From yurii.aulchenko at gmail.com  Thu Jun 13 14:37:07 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 13 Jun 2013 14:37:07 +0200
Subject: [GenABEL-dev] Fwd: [R-Forge] Complete Site/Services Downtime
References: <20130613121338.0676D185954@r-forge.r-project.org>
Message-ID: <4086179510995365293@unknownmsgid>

FYI

----------------------
Yurii Aulchenko
(sent from mobile device)

Begin forwarded message:

*From:* <noreply at r-forge.r-project.org>
*Date:* 13 June 2013 14:13:37 CEST
*To:* yurii.aulchenko at gmail.com
*Subject:* *[R-Forge] Complete Site/Services Downtime*

Dear R-Forge users

The WU Vienna University of Economics and Business will be moving to a new
campus location this summer. Since the server that hosts the website and
its services is located there, it will also need to be moved to the new
location.

The infrastructure and capacities of the buildings in Vienna?s ninth
district are no longer adequate for the demands placed on them and the
university is ?bursting at the seams.? To remedy this, WU and the
Bundesimmobilien Gesellschaft (a company which manages publicly owned real
estate in Austria) have built a new location to house the university.

According to the moving schedule the R-Forge servers (and resulting
downtime) will be relocated as follows:
June 24 (expected until 29 June): Complete downtime (website, mailing
lists, package build process, svn repos, etc.)
July 8 (expected until 12 July): Build process down (no packages will get
built during this time)

Sometime during this time period, the server will be shut down and remain
off-line until reconnected at the new campus. The downtime is expected to
around one day at minimum, however it can extend up to several days if
complications arise.

We will try to keep the downtime as short as possible and apologize for any
inconvenience

R-Forge Team
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From yurii.aulchenko at gmail.com  Sat Jun 15 17:58:03 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 15 Jun 2013 17:58:03 +0200
Subject: [GenABEL-dev] GenABEL tutorials to SVN - figures
In-Reply-To: <CAHX9t6+ZhdYF2gf9dSvzKfruhCPEqPyQRGEjqs2071YbOyk5ZA@mail.gmail.com>
References: <CAHX9t6+9GZip3QgU-FVo_Zza2k8mJm8fash8yfmKzDD0uH23ug@mail.gmail.com>
 <5140DB3B.5000603@karssen.org>
 <CAHX9t6+ZhdYF2gf9dSvzKfruhCPEqPyQRGEjqs2071YbOyk5ZA@mail.gmail.com>
Message-ID: <CAHX9t6K9=UEKi4n5hTpBaogXTeHoey89NL_PZp=P21MCg4mp_g@mail.gmail.com>

I just had good news from Elsever: they are ok that we publish the text
(this concerns chapter "GWA analysis in presence of stratification:
theory") on the web at 0 costs.

Will put the text back into tutorial as soon as I get time for that.

Yurii

On Thu, Mar 14, 2013 at 9:41 AM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:

> > I think for one figure (figure 2 from
>
>> >
>> http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005472
>> )
>> > we are fine - see below the extract from PLoS ONE site. It looks like we
>> > do not even need to request permission.
>>
>> Good. +1 for Creative Commons and open access publishing!
>>
>>
> Agree. The problem is that it is in this chapter which overlaps quite a
> bit with  Elsevier's text. So I just killed all for the moment.
>
> >
>> > I will investigate the issue with chapter "GWA analysis in presence of
>> > stratification: theory" of the tutorial further (it overlaps - both in
>> > figures and text - with a a chapter of a published book,
>> > http://www.sciencedirect.com/science/article/pii/B9780123751423100094).
>> > For the moment it may be more safe to just skip it in the SVN.
>>
>> That's an interesting question since you are the author of that text. I
>> guess you'll need to dig a bit deeper into Elsevier's legal texts...
>>
>>
> They say that "you can re-use up to 10%" with no problem.
>
> I have sent a request to them if we can use figures; will need to figure
> out about the text... Or just update it so much that it can not count as
> old text. Still may be some problem. Well, hope to find some help and clear
> guidance from Elsevier's :)
>
> best wishes,
> Yurii
>



-- 
-----------------------------------------------------
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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From lennart at karssen.org  Sun Jun 16 13:08:31 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Sun, 16 Jun 2013 13:08:31 +0200
Subject: [GenABEL-dev] GenABEL tutorials to SVN - figures
In-Reply-To: <CAHX9t6K9=UEKi4n5hTpBaogXTeHoey89NL_PZp=P21MCg4mp_g@mail.gmail.com>
References: <CAHX9t6+9GZip3QgU-FVo_Zza2k8mJm8fash8yfmKzDD0uH23ug@mail.gmail.com>
 <5140DB3B.5000603@karssen.org>
 <CAHX9t6+ZhdYF2gf9dSvzKfruhCPEqPyQRGEjqs2071YbOyk5ZA@mail.gmail.com>
 <CAHX9t6K9=UEKi4n5hTpBaogXTeHoey89NL_PZp=P21MCg4mp_g@mail.gmail.com>
Message-ID: <51BD9CAF.8090001@karssen.org>

That is excellent news!
Great work and thanks Elsevier!
Did they specify anything w.r.t. copyright or acknowledgements?


Best,

Lennart.

On 15-06-13 17:58, Yurii Aulchenko wrote:
> I just had good news from Elsever: they are ok that we publish the text
> (this concerns chapter "GWA analysis in presence of stratification:
> theory") on the web at 0 costs.
> 
> Will put the text back into tutorial as soon as I get time for that.
> 
> Yurii
> 
> On Thu, Mar 14, 2013 at 9:41 AM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     > I think for one figure (figure 2 from
> 
>         >
>         http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0005472)
>         > we are fine - see below the extract from PLoS ONE site. It
>         looks like we
>         > do not even need to request permission.
> 
>         Good. +1 for Creative Commons and open access publishing!
> 
> 
>     Agree. The problem is that it is in this chapter which overlaps
>     quite a bit with  Elsevier's text. So I just killed all for the moment.
> 
>         >
>         > I will investigate the issue with chapter "GWA analysis in
>         presence of
>         > stratification: theory" of the tutorial further (it overlaps -
>         both in
>         > figures and text - with a a chapter of a published book,
>         >
>         http://www.sciencedirect.com/science/article/pii/B9780123751423100094).
>         > For the moment it may be more safe to just skip it in the SVN.
> 
>         That's an interesting question since you are the author of that
>         text. I
>         guess you'll need to dig a bit deeper into Elsevier's legal texts...
> 
> 
>     They say that "you can re-use up to 10%" with no problem. 
> 
>     I have sent a request to them if we can use figures; will need to
>     figure out about the text... Or just update it so much that it can
>     not count as old text. Still may be some problem. Well, hope to find
>     some help and clear guidance from Elsevier's :)
> 
>     best wishes,
>     Yurii
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]

-- 
-----------------------------------------------------------------
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
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Wed Jun 19 14:38:24 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 19 Jun 2013 14:38:24 +0200
Subject: [GenABEL-dev] updated tutorial (chapter on theory of stratification
	back)
Message-ID: <CAHX9t6JEcirZuTP5DaLtLkLZ7SgSpUvACLmWV-YAHYFCx69e7w@mail.gmail.com>

Dear All,

I have updated the SVN with latest version of the tutorial (now we are at
261 pages :) ) and put the PDF/HTML on the web-site as well. The latter is
a hassle - we need to think how to automate this (Jenkins?!).

There is still something very weird - while HTML update was ok (though this
is just by-passing drupal in a way) the PDF gives a trouble. With FTP, I
put the PDF to /domains/genabel.org/htdocs/genabel/sites/default/files/pdfsand
can get it back (marked June 19). With Chrome (even after cleaning the
cache), Mozilla, with my telephone, with

wget http://genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf

I get an old copy (marked April 15!). No idea what is going on; ran out of
ideas how to solve this. Very frustrating.

best wishes,
Yurii
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From yurii.aulchenko at gmail.com  Wed Jun 19 22:19:54 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 19 Jun 2013 22:19:54 +0200
Subject: [GenABEL-dev] GenABEL logo
Message-ID: <6010936630980818034@unknownmsgid>

Dear All,

I wonder why don't we ask the users to come up with suggestions for
logo - e.g. we can ask through forum and our news line on the site.

