check it out! It's working great for us, but looks like I need to add external facing documentation.

anglekan I’m interested

I'm also in computer science and interested in Bioinformatics. I emailed a local university about a bioinformatics masters and she suggested basic (first year, introductory) bio courses just so you know what's going on, but she also mentioned it wasn't completely necessary, you'd require a bit of catchup, but if you're genuinely interested in bio I wouldn't worry too much! that's what I've learned :)

For what it's worth, I have an internship in fall in a bioinformatics lab. I'm a CS major.. I asked the employer what knowledge of biology I needed and he basically said I'll learn it all on the job and to not worry about it too much. Results may vary depending on the particular company / lab you want to join though

@@johnfedorov8089 How did it go? Ps. Im a CS major too

​@@aditya9711 Overall it was a very good experience, the first few weeks I had to learn quite a bit about biology / bioinformatics, everything from basic things like DNA and prokaryotes to advanced stuff like sequencing techniques and bioinformatic related algorithms. I helped finish up software thats used for anti-microbial resistance detection (basically to find out if a particular strain of bacteria is immune to certain antibiotics), I also refactored a lot of tools written in R to be used in python instead for efficiency reasons and integrated them with their computing clusters.

@@johnfedorov8089 hey John, what do you think helped you land the internship? Any projects you had on there that are related to Bioinformatics? I am currently a CS major and have been very interested in pursuing a career in Bioinformatics. Any tips or advice would be appreciated, thanks.

Hey! Great question. I'll give some general advice for anyone else reading this before asking you more about yourself: I think you can essentially jump right in and look for a masters, PhD, or job in bioinformatics, whichever you would prefer :) The biology is always going to be super specific, so you can pick that up by scanning a textbook for context and then digging deep into the research papers. Note that some fields of biology are more geared towards math and physics methods, and you will often find professors with those backgrounds working there. Here's an example: www.cshl.edu/research/faculty-staff/justin-kinney/ Are you looking for a grad student position, post-doc, industry job, or something else? What is your background so far, and where do you want to go next? Finally, what attracts you to bioinformatics?

Hi. Thanks for your prompt reply, and sorry for the delay in mine. That's good news for me. How long do you think it might take to be able to get to the point of being able to read a biology paper and get something out of it. In physics it took me years before I could get to that point and I still find it very hard to read papers. My background is a BS, MS and PhD (expected this summer) in physics. My research is in a more computational, statistical/stochastic modeling of inverse problems sort of area. So I think that I am in a good position to go into bioinformatics. I also have some graduate coursework in machine learning and Bayesian modeling. I would like to get a research position in bioinformatics (postdoc if necessary, but hopefully something permanent, although I doubt that'd be an option). I am interested in bioinformatics for the statistical and stochastic modeling that it demands. I am very interested in machine learning/statistical learning algorithm development, really in any field, but I would love it if my work could help people more directly (even if not immediately). Since I am not familiar with what each subfield entails, I don't know what I can say more specifically, but if there is anything in epigenetics that'd be awesome. I would be very interested in genetics of diseases as well. I may have said something biologically unreasonable without even knowing it, so any advice, thoughts, comments and opinions are greatly welcome! Thanks so much!

I think it will be good idea to reach for doctors/ professors that work in that field and ask them what sorts of things you could learn so you can make projects with them or something.

I highly recommend doing Andrew Ng's Machine Learning course on Coursera, from Stanford. He explains everything very clearly, and you can decide whether to follow along and do the linear-algebra-heavy homework assignments, or just get the concepts. Same as the advice in this video, just watching the Machine Learning course will get you that foundation and make you aware of the different techniques, and then you can do a project with a particular technique if you want to learn or if it applies to your research. As an example project, you can download HapMap data and run PCA on it to see if people from different regions of the world separate into neat clusters based on their SNPs. I did that in college (with data wrangling in Python and PCA in Matlab), but I haven't actually used machine learning in my research since. Check out Scikit-learn for doing machine learning in Python (haven't used it myself yet but it is universally highly recommended).

