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

Wed Jul 3 22:44:58 CEST 2013

Dear All,

I just discovered that we already had this discussion (under slightly
different angle) a couple of years ago, see

https://lists.r-forge.r-project.org/pipermail/genabel-devel/2011-October/000367.html

In the light of that discussion I have added questions

* Legal issues
** Is there a clear (standard) license?
** Is the license GNU GPL-compatible?

to the reviewer's list

YA

On Thu, Jun 27, 2013 at 11:10 AM, Nicola Pirastu <
nicola.pirastu at burlo.trieste.it> wrote:

>  Sorry for the late reply.
>
>  Great! I'll look at the comments and modify the package accordingly.
>
>  I'll let you know when I'm done.
>
>  Thanks a lot.
>
>  Best
>
>  Nicola
>
>
>
> Dr. Nicola Pirastu PhD
> Research Fellow
> Medical Sciences, Chirurgical and Health Department
> University of Trieste
> Medical Genetics
> IRCCS Burlo Garofolo
> Via dell'Istria 65/1
> 34137 Italy
> tel. +390403785539
>
>  Il giorno 20/giu/2013, alle ore 23:33, Yurii Aulchenko <
> yurii.aulchenko at gmail.com> ha scritto:
>
> ok, draft review form (and a review of RegionABEL) completed at
> http://piratepad.net/9ExdfmuJHV
>
>  Definitely not all comments are equal - some are minor/suggestive,
> others more important.
>
>  Nicola, may be you can reply directly in that form to my concerns
>
>  I would really like if someone else will do the next round of review - I
> feel I am really biased - any volunteers?
>
>  YA
>
> On Thu, Jun 20, 2013 at 1:09 AM, Yurii Aulchenko <
> yurii.aulchenko at gmail.com> wrote:
>
>> 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
>>>> >
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>>>>
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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/> ]
>>>
>>>
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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/> ]
>>
>
>
>
>  --
> -----------------------------------------------------
> Yurii S. Aulchenko
>
>  [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter<http://twitter.com/YuriiAulchenko>] [
> Blog <http://yurii-aulchenko.blogspot.nl/> ]
>  _______________________________________________
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>
>
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> ricevuto il messaggio per errore, siete pregati di non trascriverlo,
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> 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
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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/> ]
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