YA

----------------------
Yurii Aulchenko
(sent from mobile device)

From yurii.aulchenko at gmail.com  Wed Jun 19 22:39:58 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Wed, 19 Jun 2013 22:39:58 +0200
Subject: [GenABEL-dev] updated tutorial (chapter on theory of
	stratification back)
In-Reply-To: <CAHX9t6JEcirZuTP5DaLtLkLZ7SgSpUvACLmWV-YAHYFCx69e7w@mail.gmail.com>
References: <CAHX9t6JEcirZuTP5DaLtLkLZ7SgSpUvACLmWV-YAHYFCx69e7w@mail.gmail.com>
Message-ID: <CAHX9t6L2jD77z0R=bRv0WJP1M_XWWuFMwoZDRyhxqAnXiLLyaw@mail.gmail.com>

Upon Maarten's suggestion I renamed the file (to GenABEL-tutorial1.pdf) and
deleted the old one; changed the link. Now the link

http://www.genabel.org/sites/default/files/pdfs/GenABEL-tutorial1.pdf

seems to function properly, but there are funny things still going on:

http://www.genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf

serves the "new" (but non-existent on FTP!) file from June 19

http://genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf

serves old (also non-existent on FTP!) file from April 15

On Wed, Jun 19, 2013 at 2:38 PM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:

> Dear All,
>
> I have updated the SVN with latest version of the tutorial (now we are at
> 261 pages :) ) and put the PDF/HTML on the web-site as well. The latter is
> a hassle - we need to think how to automate this (Jenkins?!).
>
> There is still something very weird - while HTML update was ok (though
> this is just by-passing drupal in a way) the PDF gives a trouble. With FTP,
> I put the PDF to /domains/
> genabel.org/htdocs/genabel/sites/default/files/pdfs and can get it back
> (marked June 19). With Chrome (even after cleaning the cache), Mozilla,
> with my telephone, with
>
> wget http://genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf
>
> I get an old copy (marked April 15!). No idea what is going on; ran out of
> ideas how to solve this. Very frustrating.
>
> best wishes,
> Yurii
>
>


-- 
-----------------------------------------------------
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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From yurii.aulchenko at gmail.com  Thu Jun 20 00:13:14 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 20 Jun 2013 00:13:14 +0200
Subject: [GenABEL-dev] time to announce SVN tutorial?
Message-ID: <CAHX9t6+2r+uw80oVqoDFvHPg1qyAxk6-bAkXDc6xy9aoHF3cuQ@mail.gmail.com>

Dear All,

I think this may be already good time to announce the fact that the GenA
became even more open with open source tutorial on SVN.

Please let me know what you think and look through the
preliminary announcement text below

Yurii

The GenABEL project: more open than ever!

We are glad and proud to announce that the open source GenABEL project
became even more open with the release of the source code of the "GenABEL
tutorial" . under the E CREATIVE COMMONS ATTRIBUTION-
SHAREALIKE 3.0 UNPORTED LICENSE.

The code is released under <a href="
http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA 3.0
license</a>. Everybody is invited to copy, modify, extend, and share the
code further. The code can be found in <a href="
http://r-forge.r-project.org/scm/?group_id=505">the GenABEL project SCM at
the RForge</a>.
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From yurii.aulchenko at gmail.com  Thu Jun 20 00:26:48 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 20 Jun 2013 00:26:48 +0200
Subject: [GenABEL-dev] time to announce SVN tutorial?
In-Reply-To: <CAHX9t6+2r+uw80oVqoDFvHPg1qyAxk6-bAkXDc6xy9aoHF3cuQ@mail.gmail.com>
References: <CAHX9t6+2r+uw80oVqoDFvHPg1qyAxk6-bAkXDc6xy9aoHF3cuQ@mail.gmail.com>
Message-ID: <CAHX9t6L5TeAirR5mS-=6Ykcaty02CLaKTOE9mEg=mXy_MnvC+Q@mail.gmail.com>

Probably something to add to the announcement:

Note that not all the data used in "closed" version were transferrable to
the open version. These parts are indicated with "DATAPROBLEM" in the text.
We will appreciate your help in fixing this problems.

YA

On Thu, Jun 20, 2013 at 12:13 AM, Yurii Aulchenko <yurii.aulchenko at gmail.com
> wrote:

> Dear All,
>
> I think this may be already good time to announce the fact that the GenA
> became even more open with open source tutorial on SVN.
>
> Please let me know what you think and look through the
> preliminary announcement text below
>
> Yurii
>
> The GenABEL project: more open than ever!
>
> We are glad and proud to announce that the open source GenABEL project
> became even more open with the release of the source code of the "GenABEL
> tutorial" . under the E CREATIVE COMMONS ATTRIBUTION-
> SHAREALIKE 3.0 UNPORTED LICENSE.
>
> The code is released under <a href="
> http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA 3.0
> license</a>. Everybody is invited to copy, modify, extend, and share the
> code further. The code can be found in <a href="
> http://r-forge.r-project.org/scm/?group_id=505">the GenABEL project SCM
> at the RForge</a>.
>
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From yurii.aulchenko at gmail.com  Thu Jun 20 01:09:26 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 20 Jun 2013 01:09:26 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <E6BAADB6-B7B5-4DBF-BB6C-BED1013740AD@burlo.trieste.it>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
 <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>
 <CAHX9t6+kfOPUCosuAaOhQsJLWdtef-cTmCH509fRrnj-fuNf7A@mail.gmail.com>
 <E6BAADB6-B7B5-4DBF-BB6C-BED1013740AD@burlo.trieste.it>
Message-ID: <CAHX9t6Lmb-L9RXDspAD+8L+dQWC4OgwgG-GeHQBX3A9oMqaJ0Q@mail.gmail.com>

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
>>
>>  AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute
>> nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel
>> 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.
>>  _______________________________________________
>> 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
>>
>
>
>
>  --
> -----------------------------------------------------
> 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
> nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel
> 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> ] [
Twitter<http://twitter.com/YuriiAulchenko>] [
Blog <http://yurii-aulchenko.blogspot.nl/> ]
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From lennart at karssen.org  Thu Jun 20 09:30:34 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 20 Jun 2013 09:30:34 +0200
Subject: [GenABEL-dev] updated tutorial (chapter on theory of
 stratification back)
In-Reply-To: <CAHX9t6L2jD77z0R=bRv0WJP1M_XWWuFMwoZDRyhxqAnXiLLyaw@mail.gmail.com>
References: <CAHX9t6JEcirZuTP5DaLtLkLZ7SgSpUvACLmWV-YAHYFCx69e7w@mail.gmail.com>
 <CAHX9t6L2jD77z0R=bRv0WJP1M_XWWuFMwoZDRyhxqAnXiLLyaw@mail.gmail.com>
Message-ID: <51C2AF9A.8060704@karssen.org>

Dear Yurii,

The strange links may be the result of the disruption of the storage
platform of our hosting company.
However, somewhere at the back of my mind I seem to remember I've
observed this before. Maybe the requests end up at different webservers
of which some have a dirty cache? If this persists we should contact the
hosting company.


Lennart.

On 19-06-13 22:39, Yurii Aulchenko wrote:
> Upon Maarten's suggestion I renamed the file (to GenABEL-tutorial1.pdf)
> and deleted the old one; changed the link. Now the link
> 
> http://www.genabel.org/sites/default/files/pdfs/GenABEL-tutorial1.pdf
> 
> seems to function properly, but there are funny things still going on:
> 
> http://www.genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf
> 
> serves the "new" (but non-existent on FTP!) file from June 19
> 
> http://genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf
> 
> serves old (also non-existent on FTP!) file from April 15
> 
> On Wed, Jun 19, 2013 at 2:38 PM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     Dear All,
> 
>     I have updated the SVN with latest version of the tutorial (now we
>     are at 261 pages :) ) and put the PDF/HTML on the web-site as well.
>     The latter is a hassle - we need to think how to automate this
>     (Jenkins?!). 
> 
>     There is still something very weird - while HTML update was ok
>     (though this is just by-passing drupal in a way) the PDF gives a
>     trouble. With FTP, I put the PDF to
>     /domains/genabel.org/htdocs/genabel/sites/default/files/pdfs
>     <http://genabel.org/htdocs/genabel/sites/default/files/pdfs> and can
>     get it back (marked June 19). With Chrome (even after cleaning the
>     cache), Mozilla, with my telephone, with
> 
>     wget http://genabel.org/sites/default/files/pdfs/GenABEL-tutorial.pdf
> 
>     I get an old copy (marked April 15!). No idea what is going on; ran
>     out of ideas how to solve this. Very frustrating. 
> 
>     best wishes,
>     Yurii
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]
> 
> 
> _______________________________________________
> 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
------------------------------------------------------------------

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From lennart at karssen.org  Thu Jun 20 09:33:36 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 20 Jun 2013 09:33:36 +0200
Subject: [GenABEL-dev] time to announce SVN tutorial?
In-Reply-To: <CAHX9t6L5TeAirR5mS-=6Ykcaty02CLaKTOE9mEg=mXy_MnvC+Q@mail.gmail.com>
References: <CAHX9t6+2r+uw80oVqoDFvHPg1qyAxk6-bAkXDc6xy9aoHF3cuQ@mail.gmail.com>
 <CAHX9t6L5TeAirR5mS-=6Ykcaty02CLaKTOE9mEg=mXy_MnvC+Q@mail.gmail.com>
Message-ID: <51C2B050.2070603@karssen.org>

Hi Yurii,

I think that's a wonderful idea and a milestone for the project! The
tutorial has always been a strong point of the GenABEL courses.

