FYI, I started drafting more detailed reviewers' instructions (<a href="http://piratepad.net/9ExdfmuJHV">http://piratepad.net/9ExdfmuJHV</a>) and going to apply this template for Nicola's package. Few questions will pop up on the way, I am sure. <div>
<br></div><div>YA<br><br><div class="gmail_quote">On Tue, May 28, 2013 at 8:52 AM, Nicola Pirastu <span dir="ltr"><<a href="mailto:nicola.pirastu@burlo.trieste.it" target="_blank">nicola.pirastu@burlo.trieste.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi,
<div><br>
</div>
<div>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 :). </div>
<div><br>
</div>
<div>I'll send you the code separately with a tutorial attached so we can get started. </div>
<div><br>
</div>
<div>Best.</div>
<div><br>
</div>
<div>Nicola</div>
<div> </div>
<div><br>
<div>
<div>Il giorno 28/mag/2013, alle ore 04:39, Yurii Aulchenko <<a href="mailto:yurii.aulchenko@gmail.com" target="_blank">yurii.aulchenko@gmail.com</a>> ha scritto:</div><div><div class="h5">
<br>
<blockquote type="cite">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).
<div><br>
</div>
<div>What about following plan</div>
<div><br>
</div>
<div>1) We (Nicola, Yurii, ...) draft reviewer's instructions (starting with points made during this discussion) - I made a piratepad <a href="http://piratepad.net/9ExdfmuJHV" target="_blank">http://piratepad.net/9ExdfmuJHV</a> (at the moment simply a copy of latest Nicola's
email); later we will circulate the draft on the list</div>
<div><br>
</div>
<div>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. </div>
<div><br>
</div>
<div>3) Ask an external person to act as a reviewer - this is for testing our reviewers' instructions</div>
<div><br>
</div>
<div>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?<br>
<div><br>
</div>
<div>
<div>Yurii</div>
<div> <br>
<br>
<div class="gmail_quote">On Wed, May 22, 2013 at 2:55 PM, Nicola Pirastu <span dir="ltr">
<<a href="mailto:nicola.pirastu@burlo.trieste.it" target="_blank">nicola.pirastu@burlo.trieste.it</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear all,<br>
<br>
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<br>
I've just written to run gene/region wide analysis which I've called RegionABEL.<br>
<br>
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.<br>
I have beta version of the package and I've written a Tutorial to explain how to use it.<br>
<br>
So how do you think we should proceed now? Should we ask some volunteers to review it?<br>
<br>
<br>
Best.<br>
<br>
Nicola<br>
<br>
<br>
<br>
<br>
Il giorno 14/mag/2013, alle ore 00:07, L.C. Karssen <<a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a>> ha scritto:<br>
<div>
<div><br>
> Dear all,<br>
><br>
> It's been a while but this mail was still on my todo list. I agree with<br>
> Yurii that we should start establishing procedures for projects wanting<br>
> to join the GenABEL project umbrella. Software lifecycle management is<br>
> too often overlooked when developing a package and we don't want to<br>
> 'degrade' the GenABEL project brand name by including packages that are<br>
> not maintained anymore after the initial paper is published. Or, another<br>
> argument I've come across: we make it open source so everyone can<br>
> contribute to it (and therefore it will 'somehow' be maintained without<br>
> us putting more effort into it). That's not how it works. The software<br>
> ecosystem in which a package lives is dynamic and a package should adapt<br>
> to that.<br>
><br>
> As Yurii wrote we discussed this at the EMGM conference and agreed that<br>
> code review should be part of it. This neatly ties into the discussion<br>
> we had on thils list some time ago about coding standards. This does not<br>
> mean we force everybody to use four spaces instead of eight when<br>
> indenting code, but more serious stuff like variables named "a" or "df"<br>
> are not helpful when someone wants to contribute or take over<br>
> maintenance of the package.<br>
><br>
> I've just committed the draft document of the coding standards to the<br>
> www folder of the SVN repo (rev. 1215). It's a (plain text) Org-mode<br>
> file; the HTML file is created from this Org file (using org-mode allows<br>
> us to easily export the text in various formats). Those of you who want<br>
> to convert without ever opening emacs can run the command<br>
> emacs --batch --eval '(and (find-file "<a href="http://codingstyle.org/" target="_blank">codingstyle.org</a>")<br>
> (org-export-as-html nil))'<br>
> from the command line.<br>
><br>
> Looking forward to your comments, both on this e-mail and the coding<br>
> standards.<br>
><br>
><br>
> Lennart.<br>
><br>
> On 02-05-13 15:15, Yurii Aulchenko wrote:<br>
>> Dear All,<br>
>><br>
>> I have recently received several requests from people who would like to<br>
>> join to the GenABEL project with their software. Given this is a<br>
>> community-based project, neither me nor someone else is in a position to<br>
>> say 'yes' or 'no' - we need to develop some procedure how a software<br>
>> joins the project.<br>
>><br>
>> We have discussed this with Nicola and Lennart during EMGM-2013, and we<br>
>> think that we do need a technical review as a part of the procedure<br>
>> (addressing the issues of license, clarity of the code, integration with<br>
>> other packages, etc.). We also need to think how we do maintenance: the<br>
>> suggestion would be to request that the author joins the forum and the<br>
>> list. If we see that a package is not actively maintained (e.g. we can<br>
>> not reach the maintainer), we should tag such a package as 'orphaned'.<br>
>><br>
>> In many respects, we can base our procedure on the procedures developed<br>
>> by Bioconductor. In our procedures we need to achieve two conflicting<br>
>> goals: a) we do not want to repel potential contributors by a long list<br>
>> of technical requirements but at the same time b) in the sake of<br>
>> maintainability we need the code to comply to some requirements.<br>
>> Probably we should have 'minimal' and 'complete' requirements with<br>
>> packages clearly tagged on the web pages.<br>
>><br>
>> Let us know what you think. I will initiate a PiratPad document after<br>
>> having initial response from you.<br>
>><br>
>> best regards,<br>
>> YA<br>
>><br>
>><br>
>> _______________________________________________<br>
>> genabel-devel mailing list<br>
>> <a href="mailto:genabel-devel@lists.r-forge.r-project.org" target="_blank">genabel-devel@lists.r-forge.r-project.org</a><br>
>> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel" target="_blank">
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel</a><br>
>><br>
><br>
> --<br>
> -----------------------------------------------------------------<br>
> L.C. Karssen<br>
> Utrecht<br>
> The Netherlands<br>
><br>
> <a href="mailto:lennart@karssen.org" target="_blank">lennart@karssen.org</a><br>
> <a href="http://blog.karssen.org/" target="_blank">http://blog.karssen.org</a><br>
><br>
> Stuur mij aub geen Word of Powerpoint bestanden!<br>
> Zie <a href="http://www.gnu.org/philosophy/no-word-attachments.nl.html" target="_blank">
http://www.gnu.org/philosophy/no-word-attachments.nl.html</a><br>
> ------------------------------------------------------------------<br>
><br>
> _______________________________________________<br>
> genabel-devel mailing list<br>
> <a href="mailto:genabel-devel@lists.r-forge.r-project.org" target="_blank">genabel-devel@lists.r-forge.r-project.org</a><br>
> <a href="https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel" target="_blank">
https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel</a><br>
<br>
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