Question: Biology side of bioinformatics
1
gravatar for dshulgin
6 months ago by
dshulgin250
Belarus
dshulgin250 wrote:

Hi, everyone!

I was thinking about what i should know in biology as a bioinformatician? I came in biotech with CS background, so i guess that i'm a programmer mostly, but i really like to study biology, especially cell biology and gene interactions. But where is the finish line? I understand, that as CS employee i should know technical part preferably, but i feel that i have to know more in biology to ask the right questions while i'm solving bio issues. What would you recommend me? How employer usually estimate bio background of non-biologist? Is it serious? Where is the minimum that's required for bioinformatician?

I'm reading now Albert's (Essencials of Cell Biology and Molecular biology of the Cell as well) just to make my general knowledge of biology better. I've heard that's pretty good biology books.

Thanks.

biology gene genome • 349 views
ADD COMMENTlink modified 6 months ago by diallobakary40 • written 6 months ago by dshulgin250

hi, WouterDeCoster's suggestion is right. Thats a better approach to 'get a hang' of problems biologists face. Apart from rosalind, I would recommend checking out people who have successfully bridged CS/ non-bio background with intresting bio. research themes. Pavel Pevzner's courses on Coursera are very motivating in that respect.

In context of getting up to what's hip in biology, following News section of popular journals like Nature/ Science is a good place. These are not jargon-thick and easy to absorb and of course fire your imagination. Also occasionally checking science blogs (e.g.) or following popular science writers/ communicators (e.g. 1 & 2) on twitter are fun way.

ADD REPLYlink written 6 months ago by Amitm1.2k

I know all of these resources, but the main point is all of them we can call as "biology for programmers" but it's not good, i suppose, because it gives you only projection of whole processes in DNA.

ADD REPLYlink written 6 months ago by dshulgin250

I really like the old school approach, reading a book is a great way to get a strong and wide general knowledge. I'm not familiar with the book you are reading, I enjoyed Lehninger very much. Molecular biology and biochemistry are the basics.

ADD REPLYlink written 6 months ago by Asaf4.0k
2
gravatar for WouterDeCoster
6 months ago by
Belgium
WouterDeCoster13k wrote:

A wonderful resource to learn biology and programming at the same time is http://rosalind.info/, in which you get confronted with biologic problems of increasing difficulty with well written background information about the biological processes underlying the question.

ADD COMMENTlink written 6 months ago by WouterDeCoster13k
1

I don't agree with you totally, i know rosalind and i used to solve issues there, but it's just describe main terms of issues with links on wikipedia often, but it doesn't give you whole picture ob biology and description of bio processes, gene interactions, SOS-reparation system etc. I mean, it doesn't teach you biology, just giving terms related to issue.

ADD REPLYlink modified 6 months ago • written 6 months ago by dshulgin250

Above each problem is a 'background' text block. But it's not a text book indeed. I guess for someone coming from computer science it can be an interesting resource. It can work as an introduction? I studied biochemistry and I'm not learning new stuff.

ADD REPLYlink modified 6 months ago • written 6 months ago by WouterDeCoster13k
1
gravatar for kirannbishwa01
6 months ago by
United States
kirannbishwa01260 wrote:

As, a biologist I have problems on the programming side. I think it will best for you to start with:

1) Understanding the linear structure of the DNA

2) nucleotides in DNA and RNA

3) IUPAC codes

4) mRNA to protein translation codes

5) start, stop codons

6) recombination

This is the most things you will need to understand as a beginner.

Apart from this developing a bioinformatics or file manipulation tools will need understanding of biology in the frame of context - like evolution, natural selection, inducing of mutations, parental-child relationships, population structure, several others, etc.

Most of the higher levels tools are designed by considering the context - of the experimental design, biology of the organism and several underlying assumptions of the individuals and populations. Understanding these are highly important for aligning the tool design with biology in mind. You will learn as you go but will probably need some collaborations and discussions.

  • Cheers !
ADD COMMENTlink written 6 months ago by kirannbishwa01260

Thanks a lot for your answer!

ADD REPLYlink written 6 months ago by dshulgin250

Hi @dshulgin

I wanted to PM you but couldn't get your full email. Like I mentioned earlier I am a biologist working with NGS. I have some scripting skills, but very mild programming skill with awk, grep, sed. I have just started to learn python but its has become more like a learning thing and less of what I am really supposed to be doing.

In some of these data I have generated variant files (vcfs), curated bam and other. But, I need some help with programming to do exactly what I need to do. I am very clear on the conceptual side of biology and what needs to be done with data and data manipulation, but on the technical side it been more of a struggle. Do you think you can be of some help with regards to some of my objective? I will be more than happy to discuss with you.

Thanks, - Bishwa K.

ADD REPLYlink modified 5 months ago • written 6 months ago by kirannbishwa01260

Hi @kirannbishwa01 I have also a background in biology, currently learning python. I'm interested to what process you want to do with you vcf file.

ADD REPLYlink written 6 months ago by diallobakary40

Here is one of the questions I recently posted. How to add custom fields to the VCF files?

I am trying to find solutions to several different vcf manipulation.

Let me know how can I reach you.

Thanks,

ADD REPLYlink modified 6 months ago • written 6 months ago by kirannbishwa01260

my email is diallobakary4@gmail.com Thanks

ADD REPLYlink written 5 months ago by diallobakary40

you can send me an email on dshulgin1@gmail.com. Thanks.

ADD REPLYlink written 6 months ago by dshulgin250
0
gravatar for diallobakary4
6 months ago by
diallobakary40 wrote:

I think learning biology through resources like coursera and edx is great. Some time ago I followed an introductory course on edx by prof Eric Lander, covering much of the essential of biology. This article may help you select the courses you need in biology: http://journals.plos.org/ploscompbiol/article?id=info:doi/10.1371/journal.pcbi.1002632 You can also look here : https://github.com/open-source-society/bioinformatics/blob/master/Subject_Domains.md

ADD COMMENTlink written 6 months ago by diallobakary40
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