Maybe also add a short paragraph that encourages people to submit
corrections (I would also include a link to the R-forge SVN web interface).


Great work!

Lennart.

On 20-06-13 00:26, Yurii Aulchenko wrote:
> Probably something to add to the announcement:
> 
> Note that not all the data used in "closed" version were transferrable
> to the open version. These parts are indicated with "DATAPROBLEM" in the
> text. We will appreciate your help in fixing this problems.
> 
> YA
> 
> On Thu, Jun 20, 2013 at 12:13 AM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     Dear All,
> 
>     I think this may be already good time to announce the fact that the
>     GenA became even more open with open source tutorial on SVN.
> 
>     Please let me know what you think and look through the
>     preliminary announcement text below
> 
>     Yurii
> 
>     The GenABEL project: more open than ever!
> 
>     We are glad and proud to announce that the open source GenABEL
>     project became even more open with the release of the source code of
>     the "GenABEL tutorial" . under the E CREATIVE COMMONS ATTRIBUTION-
>     SHAREALIKE 3.0 UNPORTED LICENSE. 
> 
>     The code is released under <a
>     href="http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA
>     3.0 license</a>. Everybody is invited to copy, modify, extend, and
>     share the code further. The code can be found in <a
>     href="http://r-forge.r-project.org/scm/?group_id=505">the GenABEL
>     project SCM at the RForge</a>.
> 
> 
> 
> 
> _______________________________________________
> 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
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Thu Jun 20 09:34:54 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 20 Jun 2013 09:34:54 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
 <51671169.5090608@gmail.com> <51671992.9070100@karssen.org>
 <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>
 <5167B525.6030608@gmail.com> <7783033322271622686@unknownmsgid>
 <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
Message-ID: <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>

Please find attached few more logo variants

Yurii

On Mon, Apr 29, 2013 at 10:15 PM, Yurii Aulchenko <yurii.aulchenko at gmail.com
> wrote:

> Agree.
>
> We have discussed this a bit during EMGM-2013 with Lennart and Nicola, and
> our suggestion (N, L, please correct me if I am wrong) is to
>
> 1) Pick up Maarten's variant
>
> 2) Replace "project" with "Statistical Genomics" as suggested below
>
> 3) Send this to a professional designer to make it 'nice' (I am willing to
> pay it unless it is too expensive)
>
> And of cause the logo can evolve later on if we get better ideas :)
>
> Please let us know what you think.
>
> YA
>
>
> On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org>wrote:
>
>> Short is better in marketing, so in that sense I agree with Maarten and
>> Yurii. But it should cover what we do in/with the project.
>> What about:
>>
>> GenABEL
>> Statistical Genetics
>>
>>
>> Methodology is too "open", our project is focused on statistical
>> genetics (in all its aspects, from methodology development to
>> implementation and user support, but the core is about analysing genetic
>> data).
>>
>>
>> Best,
>>
>> Lennart.
>>
>> On 20/04/13 18:22, Yurii Aulchenko wrote:
>> > Dear All,
>> >
>> > I now tend to agree with Maarten. I have discussed the logos with a
>> > couple of people who know more about design, and it seems that
>> > introducing Greek letters, 0/1 etc may be bad idea - the logo must be
>> > simple. So if we want to deliver extra message it should probably go
>> > to "subheading". The subheading "project" does not carry much info, I
>> > think. I personally like the "statistical toolkit", but I think it may
>> > miss the point that the idea of the project is a bit broader than the
>> > software.
>> >
>> > So, on the top of Maarten's suggestions, what about:
>> >
>> > - methodology project
>> > - open methodology
>> > - methodological toolbox
>> > - methodology
>> > - agile methodology
>> >
>> > YA
>> > ----------------------
>> > Yurii Aulchenko
>> > (sent from mobile device)
>> >
>> > On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com> wrote:
>> >
>> >> I think a logo must deliver the message in one go. I think it misses
>> is goal if you have to play "where is Waldo?" in a logo: the simpler the
>> better. Adding some greek symbols somewhere increase the "where is
>> Waldo?"-effect.
>> >>
>> >> Maybe it is a idea to replace "project" with "Statistical toolkit" or
>> "statistics project"(or is this plainly rude?)
>> >>
>> >> Maarten
>> >>
>> >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>> >>> I think that the greek letters are a good idea although in GenABEL
>> would look very much the same, maybe in project?
>> >>>
>> >>> N.
>> >>>
>> >>> Inviato da iPhone
>> >>>
>> >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko <
>> yurii.aulchenko at gmail.com> ha scritto:
>> >>>
>> >>>> What about replacing some letters with Greek ones - this may give
>> some
>> >>>> math flavor?
>> >>>>
>> >>>> YA
>> >>>>
>> >>>> ----------------------
>> >>>> Yurii Aulchenko
>> >>>> (sent from mobile device)
>> >>>>
>> >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen" <lennart at karssen.org>
>> wrote:
>> >>>>
>> >>>>> Not bad! I really like the way you mixed the G and the DNA.
>> >>>>> Can't we make a combination with Nicola's creation so that we get
>> some
>> >>>>> math in as well? That would nicely integrate two major components
>> of the
>> >>>>> project (only programming would be missing).
>> >>>>>
>> >>>>>
>> >>>>> Lennart
>> >>>>>
>> >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>> >>>>>> Dear All,
>> >>>>>>
>> >>>>>> I made also a small sketch of a logo. It is pretty raw, colours are
>> >>>>>> wrong , etcetera, etcetera.
>> >>>>>>
>> >>>>>> To quote Nicola:
>> >>>>>> " If you hate it or think it should go in another direction, I'm
>> not
>> >>>>>> touchy so please do tell me. "
>> >>>>>>
>> >>>>>>
>> >>>>>> Cheers,
>> >>>>>>
>> >>>>>> Maarten
>> >>>>>>
>> >>>>>>
>> >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>> >>>>>>> Dear all,
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> I gave a shot at the logo, it's very simple. Let me know if you
>> like
>> >>>>>>> the general idea, if you'd like to add something or change it.
>> >>>>>>>
>> >>>>>>> As colors I've sticked to those of the website but they can be
>> >>>>>>> changed. Also the pattern for the formulas have some white
>> spaces, but
>> >>>>>>> this is just a quick draft.
>> >>>>>>>
>> >>>>>>> If you hate it or think it should go in another direction, I'm not
>> >>>>>>> touchy so please do tell me.
>> >>>>>>>
>> >>>>>>> Best.
>> >>>>>>>
>> >>>>>>> Nicola
>> >>>>>>
>> >>>>>>> Dear all,
>> >>>>>>>> I really like the proposal, I just to add a few ideas to the
>> discussion.
>> >>>>>>>> I think that there are some important concepts that could be
>> used for
>> >>>>>>>> a logo:
>> >>>>>>>>
>> >>>>>>>> 1) ABEL which is able in the end could be something like a
>> hammer or a
>> >>>>>>>> tool of some sort.
>> >>>>>>>>
>> >>>>>>>> 2) I think that the great thing about the *ABEL project is that
>> it is not
>> >>>>>>>> a single group but it is a network of people and we could
>> rappresent that
>> >>>>>>>> also.
>> >>>>>>>>
>> >>>>>>>> 3) the * in *ABEL could be made by two crossed Chromosomes or
>> something
>> >>>>>>>> else or maybe a DNA strand a tool and something else (Although I
>> do
>> >>>>>>>> realize that it could remind of the comunist party this way :) ).
>> >>>>>>>>
>> >>>>>>>> 4) I do like animals, but I it should be meanigful somehow
>> (although
>> >>>>>>>> Linux
>> >>>>>>>> does have a penguin for some obscure reason).
>> >>>>>>>>
>> >>>>>>>> Best
>> >>>>>>>>
>> >>>>>>>> Nicola
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>
>> >>>>>>>>> Dear Maarten,
>> >>>>>>>>>
>> >>>>>>>>> I have also some irritation about the fact that there is no
>> recognisable
>> >>>>>>>>>> logo on the page. I looks like a complete default page to me:
>> which
>> >>>>>>>>>> gives
>> >>>>>>>>>> me the impression that there is not any on it. Does someone has
>> >>>>>>>>>> graphical
>> >>>>>>>>>> skills to create a nice logo which we can use on the site,
>> posters or
>> >>>>>>>>>> presentations? Having a neat logo, is like wearing a suite:
>> people
>> >>>>>>>>>> think
>> >>>>>>>>>> at
>> >>>>>>>>>> first sight you are more trustworthy,intelligent etc ect. ;)
>> >>>>>>>>> Completely agree and fully support the idea! I even tried to
>> design
>> >>>>>>>>> something myself, but it was SO bad :)
>> >>>>>>>>>
>> >>>>>>>>> Part of the problem is that obvious meaningful symbols (like
>> >>>>>>>>> chromosomes,
>> >>>>>>>>> sigmas and Gaussians) are boring and used for long time.
>> Another part is
>> >>>>>>>>> that we can not just pick say a cute kitty and stop - there
>> should
>> >>>>>>>>> be some
>> >>>>>>>>> meaning to the symbol (or not?).
>> >>>>>>>>>
>> >>>>>>>>> Do we have examples of successful, recognizable logos we like?I
>> like
>> >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
>> distinguished.
>> >>>>>>>>>
>> >>>>>>>>> Yurii
>> >>>>>>>>> _______________________________________________
>> >>>>>>>>> genabel-devel mailing list
>> >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>> >>>>>>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>>>>>>>
>> >>>>>>>> _______________________________________________
>> >>>>>>>> genabel-devel mailing list
>> >>>>>>>> genabel-devel at lists.r-forge.r-project.org
>> >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org>
>> >>>>>>>>
>> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>> >>>>>>>
>> >>>>>>>
>> >>>>>>> _______________________________________________
>> >>>>>>> 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
>> >>>>>>
>> >>>>>>
>> >>>>>> _______________________________________________
>> >>>>>> 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
>> >>>> _______________________________________________
>> >>>> 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
>> >>> _______________________________________________
>> >>> 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
>> >>
>> >> _______________________________________________
>> >> 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
>> > _______________________________________________
>> > 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
>>
>
>
>
> --
> -----------------------------------------------------
> 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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From lennart at karssen.org  Thu Jun 20 09:45:40 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 20 Jun 2013 09:45:40 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>
Message-ID: <51C2B324.1010706@karssen.org>

