Some People Want to Race Cars. Others Need a Vehicle to Get Their Groceries

Some People Want to Race Cars. Others Need a Vehicle to Get Their Groceries

BioMickWatson (BMW) is angry again !!

Bioinformatics is not something you are taught, its a way of life

That is what happens, when you take a terrific car-racer and ask him to train others to drive. Those, who come to the class, are not very interested in knowing how a fast car goes around the corner, or in figuring out how to cross every other racer in front of him. Many are simply happy to let the other person go ahead and move to the slowest lane. Some of them will probably be racers in future, but most will be happy to get their groceries and maybe weekend trips to the coast.

How do we teach driving to this motley crew? BioMickWatson has ‘one size fits all’ solution.

The future of bioinformatics training?

Imagine for a minute that you pay a few hundred pounds to attend a two-day training course on genome assembly. You get there, and are presented with a Linux PC, some amazon vouchers and the simple instructions Download a Salmonella genome from the SRA and assemble it. Thats it. Theres nothing more, except a few bioinformatics experts ready to answer (some of) your questions.

Our solution is possibly not much better. Let us call it ‘five size fits all’ for lack of a better alternative.

A beginners guide to bioinformatics part I

A beginners guide to bioinformatics part II

We divided the interested people into five groups based on their background and skills, and fed them five different stews instead of one.

**Layer 1 Using web to analyze biological data

Layer 2 Ability to install and run new programs

Layer 3 Writing own scripts for analysis in PERL, python and R, and being able to use SQL (suggested by Molecular Modelling Blog)

Layer 4 High level coding in C/C++, Java for implementing existing algorithms or modifying existing codes for new functionality

Layer 5 Thinking mathematically, developing own algorithms and implementing in C/C++/Java codes**

The details are provided in the earlier links.

We absolutely agree with BMW on one part of his comment. Spoon-fed courses are unnecessary in the era of internet. Internet has so much free resources that there is no need to fly to a different country and take courses on bioinformatics.

Just do it!

This isnt just a rather cheesy Nike slogan, its a pretty good piece of advice the internet is stuffed full of information on how to do a whole variety of bioinformatics tasks get yourself a Linux PC and just do it! Its the best way to learn. Then, when you get stuck, use Biostars or SeqAnswers.

Another wonderful aspect of the internet is that you can pick websites and courses based on the type of problem you want to solve. If you are working on molecular dynamics of proteins and genome assembly does not interest you, we do not see how “Download a Salmonella genome from the SRA and assemble it” will make you feel any better. Thanks to the internet, you do not have to do it.

We also agree fully with the following view of BMW.

I think we can start with a statement, and maybe you will agree or not agree: the next generation of biology graduate will be computer literate, capable of analysing their own data using appropriate tool, and simple scripting tasks

If you agree with that, then the question is how we get there. Certainly in the UK, too many universities produce biology graduates who are not mathematically literate and who are not computer literate. This has to stop.

Then the question is what we do with the young students and post docs out there now do we just abandon them? Or do we try and make them maths and computer literate? And how best to do that?

Many of the comments are applicable for the internet as well, because in 1998 it appeared absolutely essential to learn at least a bit of HTML and SQL coding to use the internet effectively and communicate with the world. So, we can go over the history of web-programming languages to explain how they made the transition, because bioinformaticians are essentially doing the same fifteen years later.

Following things happened for the internet.

i) At first thousands of training places popped up all around India, because there was a huge demand for programmers. What they called ‘programmer’ was often entry level HTML and SQL coders.

ii) In USA, bookstores got filled with ‘for dummies’ series of books.

iii) Over time, the programming communities and the user communities self- organized using the internet. Free programs like Wordpress became very successful catering to those, who absolutely did not want to learn any HTML programming, but still wanted to communicate.

iv) Those, who wanted to learn web languages, formed web-based communities to discuss their skills. It was not that everyone had to learn C or PERL or python. Small (and large) communities formed to cater to each group.

v) Software-training places at every corner of big cities of India are gone.

Yes, the web turned out to be as useful as promised for communication, but many users continued to use it as a tool to solve other problems.

Written by M. //