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

Thu Jun 20 23:33:23 CEST 2013

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
>>> >
>>> 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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>> ricevuto il messaggio per errore, siete pregati di non trascriverlo,
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>> 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> ] [ 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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