Wow! Those look really nice!

I like options C and F the most. Actually a combination would be even
better IMHO: use C with capital ABEL and statistical genomics below it.


Looking forward to head the opinion of others,

Lennart.

On 20-06-13 09:34, Yurii Aulchenko wrote:
> Please find attached few more logo variants
> 
> Yurii
> 
> On Mon, Apr 29, 2013 at 10:15 PM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     Agree.
> 
>     We have discussed this a bit during EMGM-2013 with Lennart and
>     Nicola, and our suggestion (N, L, please correct me if I am wrong)
>     is to 
> 
>     1) Pick up Maarten's variant 
> 
>     2) Replace "project" with "Statistical Genomics" as suggested below
> 
>     3) Send this to a professional designer to make it 'nice' (I am
>     willing to pay it unless it is too expensive)
> 
>     And of cause the logo can evolve later on if we get better ideas :)
> 
>     Please let us know what you think. 
> 
>     YA
> 
> 
>     On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org
>     <mailto:lennart at karssen.org>> wrote:
> 
>         Short is better in marketing, so in that sense I agree with
>         Maarten and
>         Yurii. But it should cover what we do in/with the project.
>         What about:
> 
>         GenABEL
>         Statistical Genetics
> 
> 
>         Methodology is too "open", our project is focused on statistical
>         genetics (in all its aspects, from methodology development to
>         implementation and user support, but the core is about analysing
>         genetic
>         data).
> 
> 
>         Best,
> 
>         Lennart.
> 
>         On 20/04/13 18:22, Yurii Aulchenko wrote:
>         > Dear All,
>         >
>         > I now tend to agree with Maarten. I have discussed the logos
>         with a
>         > couple of people who know more about design, and it seems that
>         > introducing Greek letters, 0/1 etc may be bad idea - the logo
>         must be
>         > simple. So if we want to deliver extra message it should
>         probably go
>         > to "subheading". The subheading "project" does not carry much
>         info, I
>         > think. I personally like the "statistical toolkit", but I
>         think it may
>         > miss the point that the idea of the project is a bit broader
>         than the
>         > software.
>         >
>         > So, on the top of Maarten's suggestions, what about:
>         >
>         > - methodology project
>         > - open methodology
>         > - methodological toolbox
>         > - methodology
>         > - agile methodology
>         >
>         > YA
>         > ----------------------
>         > Yurii Aulchenko
>         > (sent from mobile device)
>         >
>         > On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com
>         <mailto:kooyman at gmail.com>> wrote:
>         >
>         >> I think a logo must deliver the message in one go. I think it
>         misses is goal if you have to play "where is Waldo?" in a logo:
>         the simpler the better. Adding some greek symbols somewhere
>         increase the "where is Waldo?"-effect.
>         >>
>         >> Maybe it is a idea to replace "project" with "Statistical
>         toolkit" or "statistics project"(or is this plainly rude?)
>         >>
>         >> Maarten
>         >>
>         >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>         >>> I think that the greek letters are a good idea although in
>         GenABEL would look very much the same, maybe in project?
>         >>>
>         >>> N.
>         >>>
>         >>> Inviato da iPhone
>         >>>
>         >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko
>         <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>>
>         ha scritto:
>         >>>
>         >>>> What about replacing some letters with Greek ones - this
>         may give some
>         >>>> math flavor?
>         >>>>
>         >>>> YA
>         >>>>
>         >>>> ----------------------
>         >>>> Yurii Aulchenko
>         >>>> (sent from mobile device)
>         >>>>
>         >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen"
>         <lennart at karssen.org <mailto:lennart at karssen.org>> wrote:
>         >>>>
>         >>>>> Not bad! I really like the way you mixed the G and the DNA.
>         >>>>> Can't we make a combination with Nicola's creation so that
>         we get some
>         >>>>> math in as well? That would nicely integrate two major
>         components of the
>         >>>>> project (only programming would be missing).
>         >>>>>
>         >>>>>
>         >>>>> Lennart
>         >>>>>
>         >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>         >>>>>> Dear All,
>         >>>>>>
>         >>>>>> I made also a small sketch of a logo. It is pretty raw,
>         colours are
>         >>>>>> wrong , etcetera, etcetera.
>         >>>>>>
>         >>>>>> To quote Nicola:
>         >>>>>> " If you hate it or think it should go in another
>         direction, I'm not
>         >>>>>> touchy so please do tell me. "
>         >>>>>>
>         >>>>>>
>         >>>>>> Cheers,
>         >>>>>>
>         >>>>>> Maarten
>         >>>>>>
>         >>>>>>
>         >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>         >>>>>>> Dear all,
>         >>>>>>>
>         >>>>>>>
>         >>>>>>> I gave a shot at the logo, it's very simple. Let me know
>         if you like
>         >>>>>>> the general idea, if you'd like to add something or
>         change it.
>         >>>>>>>
>         >>>>>>> As colors I've sticked to those of the website but they
>         can be
>         >>>>>>> changed. Also the pattern for the formulas have some
>         white spaces, but
>         >>>>>>> this is just a quick draft.
>         >>>>>>>
>         >>>>>>> If you hate it or think it should go in another
>         direction, I'm not
>         >>>>>>> touchy so please do tell me.
>         >>>>>>>
>         >>>>>>> Best.
>         >>>>>>>
>         >>>>>>> Nicola
>         >>>>>>
>         >>>>>>> Dear all,
>         >>>>>>>> I really like the proposal, I just to add a few ideas
>         to the discussion.
>         >>>>>>>> I think that there are some important concepts that
>         could be used for
>         >>>>>>>> a logo:
>         >>>>>>>>
>         >>>>>>>> 1) ABEL which is able in the end could be something
>         like a hammer or a
>         >>>>>>>> tool of some sort.
>         >>>>>>>>
>         >>>>>>>> 2) I think that the great thing about the *ABEL project
>         is that it is not
>         >>>>>>>> a single group but it is a network of people and we
>         could rappresent that
>         >>>>>>>> also.
>         >>>>>>>>
