[GenABEL-dev] joining the GenABEL project - what is the procedure?

Thu Jun 20 01:09:26 CEST 2013

FYI, I started drafting more detailed reviewers' instructions (
http://piratepad.net/9ExdfmuJHV) and going to apply this template for
Nicola's package. Few questions will pop up on the way, I am sure.

YA

On Tue, May 28, 2013 at 8:52 AM, Nicola Pirastu <
nicola.pirastu at burlo.trieste.it> wrote:

>  Hi,
>
>  I think this is a very good plan. As for time I think a couple of months
> is fine, I still need to do some work to demonstrate that everything works
> fine (simulations, etc etc….). Actually if some one would like to lend a
> hand on that side he/she would be more than welcome :).
>
>  I'll send you the code separately with a tutorial attached so we can get
> started.
>
>  Best.
>
>  Nicola
>
>
>  Il giorno 28/mag/2013, alle ore 04:39, Yurii Aulchenko <
> yurii.aulchenko at gmail.com> ha scritto:
>
> I think it may be indeed a good idea to start with a 'case' and
> develop/tune the recommendations on the way. Nicola's new package would
> provide a good starting point (then we actually can think of re-review of
> some of the packages which are in the GenABEL suite already).
>
>  What about following plan
>
>  1) We (Nicola, Yurii, ...) draft reviewer's instructions (starting with
> points made during this discussion) - I made a piratepad
> http://piratepad.net/9ExdfmuJHV (at the moment simply a copy of latest
> Nicola's email); later we will circulate the draft on the list
>
>  2) Take RegionABEL as an example (I am volunteering to be the 'test'
> reviewer), and explore this case to check the review procedure. Nicola, may
> be you can send me the code already.
>
>  3) Ask an external person to act as a reviewer - this is for testing our
> reviewers' instructions
>
>  The whole process (esp if we want to go for (3)) may take a couple of
> months. Nicola, how much in hurry are you with publication?
>
>  Yurii
>
>
> On Wed, May 22, 2013 at 2:55 PM, Nicola Pirastu <
> nicola.pirastu at burlo.trieste.it> wrote:
>
>> Dear all,
>>
>> I think that the best way we can discuss about this is to start with a
>> real case. I would propose to start from the package
>> I've just written to run gene/region wide analysis which I've called
>> RegionABEL.
>>
>> It basically gives gene wide value with real or imputed data, with or
>> without kinship included. It is not for analyzing rare variants, so it is
>> not like SKAT. If you want to think of it in terms of existing software it
>> is like VEGAS or plink-ave. The main advance is that since it does not use
>> simulation/permutations to get pvalues it is much faster (4 hours on 1000G
>> data vs 12-16 of VEGAS on HapMap 2.5). The other great advantage is that it
>> does not require prior knowledge of LD as in other methods.
>> I have beta version of the package and I've written a Tutorial to explain
>> how to use it.
>>
>> So how do you think we should proceed now? Should we ask some volunteers
>> to review it?
>>
>>
>> Best.
>>
>> Nicola
>>
>>
>>
>>
>> Il giorno 14/mag/2013, alle ore 00:07, L.C. Karssen <lennart at karssen.org>
>> ha scritto:
>>
>> > Dear all,
>> >
>> > It's been a while but this mail was still on my todo list. I agree with
>> > Yurii that we should start establishing procedures for projects wanting
>> > to join the GenABEL project umbrella. Software lifecycle management is
>> > too often overlooked when developing a package and we don't want to
>> > 'degrade' the GenABEL project brand name by including packages that are
>> > not maintained anymore after the initial paper is published. Or, another
>> > argument I've come across: we make it open source so everyone can
>> > contribute to it (and therefore it will 'somehow' be maintained without
>> > us putting more effort into it). That's not how it works. The software
>> > ecosystem in which a package lives is dynamic and a package should adapt
>> > to that.
>> >
>> > As Yurii wrote we discussed this at the EMGM conference and agreed that
>> > code review should be part of it. This neatly ties into the discussion
>> > we had on thils list some time ago about coding standards. This does not
>> > mean we force everybody to use four spaces instead of eight when
>> > indenting code, but more serious stuff like variables named "a" or "df"
>> > are not helpful when someone wants to contribute or take over