Do you use machine learning or AI in your research and workflow

I think the specification matters most. HP, ASUS, DELL and co.. It should just have more RAM for smooth running like 8Gig upward(I'm a learner using 4Gig and 6gIG PCs though). Nevertheless, there will still be some analysis you can't run on your PC but will have to use an Institution or researcher centre's supercomputer(communicating maybe through a LINUX system from your normal PC). Macbook is great though. I hope this you'll fine this helpful.

Wonderful to see you are starting out and excited about bioinformatics. That's a great question, and it's very dependent on what kind of research you do. Since you already have data, I suggest something like writing a python script that analyzes that data and maybe summarizes it in some way, and maybe it makes a few plots relevant to that data. I can't tell you exactly what to do of course since you know your field and what's relevant for your data better than I do. Good luck!

Biology is a huge field, and therefore so is bioinformatics. We all end up having to focus, so I wouldn’t be too discouraged that you can’t learn everything in detail. The basics are important, but we can also never stop learning and delving deeper into the part we choose to focus on. You may be able to find a postdoc position that requires more CS and less actual credits of biology if you don’t have more semesters in school to get those in. Good luck!

That is a good question. I should definitely do an episode on that. I'll add it to the stack! Thanks :) To answer your question in text form though: From what I can tell, the career prospects for bioinformatics are really good. I recently talked to a professor who pays his bioinformatics post-docs about $15k more per year than the wet-lab post-docs, because that is the market. He also has trouble finding bioinformatics post-docs (and this is an influential, young, successful lab) because they get paid more in biotech industry, or some even run off and do data science at Facebook. So if you are a wet-lab scientist and switch to dry-lab bioinformatics work, you will probably have an easier time finding jobs in academia and in industry, and the ones you get will likely pay you more. Also bioinformatics is fun, and even if you don't decide to switch completely, you still need at least some basic R skills to analyze your own data.

are you asking about jobs you can have without a PhD, or something more along the lines of how to learn bioinformatics as preparation for a PhD?

Yes! I'm not ready to move on the my Masters degree, and I have a degree in mathematics and computer science, but Im not finding too many positions that work for me. Thanks!

That's funny, someone asked almost the exact same question in the comments on my "what is bioinformatics" video. I recommend that you get some familiarity in at least computer science and statistics. You can take some courses online like on Coursera, or check out my R tutorials, especially the Plotting in R for Biologists series -- which happens to be a good beginner introduction to programming in R, which is a great language to start with for bioinformatics in general since so many people are using it in the field.

OMGenomics sorry but, I am not completely dumb in computer science and statistics though, just have some basic knowledge only. And uh didn't clear it for me, if it is a good decision or not. Plz

Well, are you interested in bioinformatics? I can't answer whether it's a good decision without knowing you and your motivations a lot better. You can learn anything, but do you want to?

OMGenomics okay, let me tell you the exact thing, the matter is the universities I applied for life sciences mater's, I cdnt get in unfortunately, n there are still little chances of getting in, so I got this stream as a second priority. I was actually more interested in animal sciences, and if something much more related to animals , bioinformatics can help me to learn , I will choose it. I am more interested in research courses.

Umm those are pretty big questions you have to decide for yourself :)

Hi, I did! I was a software engineer and now i'm doing a master degree on bioinformatics. So you can

Ana Will if a computer science graduate wanna do few biology projects ... Interested in the whole dna thing going around how to start biology is a big topic is there is like small crash course or points that I need to focus in and then I can do cool project .... Or maybe what do I need to know to work with a another biologist.., Oooh also projects like : AI to identify cells that have cancer ( I know for you this may make no since but I hope you know what I mean )

I screenshotted your comment bro because I was thinking about doing a Masters in Bioinformatics but my passion is Medicine, I love computer programming and I love biochemistry but I don't think my passion is purely bioinformatics I think learning the skills themselves are more important than studying it in university, I appreciate your comment and it really helped me think more about what's important to me ^^

Anyone can learn!

Just install it (apt install python) and then start it using 'python'.

Duh 😊

The E on your shirt is in a nice font. - Is that enough of a compliment for you? Dumbass.