Forum: How Did You Learn Good Practice In Bioinformatics/Computational Biology?
16
gravatar for epigene
6.8 years ago by
epigene490
United States
epigene490 wrote:

I came from a wet lab background and now doing a Ph.D. in genomics. Our lab is pretty decent in publication and my advisor often says the training we received in handling large amount of data is very desirable out there, etc. I can sense the need for this type of training is strong but I don't feel I'm getting the best or most effective training in how to handle data or being a good bioinformatics even though our program is ranked pretty high in US.

Just looking at my peers, I felt there is a great level of variation in the level of technical skills students have in the genomics filed. I struggle to find a "textbook" on the best practice type of thing. How did you learn it or suggest to do so in an efficient, systematic way, for students with biology, non-computer science background?

bioinformatics forum • 16k views
ADD COMMENTlink modified 3.7 years ago by robson0 • written 6.8 years ago by epigene490
15
gravatar for Irsan
6.8 years ago by
Irsan7.2k
Amsterdam
Irsan7.2k wrote:

Reading text books is a good start but the best way to learn good practice is by experience. Analyzing data is something different from reading about analyzing data. When you stumble on a technical difficulty that you find hard to tackle, in my opinion posting a question on a dedicated Q&A site like biostars or stack overflow gives you faster and better answers then asking someone in your lab/proximity (in my case at least, I'm the only bio-informatician within our section). Even when you have more general questions like you feel you are missing something or you want to hear about experiences and/or practices of others, Q&A sites (biostars in particular) help you a lot.

ADD COMMENTlink modified 5.8 years ago • written 6.8 years ago by Irsan7.2k
1

I agree, I was amazed by how quickly people respond on stackoverflow

ADD REPLYlink modified 3.7 years ago • written 6.8 years ago by epigene490
14
gravatar for Medhat
6.8 years ago by
Medhat8.8k
Texas
Medhat8.8k wrote:

Hi,

As @Irsan said most of the time you will learn by doing that is the hard way, but it will give you a keen solid stand-in bioinformatics field, also to have a basic knowledge by reading books or watching lectures is good, somehow it paves the way and make things little bit easy to follow.

Here is the most useful rules that I think you shall follow;

Advice for newcomers to the bioinformatics field

Then please read this

10 Steps to Success in Bioinformatics

I want to learn bioinformatics! A guide for complete beginners.

A beginner's guide to bioinformatics - part I

A beginner's guide to bioinformatics - part II

and If you are alone or searching for new knowledge follow this;

A guide for the lonely bioinformatician

Lastly spend a lot of time in Biostars and seqanswers you will learn a lot, I hope that helps :)

ADD COMMENTlink modified 22 months ago • written 6.8 years ago by Medhat8.8k

Thanks a lot. I got a mail exchange with someone who contacted me for advice about switching to bioinformatics. This will be handy!

ADD REPLYlink written 6.8 years ago by Eric Normandeau10k

It is my pleasure you are welcome any time :) that is the purpose of the community

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by Medhat8.8k
8
gravatar for GANI
6.8 years ago by
GANI220
United States
GANI220 wrote:

The following PLOS article summarizes many courses related to Bioinformatics in a systematic way. You can choose the courses based on you level of your experience in the particular field. I would suggest the Math and Computer Science departments for you.

http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1002632

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by GANI220
1

yeah, good to know this!

ADD REPLYlink written 6.8 years ago by epigene490
6
gravatar for lexnederbragt
6.8 years ago by
lexnederbragt1.2k
Oslo, Norway
lexnederbragt1.2k wrote:

I can recommend these articles: Best Practices for Scientific Computing and So you want to be a computational biologist?. Beyond that, I would take a Software Carpentry Bootcamp, see http://software-carpentry.org/.

ADD COMMENTlink written 6.8 years ago by lexnederbragt1.2k
4
gravatar for Zev.Kronenberg
6.8 years ago by
United States
Zev.Kronenberg11k wrote:

Implement everything you can, within reason. Someone who can teach themselves new methods / algorithms is much more desirable than someone trained in "big data".

Also take as many statistics courses as humanly possible.

ADD COMMENTlink written 6.8 years ago by Zev.Kronenberg11k
4
gravatar for Biojl
6.8 years ago by
Biojl1.7k
Barcelona
Biojl1.7k wrote:

Committing lots (LOTS) of errors and looking at other people's code.

ADD COMMENTlink written 6.8 years ago by Biojl1.7k
3
gravatar for Csaba Kerepesi
6.8 years ago by
Hungary
Csaba Kerepesi330 wrote:

This is a very good and practical textbook with computer science basics: James Tisdall: Beginning Perl for Bioinformatics

ADD COMMENTlink written 6.8 years ago by Csaba Kerepesi330
1

This is a great resource, but unfortunately that book is nearly 13 years old now. Here is a link to a free, modern perl book which is a bit more up-to-date.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by SES8.4k
4

Sure this is very up to date book,But should not we advice with python better?

ADD REPLYlink written 6.8 years ago by Medhat8.8k
3

That would be an opinion and not relevant for how to learn bioinformatics or be successful in the field. Without question though, learning to program from a book that is 13 years old will lead to a lot of problems, regardless of the language. That was my point, not that you should learn Perl. Sorry if that was not clear. You can be successful with any modern programming language and everyone can benefit by learning more than one.

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by SES8.4k

Totally agree sorry for miss understanding :)

ADD REPLYlink written 6.8 years ago by Medhat8.8k

My comment was rather terse, it's my fault. I do think learning good programming habits is essential, like modern best practices in whatever your language.

ADD REPLYlink written 6.8 years ago by SES8.4k
3
gravatar for Sudeep
6.8 years ago by
Sudeep1.6k
.
Sudeep1.6k wrote:

This might also be a good read: How Not to Be a Bioinformatician

ADD COMMENTlink written 6.8 years ago by Sudeep1.6k

Do not provide a graphical user interface: command line is always more effective. Force your end-users to use the command line

I don't understand this part, some of the most commonly used bioinformatic tools are command line based and do not come with a GUI.

ADD REPLYlink modified 11 months ago by RamRS30k • written 6.6 years ago by Vivek2.4k
3
gravatar for PoGibas
6.8 years ago by
PoGibas4.8k
Vilnius
PoGibas4.8k wrote:

You can/should try online courses (mentioned #1 in suggested PLOS article by GANI).
There is Data Analysis for Genomics coming up later this year. I already signed in and going to invest some time into this.

Take a note that prerequisites to this course are "programming skills, basic familiarity with the R programming language" and for this I strongly recommend learning sites like DataCamp and R-Fiddle.

ADD COMMENTlink modified 6.8 years ago • written 6.8 years ago by PoGibas4.8k
3
gravatar for epigene
3.7 years ago by
epigene490
United States
epigene490 wrote:

I realized that I asked this question 3 years ago. Now I've got a bit more experience and would like to share some of my personal thoughts on the question.

  1. Learn by doing. I ended up picking up most of what I know by working on the problems and trying to find answers from the internet, mostly from stackoverflow and related sites, some from biostars. It's a painful and kind of slow process but I guess you have to go through it to really master certain skills.

  2. Keep a good technical notes about all the problems you encountered. Either keep it to yourself or write it in a blog. Summarize them from time to time. I often revisit the same thing again and again later.

  3. Read other people's code, especially the commonly used tools (samtools, bedtools, etc) and learn how they implement certain things.

  4. Go to conferences. You will meet like-minded people, hear new development, tools in the field.

ADD COMMENTlink written 3.7 years ago by epigene490
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