>         >>>>>>>> 3) the * in *ABEL could be made by two crossed
>         Chromosomes or something
>         >>>>>>>> else or maybe a DNA strand a tool and something else
>         (Although I do
>         >>>>>>>> realize that it could remind of the comunist party this
>         way :) ).
>         >>>>>>>>
>         >>>>>>>> 4) I do like animals, but I it should be meanigful
>         somehow (although
>         >>>>>>>> Linux
>         >>>>>>>> does have a penguin for some obscure reason).
>         >>>>>>>>
>         >>>>>>>> Best
>         >>>>>>>>
>         >>>>>>>> Nicola
>         >>>>>>>>
>         >>>>>>>>
>         >>>>>>>>
>         >>>>>>>>
>         >>>>>>>>
>         >>>>>>>>
>         >>>>>>>>> Dear Maarten,
>         >>>>>>>>>
>         >>>>>>>>> I have also some irritation about the fact that there
>         is no recognisable
>         >>>>>>>>>> logo on the page. I looks like a complete default
>         page to me: which
>         >>>>>>>>>> gives
>         >>>>>>>>>> me the impression that there is not any on it. Does
>         someone has
>         >>>>>>>>>> graphical
>         >>>>>>>>>> skills to create a nice logo which we can use on the
>         site, posters or
>         >>>>>>>>>> presentations? Having a neat logo, is like wearing a
>         suite: people
>         >>>>>>>>>> think
>         >>>>>>>>>> at
>         >>>>>>>>>> first sight you are more trustworthy,intelligent etc
>         ect. ;)
>         >>>>>>>>> Completely agree and fully support the idea! I even
>         tried to design
>         >>>>>>>>> something myself, but it was SO bad :)
>         >>>>>>>>>
>         >>>>>>>>> Part of the problem is that obvious meaningful symbols
>         (like
>         >>>>>>>>> chromosomes,
>         >>>>>>>>> sigmas and Gaussians) are boring and used for long
>         time. Another part is
>         >>>>>>>>> that we can not just pick say a cute kitty and stop -
>         there should
>         >>>>>>>>> be some
>         >>>>>>>>> meaning to the symbol (or not?).
>         >>>>>>>>>
>         >>>>>>>>> Do we have examples of successful, recognizable logos
>         we like?I like
>         >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
>         distinguished.
>         >>>>>>>>>
>         >>>>>>>>> Yurii
>         >>>>>>>>> _______________________________________________
>         >>>>>>>>> genabel-devel mailing list
>         >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>>
>         >>>>>>>>>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>         >>>>>>>>
>         >>>>>>>> _______________________________________________
>         >>>>>>>> genabel-devel mailing list
>         >>>>>>>> genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>>
>         >>>>>>>>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>         >>>>>>>
>         >>>>>>>
>         >>>>>>> _______________________________________________
>         >>>>>>> genabel-devel mailing list
>         >>>>>>> genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         >>>>>>>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>         >>>>>>
>         >>>>>>
>         >>>>>> _______________________________________________
>         >>>>>> genabel-devel mailing list
>         >>>>>> genabel-devel at lists.r-forge.r-project.org
>         <mailto: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 <mailto: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
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         >>>>>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>         >>>> _______________________________________________
>         >>>> genabel-devel mailing list
>         >>>> genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         >>>>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>         >>> _______________________________________________
>         >>> genabel-devel mailing list
>         >>> genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         >>>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>         >>
>         >> _______________________________________________
>         >> genabel-devel mailing list
>         >> genabel-devel at lists.r-forge.r-project.org
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         >>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>         > _______________________________________________
>         > genabel-devel mailing list
>         > genabel-devel at lists.r-forge.r-project.org
>         <mailto: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 <mailto: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
>         <mailto:genabel-devel at lists.r-forge.r-project.org>
>         https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> 
> 
> 
>     -- 
>     -----------------------------------------------------
>     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/> ]
> 
> 
> _______________________________________________
> 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
------------------------------------------------------------------

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From lennart at karssen.org  Thu Jun 20 09:46:17 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Thu, 20 Jun 2013 09:46:17 +0200
Subject: [GenABEL-dev] GenABEL logo
In-Reply-To: <6010936630980818034@unknownmsgid>
References: <6010936630980818034@unknownmsgid>
Message-ID: <51C2B349.1090605@karssen.org>

Excellent idea! Why didn't I think of that before :-) ??


Lennart

On 19-06-13 22:19, Yurii Aulchenko wrote:
> Dear All,
> 
> I wonder why don't we ask the users to come up with suggestions for
> logo - e.g. we can ask through forum and our news line on the site.
> 
> YA
> 
> ----------------------
> Yurii Aulchenko
> (sent from mobile device)
> _______________________________________________
> 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
------------------------------------------------------------------

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From nicola.pirastu at burlo.trieste.it  Thu Jun 20 10:14:46 2013
From: nicola.pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Thu, 20 Jun 2013 10:14:46 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <51C2B324.1010706@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
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 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>
 <51C2B324.1010706@karssen.or g>
Message-ID: <EF81F137-675E-4A09-A915-81E37C570AD8@burlo.trieste.it>

They do look great.

Who came up with these?

I like C best also, although I'm wondering if we should not change the palette of the forum and website if we use that one.

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 09:45, "L.C. Karssen" <lennart at karssen.org> ha scritto:

> Wow! Those look really nice!
>
> I like options C and F the most. Actually a combination would be even
> better IMHO: use C with capital ABEL and statistical genomics below it.
>
>
> Looking forward to head the opinion of others,
>
> Lennart.
>
> On 20-06-13 09:34, Yurii Aulchenko wrote:
>> Please find attached few more logo variants
>>
>> Yurii
>>
>> On Mon, Apr 29, 2013 at 10:15 PM, Yurii Aulchenko
>> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
>>
>>    Agree.
>>
>>    We have discussed this a bit during EMGM-2013 with Lennart and
>>    Nicola, and our suggestion (N, L, please correct me if I am wrong)
>>    is to
>>
>>    1) Pick up Maarten's variant
>>
>>    2) Replace "project" with "Statistical Genomics" as suggested below
>>
>>    3) Send this to a professional designer to make it 'nice' (I am
>>    willing to pay it unless it is too expensive)
>>
>>    And of cause the logo can evolve later on if we get better ideas :)
>>
>>    Please let us know what you think.
>>
>>    YA
>>
>>
>>    On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org
>>    <mailto:lennart at karssen.org>> wrote:
>>
>>        Short is better in marketing, so in that sense I agree with
>>        Maarten and
>>        Yurii. But it should cover what we do in/with the project.
>>        What about:
>>
>>        GenABEL
>>        Statistical Genetics
>>
>>
>>        Methodology is too "open", our project is focused on statistical
>>        genetics (in all its aspects, from methodology development to
>>        implementation and user support, but the core is about analysing
>>        genetic
>>        data).
>>
>>
>>        Best,
>>
>>        Lennart.
>>
>>        On 20/04/13 18:22, Yurii Aulchenko wrote:
>>> Dear All,
>>>
>>> I now tend to agree with Maarten. I have discussed the logos
>>        with a
>>> couple of people who know more about design, and it seems that
>>> introducing Greek letters, 0/1 etc may be bad idea - the logo
>>        must be
>>> simple. So if we want to deliver extra message it should
>>        probably go
>>> to "subheading". The subheading "project" does not carry much
>>        info, I
>>> think. I personally like the "statistical toolkit", but I
>>        think it may
>>> miss the point that the idea of the project is a bit broader
>>        than the
>>> software.
>>>
>>> So, on the top of Maarten's suggestions, what about:
>>>
>>> - methodology project
>>> - open methodology
>>> - methodological toolbox
>>> - methodology
>>> - agile methodology
>>>
>>> YA
>>> ----------------------
>>> Yurii Aulchenko
>>> (sent from mobile device)
>>>
>>> On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com
>>        <mailto:kooyman at gmail.com>> wrote:
>>>
>>>> I think a logo must deliver the message in one go. I think it
>>        misses is goal if you have to play "where is Waldo?" in a logo:
>>        the simpler the better. Adding some greek symbols somewhere
>>        increase the "where is Waldo?"-effect.
>>>>
>>>> Maybe it is a idea to replace "project" with "Statistical
>>        toolkit" or "statistics project"(or is this plainly rude?)
>>>>
>>>> Maarten
>>>>
>>>> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
>>>>> I think that the greek letters are a good idea although in
>>        GenABEL would look very much the same, maybe in project?
>>>>>
>>>>> N.
>>>>>
>>>>> Inviato da iPhone
>>>>>
>>>>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko
>>        <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>>
>>        ha scritto:
>>>>>
>>>>>> What about replacing some letters with Greek ones - this
>>        may give some
>>>>>> math flavor?
>>>>>>
>>>>>> YA
>>>>>>
>>>>>> ----------------------
>>>>>> Yurii Aulchenko
>>>>>> (sent from mobile device)
>>>>>>
>>>>>> On 11 Apr 2013, at 22:14, "L.C. Karssen"
>>        <lennart at karssen.org <mailto:lennart at karssen.org>> wrote:
>>>>>>
>>>>>>> Not bad! I really like the way you mixed the G and the DNA.
>>>>>>> Can't we make a combination with Nicola's creation so that
>>        we get some
>>>>>>> math in as well? That would nicely integrate two major
>>        components of the
>>>>>>> project (only programming would be missing).
>>>>>>>
>>>>>>>
>>>>>>> Lennart
>>>>>>>
>>>>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
>>>>>>>> Dear All,
>>>>>>>>
>>>>>>>> I made also a small sketch of a logo. It is pretty raw,
>>        colours are
>>>>>>>> wrong , etcetera, etcetera.
>>>>>>>>
>>>>>>>> To quote Nicola:
>>>>>>>> " If you hate it or think it should go in another
>>        direction, I'm not
>>>>>>>> touchy so please do tell me. "
>>>>>>>>
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> Maarten
>>>>>>>>
>>>>>>>>
>>>>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
>>>>>>>>> Dear all,
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> I gave a shot at the logo, it's very simple. Let me know
>>        if you like
>>>>>>>>> the general idea, if you'd like to add something or
>>        change it.
>>>>>>>>>
>>>>>>>>> As colors I've sticked to those of the website but they
>>        can be
>>>>>>>>> changed. Also the pattern for the formulas have some
>>        white spaces, but
>>>>>>>>> this is just a quick draft.
>>>>>>>>>
>>>>>>>>> If you hate it or think it should go in another
>>        direction, I'm not
>>>>>>>>> touchy so please do tell me.
>>>>>>>>>
>>>>>>>>> Best.
>>>>>>>>>
>>>>>>>>> Nicola
>>>>>>>>
>>>>>>>>> Dear all,
>>>>>>>>>> I really like the proposal, I just to add a few ideas
>>        to the discussion.
>>>>>>>>>> I think that there are some important concepts that
>>        could be used for
>>>>>>>>>> a logo:
>>>>>>>>>>
>>>>>>>>>> 1) ABEL which is able in the end could be something
>>        like a hammer or a
>>>>>>>>>> tool of some sort.
>>>>>>>>>>
>>>>>>>>>> 2) I think that the great thing about the *ABEL project
>>        is that it is not
>>>>>>>>>> a single group but it is a network of people and we
>>        could rappresent that
>>>>>>>>>> also.
>>>>>>>>>>
>>>>>>>>>> 3) the * in *ABEL could be made by two crossed
>>        Chromosomes or something
>>>>>>>>>> else or maybe a DNA strand a tool and something else
>>        (Although I do
>>>>>>>>>> realize that it could remind of the comunist party this
>>        way :) ).
>>>>>>>>>>
>>>>>>>>>> 4) I do like animals, but I it should be meanigful
>>        somehow (although
>>>>>>>>>> Linux
>>>>>>>>>> does have a penguin for some obscure reason).
>>>>>>>>>>
>>>>>>>>>> Best
>>>>>>>>>>
>>>>>>>>>> Nicola
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>> Dear Maarten,
>>>>>>>>>>>
>>>>>>>>>>> I have also some irritation about the fact that there
>>        is no recognisable
>>>>>>>>>>>> logo on the page. I looks like a complete default
>>        page to me: which
>>>>>>>>>>>> gives
>>>>>>>>>>>> me the impression that there is not any on it. Does
>>        someone has
>>>>>>>>>>>> graphical
>>>>>>>>>>>> skills to create a nice logo which we can use on the
>>        site, posters or
>>>>>>>>>>>> presentations? Having a neat logo, is like wearing a
>>        suite: people
>>>>>>>>>>>> think
>>>>>>>>>>>> at
>>>>>>>>>>>> first sight you are more trustworthy,intelligent etc
>>        ect. ;)
>>>>>>>>>>> Completely agree and fully support the idea! I even
>>        tried to design
>>>>>>>>>>> something myself, but it was SO bad :)
>>>>>>>>>>>
>>>>>>>>>>> Part of the problem is that obvious meaningful symbols
>>        (like
>>>>>>>>>>> chromosomes,
>>>>>>>>>>> sigmas and Gaussians) are boring and used for long
>>        time. Another part is
>>>>>>>>>>> that we can not just pick say a cute kitty and stop -
>>        there should
>>>>>>>>>>> be some
>>>>>>>>>>> meaning to the symbol (or not?).
>>>>>>>>>>>
>>>>>>>>>>> Do we have examples of successful, recognizable logos
>>        we like?I like
>>>>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
>>        distinguished.
>>>>>>>>>>>
>>>>>>>>>>> Yurii
>>>>>>>>>>> _______________________________________________
>>>>>>>>>>> genabel-devel mailing list
>>>>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>>
>>>>>>>>>>>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> genabel-devel mailing list
>>>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>>
>>>>>>>>>>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> _______________________________________________
>>>>>>>>> genabel-devel mailing list
>>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>>>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> genabel-devel mailing list
>>>>>>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto: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 <mailto: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
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>>> _______________________________________________
>>>>>> genabel-devel mailing list
>>>>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>> _______________________________________________
>>>>> genabel-devel mailing list
>>>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>>>
>>>> _______________________________________________
>>>> genabel-devel mailing list
>>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>>>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>> _______________________________________________
>>> genabel-devel mailing list
>>> genabel-devel at lists.r-forge.r-project.org
>>        <mailto: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 <mailto: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
>>        <mailto:genabel-devel at lists.r-forge.r-project.org>
>>        https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
>>
>>
>>
>>
>>    --
>>    -----------------------------------------------------
>>    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/> ]
>>
>>
>> _______________________________________________
>> 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

AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel 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.

From yurii.aulchenko at gmail.com  Thu Jun 20 13:23:34 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 20 Jun 2013 13:23:34 +0200
Subject: [GenABEL-dev] Fwd: [R-Forge] Update Complete Site/Services Downtime
References: <20130620091736.74F1A1857F3@r-forge.r-project.org>
Message-ID: <-8142959987905897234@unknownmsgid>

FYI

----------------------
Yurii Aulchenko
(sent from mobile device)

Begin forwarded message:

*From:* <noreply at r-forge.r-project.org>
*Date:* 20 June 2013 11:17:36 CEST
*To:* yurii.aulchenko at gmail.com
*Subject:* *[R-Forge] Update Complete Site/Services Downtime*

Dear R-Forge users

There is an update on the planned Site downtime which was scheduled to be
next week:
All services will remain fully online until July 8th.
There will be only one downtime period (as opposed to 2) on July 8th and
the downtime is planned to last 1 day (if no complications arise).
In any case we will still try to keep the downtime as short as possible and
apologize for any inconvenience.

