[GenABEL-dev] The three layers of GenABEL

[Maria G]

Sounds great :) I like that :)

18.05.2011, 01:21, "Yurii Aulchenko" <yurii.aulchenko at gmail.com>:
> 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
>
> ------------------------
> 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.
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