>> > maintenance of the package.
>> >
>> > I've just committed the draft document of the coding standards to the
>> > www folder of the SVN repo (rev. 1215). It's a (plain text) Org-mode
>> > file; the HTML file is created from this Org file (using org-mode allows
>> > us to easily export the text in various formats). Those of you who want
>> > to convert without ever opening emacs can run the command
>> > emacs --batch --eval '(and (find-file "codingstyle.org")
>> > (org-export-as-html nil))'
>> > from the command line.
>> >
>> > Looking forward to your comments, both on this e-mail and the coding
>> > standards.
>> >
>> >
>> > Lennart.
>> >
>> > On 02-05-13 15:15, Yurii Aulchenko wrote:
>> >> Dear All,
>> >>
>> >> I have recently received several requests from people who would like to
>> >> join to the GenABEL project with their software. Given this is a
>> >> community-based project, neither me nor someone else is in a position
>> to
>> >> say 'yes' or 'no' - we need to develop some procedure how a software
>> >> joins the project.
>> >>
>> >> We have discussed this with Nicola and Lennart during EMGM-2013, and we
>> >> think that we do need a technical review as a part of the procedure
>> >> (addressing the issues of license, clarity of the code, integration
>> with
>> >> other packages, etc.). We also need to think how we do maintenance: the
>> >> suggestion would be to request that the author joins the forum and the
>> >> list. If we see that a package is not actively maintained (e.g. we can
>> >> not reach the maintainer), we should tag such a package as 'orphaned'.
>> >>
>> >> In many respects, we can base our procedure on the procedures developed
>> >> by Bioconductor. In our procedures we need to achieve two conflicting
>> >> goals: a) we do not want to repel potential contributors by a long list
>> >> of technical requirements but at the same time b) in the sake of
>> >> maintainability we need the code to comply to some requirements.
>> >> Probably we should have 'minimal' and 'complete' requirements with
>> >> packages clearly tagged on the web pages.
>> >>
>> >> Let us know what you think. I will initiate a PiratPad document after
>> >> having initial response from you.
>> >>
>> >> best regards,
>> >> YA
>> >>
>> >>
>> >> _______________________________________________
>> >> genabel-devel mailing list
>> >> genabel-devel at lists.r-forge.r-project.org
>> >>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>
>> >
>> > --
>> > -----------------------------------------------------------------
>> > L.C. Karssen
>> > Utrecht
>> > The Netherlands
>> >
>> > lennart at karssen.org
>> > http://blog.karssen.org
>> >
>> > Stuur mij aub geen Word of Powerpoint bestanden!
>> > Zie http://www.gnu.org/philosophy/no-word-attachments.nl.html
>> > ------------------------------------------------------------------
>> >
>> > _______________________________________________
>> > genabel-devel mailing list
>> > genabel-devel at lists.r-forge.r-project.org
>> >
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
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>
>
>
>  --
> -----------------------------------------------------
> Yurii S. Aulchenko
>
>  [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko>] [
> Blog <http://yurii-aulchenko.blogspot.nl/> ]
>
>
>  AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute
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> messaggio, o responsabili per la sua consegna alla persona, o se avete
> ricevuto il messaggio per errore, siete pregati di non trascriverlo,
> copiarlo o inviarlo a nessuno. In tal caso vi invitiamo a cancellare il
> messaggio ed i suoi allegati. Grazie. CONFIDENTIALITY NOTICE Confidential
> information may be contained in this message or in its attachments. If you
> are not the addressee indicated in this message, or responsible for message
> delivering to that person, or if you have received this message in error,
> you may not transcribe, copy or deliver this message to anyone. In that
> case, you should delete this message and its attachments. Thank you.
>

-- 
-----------------------------------------------------
Yurii S. Aulchenko

[ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [
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Blog <http://yurii-aulchenko.blogspot.nl/> ]
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