[GenABEL-dev] The three layers of GenABEL

[Yurii Aulchenko]

Thanks for support!

Now published at
http://yurii-aulchenko.blogspot.com/2011/05/three-layers-of-genabel.html

Yurii

On Tue, May 17, 2011 at 11:49 PM, Diego Fabregat Traver
<fabregat at aices.rwth-aachen.de> wrote:
>
> Nice! Sounds good to me ;)
>
> El 17/05/11, Yurii Aulchenko  <yurii.aulchenko at gmail.com> escribió:
>
>> 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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>