Question: How To Get Started In Bioinformatics?
15
gravatar for Oli
10.3 years ago by
Oli180
Oli180 wrote:

I am a Software Engineering student (with decent background in biology) and would like to explore the field of bioinformatics. I am completely new to the field and would like some pointers on where and how to get started.

  • Is there any book I should read?
  • Any interesting online resources?
  • Any interesting blogs / online communities (apart from this one)?
  • What are some of the interesting problems bioinformatics is trying to solve?

Any advice or insight about this industry would be appreciated.

books • 9.2k views
ADD COMMENTlink modified 3.5 years ago by jp110 • written 10.3 years ago by Oli180
3

that's ok, it is fine to ask questions, but it is better if we close this topic and leave the links to other discussions. Otherwise, people will start writing here about their favorite blogs, books, resources, etc... while they should to so in the specific topics.

ADD REPLYlink written 10.3 years ago by Giovanni M Dall'Olio27k
1

Voted down because the question is IMHO way too general; see my answer.

ADD REPLYlink written 10.3 years ago by Egon Willighagen5.2k
1

Sometimes lettings things grow in their organic way my appear inefficient but leads to unexpected features that we did not foresee. Once multiple people have moderator rights then we can all vote on the right course of action

ADD REPLYlink written 10.3 years ago by Istvan Albert ♦♦ 84k

why the negative vote? It is true that the question is a bit too general (in fact, each question should go to a separate topic) but it is nothing so terrible..

ADD REPLYlink written 10.3 years ago by Giovanni M Dall'Olio27k

ok, now I understand... maybe we should close this question and leave the links to the other discussions on biostar.

ADD REPLYlink written 10.3 years ago by Giovanni M Dall'Olio27k

I do agree with your sentiment that this could be closed. On the other sometimes lettings things grow in their organic way my appear inefficient but leads to unexpected features that we did not foresee. Once multiple people have moderator then we can all vote on the right course of action.

ADD REPLYlink written 10.3 years ago by Istvan Albert ♦♦ 84k

I do agree with your sentiment that this could be closed. On the hand other sometimes lettings things grow in their organic way my appear inefficient but leads to unexpected features that one may not have foreseen. Once multiple people have moderator then we can all vote on the right course of action. My personal preference is for people to vote up questions that they like, that way the interesting stuff rises to the top, only down-vote sparingly ...

ADD REPLYlink written 10.3 years ago by Istvan Albert ♦♦ 84k

Sometimes lettings things grow in their organic way my appear inefficient but leads to unexpected features that we did not foresee. Once multiple people have moderator then we can all vote on the right course of action.

ADD REPLYlink written 10.3 years ago by Istvan Albert ♦♦ 84k
21
gravatar for Giovanni M Dall'Olio
10.3 years ago by
London, UK
Giovanni M Dall'Olio27k wrote:

Well, I will answer by redirecting you to other topics :-) :

Is there any book I should read?

Any interesting online resources?

Any interesting blogs / online communities (apart from this one)?

What are some of the interesting problems bioinformatics is trying to solve?

ADD COMMENTlink modified 10 months ago by RamRS27k • written 10.3 years ago by Giovanni M Dall'Olio27k
5
gravatar for Brandstaetter
10.3 years ago by
Brandstaetter270
Austria
Brandstaetter270 wrote:

Does your university offer bioinformatics courses? It might be a better place to start asking there...

Books: can't really recommend any. There are too many different sub-fields in bioinformatics

Online: depends what you're interested in, again.

Blogs: not really, I think. If you find any good ones, let me know.

There seem to be two opposing sides to bioinformatics currently:

  • those who studied microbiology and use bioinformatics as a tool (maybe even cobble some scripts together)
  • those who come from the software engineering side and build tools according to these standards.

Problems in bioinformatics:

  • sequence analysis, including sequence matching/searching (BLAST et al.), also databases
  • image processing (electron microscopy analysis, microarrays)
  • structure prediction (protein structure, see Folding@Home and others)

Many of these include high performance computing, so you might want to learn stuff about that.

Your question is rather broad. How did you find out about bioinformatics? What made you interested in this field?

