Forum: Too late to switch to Bioinformatics?
3
gravatar for taneuroth
3.6 years ago by
taneuroth30
United States
taneuroth30 wrote:

First let me apologize if this is not the kind of question this forums is intended for.

I am a senior CS undergraduate getting ready to apply for grad school.  I have a lot of interest in bioinformatics, but unfortunately this interest came late in my education and I have not yet taken a single biology or chemistry class. 

I'm feeling that getting up to par in biology would take too much time and I could barely fit Biology 1A into my schedule before graduation. 

How much biology and chemistry do you need to learn before doing bioinformatics or computational biology research?  Is it feasible for CS student to do this late in their education?

I am considering self study in biology and chemistry.  What specifically should I focus on (what do I need to know and what is safe to ignore )?  Or should I just work my way through standard text books? 

Thank You

education forum • 3.5k views
ADD COMMENTlink modified 3.6 years ago by lchau9120 • written 3.6 years ago by taneuroth30

Doing a masters in bioinformatics as a CS grad is feasible (but check the relevance of the course first). I've seen plenty of good MSc graduates via this route.

ADD REPLYlink written 3.6 years ago by Alastair Kerr5.2k
10
gravatar for Pawel Szczesny
3.6 years ago by
Pawel Szczesny3.2k
Poland
Pawel Szczesny3.2k wrote:

You are worry about the wrong thing. Have a look at the resume of Robert Edgar and see his publication record

Worry about building useful things, not about being too late. The party ain't over.

ADD COMMENTlink written 3.6 years ago by Pawel Szczesny3.2k
4
gravatar for predeus
3.6 years ago by
predeus400
Russia
predeus400 wrote:

I walked even more bizarre path - after getting my PhD in organic chemistry, I first switched to molecular dynamics, where I learnt some coding, and then to bioinformatics, or more like computational biology. So yeah, it's possible :) However, it will not be easy. 

However, you have to accept one thing - bioinformatics is not about coding, it's about biology. Sure, there's a ton of very bad code in bioinformatics, but it's not because the problems are so hard. It's because people who wrote them are just bad at it. Also, undergraduate courses on biology don't usually even begin to describe stuff you have to deal with in real research. However if you want to take a look,  check out MIT online courses, Coursera, etc. 

Overall, I'd suggest look for a grad school that would teach you biology, first of all - the kind you'd be most interested in. Some schools are very strong in plant biology, some deal with a lot of animal studies, and some others will be the best for human data.

If you explain your interests to grad school coordinators, you might be surprised how responsive they will get. Next-generation sequencing is as hot of a topic as it possibly could be, so a lot of departments and universities already recognize that they don't necessarily know what to do with the data once they obtained it.   

ADD COMMENTlink written 3.6 years ago by predeus400
1

You write: "bioinformatics is not about coding, it's about biology" but it seems to me that you mistake computational biology for bioinformatics. Half of the posters in this forum had never asked and answered a meaningful biological question. That doesn't make them less-scientists or something. Higgs didn't write software for LHC, neither people who wrote that software created fundamental theories in particle physics. 

ADD REPLYlink written 3.6 years ago by Pawel Szczesny3.2k
1

> That doesn't make them less-scientists or something.

In my opinion, it very much does. Without the biology part, bioinformatics is just a lot of crappy unsystematic coding. If you want to learn how to code and solve truly interesting CS problems, this is most certainly not the place to be. 

 

ADD REPLYlink written 3.6 years ago by predeus400

I already know how to program, and grad school in CS isn't mean to teach you that anyways.  I am looking for meaningful algorithmic problems to work on, and hopefully make publications about when I solve them.  Some of my inspiration comes from the CS professors at my university who specialize in algorithms but have branched out into bioinformatics and computational biology.  Their papers are very interesting and employ algorithmic techniques from graph theory, combinatorics, and machine learning,      

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by taneuroth30

Do you think expressing interest in Bioinformatics in my application, despite my lack of biology training, might help or hurt my chance of acceptance? 

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by taneuroth30

I mean, I don't really have any practical experience - I'm not a faculty or anything, so I don't want to mislead you. But I think it should definitely help. Also, try to get in touch with faculty personally, if you're good at that sort of thing. A lot of groups right now are very keen on idea of having their own bioinformatician. And who is better for this than a grad student? 

ADD REPLYlink written 3.6 years ago by predeus400

From my perspective, trying to join a bioinformatics department (such that develops a software) as a computer scientists has a much higher chance of success, than trying to join such a department as a biologist. 

ADD REPLYlink written 3.6 years ago by Pawel Szczesny3.2k

I was under the impression that most american universities did not have a bioinformatics department

ADD REPLYlink written 3.6 years ago by predeus400

It's true that there are few official "Departments of bioinformatics". I don't know how it is elsewhere but forming a new Department is very difficult and fraught with political barriers. Some Universities haven't even started Department of Genetics yet. But, there are many, many bioinformatics programs. From the student's perspective this is all that matters. You might officially belong to a Comp Sci, Biology, Statistics, etc department or a division. But your studies will follow the curriculum of your program. The critical thing in my opinion is to study that curriculum carefully and try to get a sense if it is really a well designed bioinformatics program for your goals and not just a pseudo-program hobbled together from existing materials without faculty who have a strong track record in bioinformatics.

ADD REPLYlink written 3.6 years ago by Obi Griffith16k
1
gravatar for Biomonika (Noolean)
3.6 years ago by
State College, PA, USA
Biomonika (Noolean)3.0k wrote:

As already suggested, take some Coursera (or any other online course) on bioinformatics and see how you like it. In my experience, best way to learn biology is to spend a lot of time around biologists and talk to them a lot. Ask them a lot of questions. Be curious. I never read any of those thick biology books alone at home, but I read blogs (such as http://homolog.us/), twitter (follow people who do what you might be interested in), read papers, take courses (one or two every semester is a good start) and so on..

Last but not least, be prepared that as a grad student your salary will be much lower than what you could get as computer scientist in industry. This is definitely something to consider. I myself experienced CS->Bioinformatics->Biology transition during the last 4 years.

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by Biomonika (Noolean)3.0k

>As already suggested, take some Coursera (or any other online course)

I'm taking a Coursera course, https://class.coursera.org/bioinform-001, through Johns Hopkins.  It just started today!

ADD REPLYlink written 3.6 years ago by taneuroth30
1
gravatar for lchau91
3.6 years ago by
lchau9120
United States
lchau9120 wrote:

I wouldn't worry too much about your background in biology. The bioinformatics program in my graduate school recruits people with backgrounds in computer science or biology, so the coursework consists of both bio and computer science classes. People who are strong in one field take that time to get stronger in the other field. You'll probably be around biologists too, so you'll pick up basic stuff just by talking them. 

ADD COMMENTlink written 3.6 years ago by lchau9120
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