For more Information, please see the previous email sent out (copy attached
below)

The R-Forge Team


Copy of email sent out on June 13th:

Dear R-Forge users

The WU Vienna University of Economics and Business will be moving to a new
campus location this summer. Since the server that hosts the website and
its services is located there, it will also need to be moved to the new
location.

The infrastructure and capacities of the buildings in Vienna?s ninth
district are no longer adequate for the demands placed on them and the
university is ?bursting at the seams.? To remedy this, WU and the
Bundesimmobilien Gesellschaft (a company which manages publicly owned real
estate in Austria) have built a new location to house the university.

According to the moving schedule the R-Forge servers (and resulting
downtime) will be relocated as follows:
June 24 (expected until 29 June): Complete downtime (website, mailing
lists, package build process, svn repos, etc.)
July 8 (expected until 12 July): Build process down (no packages will get
built during this time)

Sometime during this time period, the server will be shut down and remain
off-line until reconnected at the new campus. The downtime is expected to
around one day at minimum, however it can extend up to several days if
complications arise.

We will try to keep the downtime as short as possible and apologize for any
inconvenience

R-Forge Team
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From yurii.aulchenko at gmail.com  Thu Jun 20 23:33:23 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 20 Jun 2013 23:33:23 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <CAHX9t6Lmb-L9RXDspAD+8L+dQWC4OgwgG-GeHQBX3A9oMqaJ0Q@mail.gmail.com>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
 <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>
 <CAHX9t6+kfOPUCosuAaOhQsJLWdtef-cTmCH509fRrnj-fuNf7A@mail.gmail.com>
 <E6BAADB6-B7B5-4DBF-BB6C-BED1013740AD@burlo.trieste.it>
 <CAHX9t6Lmb-L9RXDspAD+8L+dQWC4OgwgG-GeHQBX3A9oMqaJ0Q@mail.gmail.com>
Message-ID: <CAHX9t6+3Bk6tyLbtmBtZX55LWtuzmSY8gj4NFhEzM99U795_QQ@mail.gmail.com>

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
>>>
>>>  AVVISO DI RISERVATEZZA Informazioni riservate possono essere contenute
>>> nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel
>>> 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.
>>>  _______________________________________________
>>> 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
>>>
>>
>>
>>
>>  --
>> -----------------------------------------------------
>> 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
>> nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel
>> 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> ] [ 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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From yurii.aulchenko at gmail.com  Fri Jun 21 09:46:36 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 21 Jun 2013 09:46:36 +0200
Subject: [GenABEL-dev] time to announce SVN tutorial?
In-Reply-To: <51C2B050.2070603@karssen.org>
References: <CAHX9t6+2r+uw80oVqoDFvHPg1qyAxk6-bAkXDc6xy9aoHF3cuQ@mail.gmail.com>
 <CAHX9t6L5TeAirR5mS-=6Ykcaty02CLaKTOE9mEg=mXy_MnvC+Q@mail.gmail.com>
 <51C2B050.2070603@karssen.org>
Message-ID: <CAHX9t6Lxm5rO=KD1PLdkf6pgRfdknRCeGtr9x1Yg=_dkQ=KXHw@mail.gmail.com>

ok, so what about

The GenABEL project: more open than ever!

We are glad and proud to announce that the open source GenABEL project
became even more open with the release of the source code of the "GenABEL
tutorial" .

The code is released under <a href="
http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA 3.0
license</a>. Everybody is invited to copy, modify, extend, and share the
code further. The code can be found in <a href="
http://r-forge.r-project.org/scm/?group_id=505">the GenABEL project SCM at
the RForge</a> (and here is the <a href="
https://r-forge.r-project.org/scm/viewvc.php/tutorials/GenABEL_general/?root=genabel">direct
link to the Tutorial code</a>).

If you are willing to help us, please feel encouraged to export the source
code ("svn export svn://
svn.r-forge.r-project.org/svnroot/genabel/tutorials/GenABEL_general"), make
the corrections (e.g. there are many typos and awkward phrasings) to the
tutorial, and submit the patches to <a href="
https://r-forge.r-project.org/mail/?group_id=505">the genabel-developers'
mailing list</a>.

Note that not all the data used in "closed" version were transferrable to
the open version. These parts are indicated with "DATAPROBLEM" in the text.
We will appreciate your help in fixing this problems.

On Thu, Jun 20, 2013 at 9:33 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Hi Yurii,
>
> I think that's a wonderful idea and a milestone for the project! The
> tutorial has always been a strong point of the GenABEL courses.
>
> Maybe also add a short paragraph that encourages people to submit
> corrections (I would also include a link to the R-forge SVN web interface).
>
>
> Great work!
>
> Lennart.
>
> On 20-06-13 00:26, Yurii Aulchenko wrote:
> > Probably something to add to the announcement:
> >
> > Note that not all the data used in "closed" version were transferrable
> > to the open version. These parts are indicated with "DATAPROBLEM" in the
> > text. We will appreciate your help in fixing this problems.
> >
> > YA
> >
> > On Thu, Jun 20, 2013 at 12:13 AM, Yurii Aulchenko
> > <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> >
> >     Dear All,
> >
> >     I think this may be already good time to announce the fact that the
> >     GenA became even more open with open source tutorial on SVN.
> >
> >     Please let me know what you think and look through the
> >     preliminary announcement text below
> >
> >     Yurii
> >
> >     The GenABEL project: more open than ever!
> >
> >     We are glad and proud to announce that the open source GenABEL
> >     project became even more open with the release of the source code of
> >     the "GenABEL tutorial" . under the E CREATIVE COMMONS ATTRIBUTION-
> >     SHAREALIKE 3.0 UNPORTED LICENSE.
> >
> >     The code is released under <a
> >     href="http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA
> >     3.0 license</a>. Everybody is invited to copy, modify, extend, and
> >     share the code further. The code can be found in <a
> >     href="http://r-forge.r-project.org/scm/?group_id=505">the GenABEL
> >     project SCM at the RForge</a>.
> >
> >
> >
> >
> > _______________________________________________
> > 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
>



-- 
-----------------------------------------------------
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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From lennart at karssen.org  Fri Jun 21 10:31:36 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 21 Jun 2013 10:31:36 +0200
Subject: [GenABEL-dev] time to announce SVN tutorial?
In-Reply-To: <CAHX9t6Lxm5rO=KD1PLdkf6pgRfdknRCeGtr9x1Yg=_dkQ=KXHw@mail.gmail.com>
References: <CAHX9t6+2r+uw80oVqoDFvHPg1qyAxk6-bAkXDc6xy9aoHF3cuQ@mail.gmail.com>
 <CAHX9t6L5TeAirR5mS-=6Ykcaty02CLaKTOE9mEg=mXy_MnvC+Q@mail.gmail.com>
 <51C2B050.2070603@karssen.org>
 <CAHX9t6Lxm5rO=KD1PLdkf6pgRfdknRCeGtr9x1Yg=_dkQ=KXHw@mail.gmail.com>
Message-ID: <51C40F68.5070601@karssen.org>

Hi Yurii,

Sounds good. The only thing I would change is the word "code" to
"source" or "source material".
Oh, and in the last line: "this problems" -> "these problems".


Should we mention that the document is written in LaTeX? We could write
that it is a simple plain text format so that fixing things like
spelling mistakes is easy and doesn't really require any LaTeX knowledge.



Lennart.