ADD COMMENTlink written 10.3 years ago by Brandstaetter270
5
gravatar for Khader Shameer
10.3 years ago by
Manhattan, NY
Khader Shameer18k wrote:

I think the best way is to get in to a lab for a rotation project / part-time project depending on your schedule and work on a live project. You may either help the group to code something, they can help you to get familiarize with some common bioinformatics tools and approaches. I think this will be the best way.

If you can work on your own, pick your language (Perl, Python, Java, Ruby) send a mail to respective bio* mailing list. You will definitely get a small project. You can help the open source community and also get to understand the field and its generic requirements.

Go ahead, Future is Open, Bioinformatics is Open. All the best !

ADD COMMENTlink written 10.3 years ago by Khader Shameer18k
5
gravatar for eka.chaykina
7.5 years ago by
eka.chaykina50
eka.chaykina50 wrote:

You can also check out ROSALIND - a free and open online educational platform for learning bioinformatics through problem solving and programming. Now there are around 90 published problems. It is quite interesting!

ADD COMMENTlink modified 7.5 years ago • written 7.5 years ago by eka.chaykina50
4
gravatar for Egon Willighagen
10.3 years ago by
Maastricht
Egon Willighagen5.2k wrote:

Note: the below answer is meant to be constructive. The best way to start in any field is just to listen, learn, and do something. By actually doing something, you best show your intentions, and you get more people listening to your questions.

I am pretty sure Google can help you with getting started, and otherwise have a look around at this forum for topics you like. I have seen questions like yours many times, like so many others before you, you have no idea where to start.

However, like all those before you, you make a classical mistake: you forget to formulate what you really like to do. Never ask others what you should do (with your life). Instead, use Google to read up on topic, look around at (Open Source) bioinformatics tools, possibly get additional non-IT education, and decide for yourself what domain question you have. Only then you should start asking around how to proceed.

The reason underlying this, is that those reading your question, like me, have no clue about your background, your interested, while at the same time, there is so many interesting things to do. You basically ask us what is the answer to the world, but I am pretty sure 42 is not the answer you are looking for.

So, first do some research yourself, pick a topic yourself, formulate questions you have on that topic that Google, Wikipedia, your university courses do not tell you, and then pose those questions.

ADD COMMENTlink modified 10.3 years ago • written 10.3 years ago by Egon Willighagen5.2k
1

You're basically telling me to Google instead of asking here. I thought I'd get a more insightful answer here than from Google but apparently, you are not interested in helping out "newbies" which I can understand.

ADD REPLYlink written 10.3 years ago by Oli180
1

"you forget to formulate what you really like to do. Never ask others what you should do (with your life)." was somewhat an overstatement. All I was asking for was book recommendation, not life advice. And I did formulate what I was interested in: bioinformatics.

ADD REPLYlink written 10.3 years ago by Oli180
1

Oli, you are misreading my answer. Asking here is fine, but you are doing it the wrong way.

ADD REPLYlink written 10.3 years ago by Egon Willighagen5.2k

I understand you get this kind of question a lot, but you could've simply ignored it or at least let me know it wasn't appropriate on this forum - in a non arrogant way.

ADD REPLYlink written 10.3 years ago by Oli180

And for the record, you asked for online resources: Google is an online resource. Alternatively, you could have just split up things and asked "What Bioinformatics blogs can I read to learn about Bioinformatics coding?"... then you would have posed a reasonable answerable question.

ADD REPLYlink written 10.3 years ago by Egon Willighagen5.2k

"And I did formulate what I was interested in: bioinformatics." Bioinformatics is a very broad subject, he's just saying that you should narrow it down.

ADD REPLYlink written 9.8 years ago by Niek De Klein2.5k
0
gravatar for jp
3.5 years ago by
jp110
jp110 wrote:

This is four years late (I know), but I wrote a small blog post with some links to good introductory articles which serves as an introduction to the bioinformatics field (especially for someone with a CS background).

https://bitsilla.com/blog/2016/12/bioinformatics-starter-pack-getting-started-in-bioinformatics/

ADD COMMENTlink modified 13 months ago • written 3.5 years ago by jp110
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