Tiago’s blog is fast becoming a favorite. He responds to an interview with Alexei Drummond and I figured I’d respond to him.
First things first, I am not a biologist, just a physical chemist who has been in the biological sciences for a long time. So programming/scripting, etc are part of what I did in my scientific career from the beginning. I do believe that there are some level of computational skills all biologists must possess, but unlike Tiago, I think the number of scientists who know how to script is actually going to go down. It is becoming less common to find many scientists, even those who do part time molecular modeling, who have ever using a *NIX machine. Many OSX users don’t even know the best part of the OS, the ability to open a shell.
The alternative is to use interfaces that are between the scientist and the script, simple drag and drop interfaces that can be used to do many of the same things (workflow engines for example). Many of those are still to complex, but if a scientist has a basic understanding of data flow and the methods behind the madness, tools that give them access to workflows are the way to go, or so I think.
On the flip side, I do believe that hacks like yours truly would have benefited greatly from some formal software development training. Being able to write good code is important. Just look at the number of great academic packages that are a nightmare to maintain and completely bloated.
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4 Comments
Well I think every biologist should at-least know one scripting language-perl , python or whatever. The justification is like the saying–if you teach a man to fish you have fed him for life.
Knowing scripting does not imply that good nebch scientists spend all their time writing and debugging code. It just means that they can then have a more meaningful conversation with their friendly neighborhood bioinformatician or scripting geek besides also querying databases and using workflow based software more effectively.
I guess what I am saying is learning a programming language gives you a good grasp of the structure of information and information flow. This is essential in this genomic age.
Oh, I agree, but I am not sure it’s going to happen. To some extent it’s the analogy of having calculators. People get so comfortable with their tools that they essentially forget simple arithmetic.
Well I think every biologist should at-least know one scripting language-perl , python or whatever. The justification is like the saying–if you teach a man to fish you have fed him for life.
Knowing scripting does not imply that good nebch scientists spend all their time writing and debugging code. It just means that they can then have a more meaningful conversation with their friendly neighborhood bioinformatician or scripting geek besides also querying databases and using workflow based software more effectively.
I guess what I am saying is learning a programming language gives you a good grasp of the structure of information and information flow. This is essential in this genomic age.
Oh, I agree, but I am not sure it's going to happen. To some extent it's the analogy of having calculators. People get so comfortable with their tools that they essentially forget simple arithmetic.
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[...] Posted by nsaunders on August 18th, 2007 A interview with the head of a bioinformatics software company got Tiago thinking about how much time biologists should devote to computing. Deepak also has a few ideas on the topic. This one is always a favourite in the “biologists versus bioinformaticians” debate and here’s my $0.02. First, I can’t answer the question “how much programming should a biologist know?” It depends on the individual and the nature of their work. What I will say is that since we live in an age where the ability to acquire, process and interpret large amounts of data is an important research skill, I’d assume that any biologist with any common sense is thinking about improving their computer skills. [...]
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