Source Code for Biology and Medicine 2012, 7:3 doi:10.1186/1751-0473-7-3
I agree, but..........
David Sexton
(2012-06-12 04:24) Baylor College of Medicine
I agree with most of what you are saying, but many of the issues around code reuse
and documentation are a problem of time. There are too few bioinformatician hired,
the key word is hired, at most institutions. This means that most bioinformaticians
are seriously over committed and are looking for easy (cheap) ways to complete work
before they are yelled at by the PI. PIs do not understand software development AT
ALL and if you do not have someone who can stand up and explain it, then these issues
will continue. I can't tell you how many times I have heard "What do you mean that
you need 4 weeks to properly analyze that data? I have the paper going out in 2 weeks"
or "How can it take 6 months to develop a pipeline? I could get a grad student to
do it in 2 weeks." The other refrain I hear is "It costs that much? I could add
1000 samples to my experiment for that amount of money." Sorry but you should have
talked to me before writing the grant. Bioinformaticians and biologists share in
the problems here.
Commentary
I agree, but..........
David Sexton (2012-06-12 04:24) Baylor College of Medicine
I agree with most of what you are saying, but many of the issues around code reuse and documentation are a problem of time. There are too few bioinformatician hired, the key word is hired, at most institutions. This means that most bioinformaticians are seriously over committed and are looking for easy (cheap) ways to complete work before they are yelled at by the PI. PIs do not understand software development AT ALL and if you do not have someone who can stand up and explain it, then these issues will continue. I can't tell you how many times I have heard "What do you mean that you need 4 weeks to properly analyze that data? I have the paper going out in 2 weeks" or "How can it take 6 months to develop a pipeline? I could get a grad student to do it in 2 weeks." The other refrain I hear is "It costs that much? I could add 1000 samples to my experiment for that amount of money." Sorry but you should have talked to me before writing the grant. Bioinformaticians and biologists share in the problems here.
Competing interests
none.
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