Biotech Graduate aiming for bioinformatics MS leading to PhD

Question

[Ehsan]

Hi,

I am going to sit for my undergrad final exam within a month.I am a student of biotechnology & genetic engineering,in Bangladesh.My expected cgpa is 3.60 on a 4.0 scale.

I dont like wet lab work much.So my teacher(who took my bioinformatics course) encouraged me very much to shift to bioinformatics as i find it too interesting.

Now,um gonna sit for GRE n then TOEFL.n eventually planning for a MS in Bioinformatics in USA.after that i will try to gain a PhD consequently.

now my question is,

1. Will it be so tough for me to succeed in the long run as a biology based graduate(comparing to CSE background graduates)?

2. Even if i succeed,then what areas can be my future sector of work?

3. Comparing to a cse graduate bioinformatician(who has A 4 yr undergrad cse certificate),what are my chances to get a high job?(academic/industrial)

thanks

[Michael]

Hello ehsansuez666666!

We believe that this post does not fit the main topic of this site.

This is not a question the community could answer, and it is not a bioinformatics question.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

[Istvan Albert]

I think questions like this are not off topic. This is a community of bioinformaticians many of whom have troubles assessing their own abilities and future prospects. While I would agree with the sentiment that we cannot predict the future for the OP these questions are more like chatting around a fire in the evening. It is ok to think about these issues every now and then.

Answer 1

[cbio]

You'll be fine. I am a biology graduate, and have been working on computational biology tasks for the past few months. Just a couple of things I wish I had done before coming into the field. As an aside, I work mostly on genomics.

1. Learn UNIX command line
2. Learn Bash
3. Learn GNU Make
4. Learn vim/vi/nano
5. Learn how to use UCSC Table Browser / Biomart
6. Learn a scripting language: Python
7. Learn R

[Thomas]

Hi, a few questions:

What is the advantage of learning GNU make?

What is the benefit of using Python instead of say Bash and/or R?

Cheers

[cbio]

There are probably not many advantages of GNU make over say, Snakemake or Ruffus for creation of pipelines. I myself use Snakemake because it's so powerful and easy to use. However, most of these are based off GNU make so it's nice to have a little bit of experience with it. You don't have to use it for automation tasks, but it's easier to learn Latin if you already know Spanish.

Python was just a simple example of a scripting language, it's generally the most favored due to a lot of different things here on Biostars, you can find more comprehensive lists of pros and cons for most programming languages with a quick search using the Biostars search bar.

R is great for creating publish quality figures, and when I say you should learn R I mean you should learn ENOUGH that you can generate these figures easily, and run some of the Bioconductor packages that can be very helpful for solving specific problems that might not be as straight-forward in Python.

In general, ANY language you WANT to learn is fine. If you'd rather learn Ruby, or Java, or Julia or whatever, they all should be fine. There are bioinformatics tools out there for almost any language. Python just generally is the most often used in bioinformatics, and thus leads to more job opportunities.

[Istvan Albert]

today if I had time I would learn Nim: http://nim-lang.org/ why:

Nim produces small executables without dependencies for easy redistribution

[cbio]

This is pretty cool.

You would learn this in place of Python or you would learn it in conjunction with Python?

What I mean is, if someone was barely starting Bioinformatics you would suggest learning Nim before Python?

[Istvan Albert]

Well of course it all depends of what one is after. If it is straight out data crunching then Python/R are the way to go. But it is important not to "chase the past" but look to the future.

I learned Turbo Pascal first, then C, then Perl, then Java and then finally Python, although admittedly most of the work was not related to bioinformatics. Overall I think it is good to start with the more difficult languages first, julia is also interesting.

I like nim and languages that create small standalone executable because these will run on small devices, like phones. I think the time when we sequence with our phones is not that far out - it will be wild!

Answer 2

[ablanchetcohen]

Your cGPA is rather low for a foreign student, which may be a problem when you apply for Master's programs, and scholarships.

1. Computer Science and engineering students have weaknesses in biology, so having a degree in computer science and engineering in bioinformatics has its own disadvantages. Of course, those students always have the option to ditch bioinformatics for a higher salary. No one is an expert in all fields. If you believe you have weaknesses just work on them. You'll definitely want to learn one or two programming languages, how to use the Unix command line, and some basic statistics.

2. With a Master's, you can be an analyst. With a PhD, a successful post-phD, a lot of luck, and good contacts, you can be a principal investigator.

3. If the CSE student is applying to CSE jobs, he will get a higher salary. If you're both applying for bioinformatics jobs, you will be on an equal footing. You may have weaknesses in programming, but he will have weaknesses in his knowledge of biology.

Answer 3

[oi.bioinf]

There is a bioinformatics subreddit, where I've seen a lot of these types of questions. You could try to search for replies there, it could be useful also to know, which way others people choose and why.