[GenABEL-dev] The three layers of GenABEL

[Yurii Aulchenko]

Here is another post on the GenABEL project. Unlike other posts, I
intend to publish this post in my blog (after your feedback): this
post rather timely (not a guidline) and expresses my personal hopes
for the project.

best wishes,
Yurii

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The three layers of GenABEL

I think there is a growing confusion about GenABEL, and I start
getting questions like: What the hell is it? To whom does it belong?
Is it free? Will it stay free? Is it supposed to make money? What
happens next? Also the rumors that I am leaving Academia spread,
building some anxiety.

To start with, please keep in mind that whatever happens, I am
dedicated to the free GenABEL in the open source spirit. The GenABEL
is and will stay open (re)source: free of charge to anyone, open
source, modifiable, and redistributable.

Ok, now to business: To start with, and may be to confuse you even
more, there is no such thing as "the GenABEL". Actually, there are
three things – the GenABEL package, the GenABEL suite, and the GenABEL
project. The GenABEL project includes the suite, which includes the
package. I will elaborate below on each of them in turn, starting with
smaller entities.

*** The GenABEL package.

What is it: This is free open source package for R (R is also, a free,
open source software).

To whom does it belong: It is released under GNU GPL, so the answer is
it free to copy, modify, and redistribute to everyone. It is "mine" in
the sense that I feel responsible to keep it in good shape. At the
same time, many other people contributed the ideas, code,
documentation, suggestions, etc. to it. In that, the package belongs
to the community. In the release 1.6-7 of the package, I have removed
my name from the DESCRIPTION file and the “GenABEL developers” are
credited as authors. You can see who has developed specific function,
and what paper should be referenced, by looking at the man page of a
function.

Will it stay free: Sure. It is released under GNU GPL, so the source
cannot be closed or charged money for. Moreover, many people
contributed; guess who can claim the ownership? I am feeling quite
happy about this.

Is it supposed to make money: Not directly. The code is available to
everyone for free (provided any derivative is also made available for
free). This does not exclude indirect uses, e.g. if a company
approaches me with a question on how to use the GenABEL package most
effectively, I may consider charging them for consultancy. The same
goes for the cases when I am invited to teach a course, or help a
company developing a software making use of the package. If someone
wants to have specific functionality extended within GenABEL package,
and is willing to pay money for it, I will not say ‘no’ to get some
extra income. Note that according to GNU GPL whatever is developed
must become a part of the free GenABEL package if the GenABEL code was
used!

What next: There are many plans about GenABEL; after 4 years, it is
still (an will remain) under active development. During 2010, we had
10 public (CRAN) releases adding and improving much if the
functionality.

*** GenABEL suite:

What is it: This is a set free open source packages, mostly for R.
However, the set also includes standalone applications (e.g. ProbABEL)
and libraries (e.g. filevector). The GenABEL package is part of the
GenABEL suite.

To whom does it belong: Right now, all packages are released under GNU
GPL, so the first answer is that the “GenABEL suite” is free to copy,
modify and redistribute. At the same time, each individual package
‘belongs’ to individuals, who contributed these packages.

Will it stay free: Sure. My position is that only the packages, which
are open source, free to use, modify, and redistribute (recursively)
should be in the GenABEL suite.

Is it supposed to make money: Not directly, but there may be many
indirect uses. For example, a company may package GenABEL suite with a
cloud computing (or whatsoever), and sell the computations as a
service. No complains here.

What next: My sincere hope is that the GenABEL suite will grow both in
quality and quantity and will become a leading software suite for
statistical analyses of polymorphic genomes.

*** GenABEL project:

What is it: this is a framework for methodology development, based on
an idea of methodology development as a three-stage process including
methodology development itself (math), implementation of this
methodology in a usable software (the GenABEL suite), and application
of the software to solve real-life problems.

To whom does it belong: this is a community effort, and it belongs to
the community. While I am currently the coordinator and in that have
most influence and control, this can (and should) change.

Will it stay free: Sure. The GenABEL project is a kind of a workshop.
If people are not satisfied with a setting of a workshop, they just
organize alternative workshop.

Is it supposed to make money: Not directly. I must admit I can also
hardly imagine how it can make money indirectly as well. See remarks
about the suite and package for more info.

What next: My sincere hope is that in the GenABEL project framework,
we will work out new standards for open methodology development and
open manuscript writing; will formulate most important (and fun)
problems of statistical genomics and come up with great new solutions
to these; develop excellent software; will publish top papers; will
apply our software to solve burning problems of biology; and will
contribute to public good.