On 21-06-13 09:46, Yurii Aulchenko wrote:
> ok, so what about
> 
> The GenABEL project: more open than ever!
> 
> We are glad and proud to announce that the open source GenABEL project
> became even more open with the release of the source code of the
> "GenABEL tutorial" . 
> 
> The code is released under <a
> href="http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA 3.0
> license</a>. Everybody is invited to copy, modify, extend, and share the
> code further. The code can be found in <a
> href="http://r-forge.r-project.org/scm/?group_id=505">the GenABEL
> project SCM at the RForge</a> (and here is the <a
> href="https://r-forge.r-project.org/scm/viewvc.php/tutorials/GenABEL_general/?root=genabel">direct
> link to the Tutorial code</a>).
> 
> If you are willing to help us, please feel encouraged to export the
> source code ("svn export
> svn://svn.r-forge.r-project.org/svnroot/genabel/tutorials/GenABEL_general <http://svn.r-forge.r-project.org/svnroot/genabel/tutorials/GenABEL_general>"),
> make the corrections (e.g. there are many typos and awkward phrasings)
> to the tutorial, and submit the patches to <a
> href="https://r-forge.r-project.org/mail/?group_id=505">the
> genabel-developers' mailing list</a>.
> 
> Note that not all the data used in "closed" version were transferrable
> to the open version. These parts are indicated with "DATAPROBLEM" in the
> text. We will appreciate your help in fixing this problems.
> 
> On Thu, Jun 20, 2013 at 9:33 AM, L.C. Karssen <lennart at karssen.org
> <mailto:lennart at karssen.org>> wrote:
> 
>     Hi Yurii,
> 
>     I think that's a wonderful idea and a milestone for the project! The
>     tutorial has always been a strong point of the GenABEL courses.
> 
>     Maybe also add a short paragraph that encourages people to submit
>     corrections (I would also include a link to the R-forge SVN web
>     interface).
> 
> 
>     Great work!
> 
>     Lennart.
> 
>     On 20-06-13 00:26, Yurii Aulchenko wrote:
>     > Probably something to add to the announcement:
>     >
>     > Note that not all the data used in "closed" version were transferrable
>     > to the open version. These parts are indicated with "DATAPROBLEM"
>     in the
>     > text. We will appreciate your help in fixing this problems.
>     >
>     > YA
>     >
>     > On Thu, Jun 20, 2013 at 12:13 AM, Yurii Aulchenko
>     > <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>
>     <mailto:yurii.aulchenko at gmail.com
>     <mailto:yurii.aulchenko at gmail.com>>> wrote:
>     >
>     >     Dear All,
>     >
>     >     I think this may be already good time to announce the fact
>     that the
>     >     GenA became even more open with open source tutorial on SVN.
>     >
>     >     Please let me know what you think and look through the
>     >     preliminary announcement text below
>     >
>     >     Yurii
>     >
>     >     The GenABEL project: more open than ever!
>     >
>     >     We are glad and proud to announce that the open source GenABEL
>     >     project became even more open with the release of the source
>     code of
>     >     the "GenABEL tutorial" . under the E CREATIVE COMMONS ATTRIBUTION-
>     >     SHAREALIKE 3.0 UNPORTED LICENSE.
>     >
>     >     The code is released under <a
>     >     href="http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA
>     >     3.0 license</a>. Everybody is invited to copy, modify, extend, and
>     >     share the code further. The code can be found in <a
>     >     href="http://r-forge.r-project.org/scm/?group_id=505">the GenABEL
>     >     project SCM at the RForge</a>.
>     >
>     >
>     >
>     >
>     > _______________________________________________
>     > genabel-devel mailing list
>     > genabel-devel at lists.r-forge.r-project.org
>     <mailto: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 <mailto: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
>     <mailto:genabel-devel at lists.r-forge.r-project.org>
>     https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> 
> 
> 
> 
> -- 
> -----------------------------------------------------
> Yurii S. Aulchenko
> 
> [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> <http://twitter.com/YuriiAulchenko> ] [ Blog
> <http://yurii-aulchenko.blogspot.nl/> ]

-- 
-----------------------------------------------------------------
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
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Tue Jun 25 22:27:20 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Tue, 25 Jun 2013 22:27:20 +0200
Subject: [GenABEL-dev] time to announce SVN tutorial?
In-Reply-To: <51C40F68.5070601@karssen.org>
References: <CAHX9t6+2r+uw80oVqoDFvHPg1qyAxk6-bAkXDc6xy9aoHF3cuQ@mail.gmail.com>
 <CAHX9t6L5TeAirR5mS-=6Ykcaty02CLaKTOE9mEg=mXy_MnvC+Q@mail.gmail.com>
 <51C2B050.2070603@karssen.org>
 <CAHX9t6Lxm5rO=KD1PLdkf6pgRfdknRCeGtr9x1Yg=_dkQ=KXHw@mail.gmail.com>
 <51C40F68.5070601@karssen.org>
Message-ID: <CAHX9t6K0vYo7WOmFsDjCTYnZiQ87ysmMzGwBJkSZiZVpcWxtBw@mail.gmail.com>

I have made suggested corrections and published these news at
http://www.genabel.org/news20130625. As usual, the social buttons allow you
to share these news with your friends and colleagues :)

Yurii

On Fri, Jun 21, 2013 at 10:31 AM, L.C. Karssen <lennart at karssen.org> wrote:

> Hi Yurii,
>
> Sounds good. The only thing I would change is the word "code" to
> "source" or "source material".
> Oh, and in the last line: "this problems" -> "these problems".
>
>
> Should we mention that the document is written in LaTeX? We could write
> that it is a simple plain text format so that fixing things like
> spelling mistakes is easy and doesn't really require any LaTeX knowledge.
>
>
>
> Lennart.
>
> On 21-06-13 09:46, Yurii Aulchenko wrote:
> > ok, so what about
> >
> > The GenABEL project: more open than ever!
> >
> > We are glad and proud to announce that the open source GenABEL project
> > became even more open with the release of the source code of the
> > "GenABEL tutorial" .
> >
> > The code is released under <a
> > href="http://creativecommons.org/licenses/by-sa/3.0/">the CC-BY-SA 3.0
> > license</a>. Everybody is invited to copy, modify, extend, and share the
> > code further. The code can be found in <a
> > href="http://r-forge.r-project.org/scm/?group_id=505">the GenABEL
> > project SCM at the RForge</a> (and here is the <a
> > href="
> https://r-forge.r-project.org/scm/viewvc.php/tutorials/GenABEL_general/?root=genabel
> ">direct
> > link to the Tutorial code</a>).
> >
> > If you are willing to help us, please feel encouraged to export the
> > source code ("svn export
> > svn://
> svn.r-forge.r-project.org/svnroot/genabel/tutorials/GenABEL_general <
> http://svn.r-forge.r-project.org/svnroot/genabel/tutorials/GenABEL_general
> >"),
> > make the corrections (e.g. there are many typos and awkward phrasings)
> > to the tutorial, and submit the patches to <a
> > href="https://r-forge.r-project.org/mail/?group_id=505">the
> > genabel-developers' mailing list</a>.
> >
> > Note that not all the data used in "closed" version were transferrable
> > to the open version. These parts are indicated with "DATAPROBLEM" in the
> > text. We will appreciate your help in fixing this problems.
> >
> > On Thu, Jun 20, 2013 at 9:33 AM, L.C. Karssen <lennart at karssen.org
> > <mailto:lennart at karssen.org>> wrote:
> >
> >     Hi Yurii,
> >
> >     I think that's a wonderful idea and a milestone for the project! The
> >     tutorial has always been a strong point of the GenABEL courses.
> >
> >     Maybe also add a short paragraph that encourages people to submit
> >     corrections (I would also include a link to the R-forge SVN web
> >     interface).
> >
> >
> >     Great work!
> >
> >     Lennart.
> >
> >     On 20-06-13 00:26, Yurii Aulchenko wrote:
> >     > Probably something to add to the announcement:
> >     >
> >     > Note that not all the data used in "closed" version were
> transferrable
> >     > to the open version. These parts are indicated with "DATAPROBLEM"
> >     in the
> >     > text. We will appreciate your help in fixing this problems.
> >     >
> >     > YA
> >     >
> >     > On Thu, Jun 20, 2013 at 12:13 AM, Yurii Aulchenko
> >     > <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>
> >     <mailto:yurii.aulchenko at gmail.com
> >     <mailto:yurii.aulchenko at gmail.com>>> wrote:
> >     >
> >     >     Dear All,
> >     >
> >     >     I think this may be already good time to announce the fact
> >     that the
> >     >     GenA became even more open with open source tutorial on SVN.
> >     >
> >     >     Please let me know what you think and look through the
> >     >     preliminary announcement text below
> >     >
> >     >     Yurii
> >     >
> >     >     The GenABEL project: more open than ever!
> >     >
> >     >     We are glad and proud to announce that the open source GenABEL
> >     >     project became even more open with the release of the source
> >     code of
> >     >     the "GenABEL tutorial" . under the E CREATIVE COMMONS
> ATTRIBUTION-
> >     >     SHAREALIKE 3.0 UNPORTED LICENSE.
> >     >
> >     >     The code is released under <a
> >     >     href="http://creativecommons.org/licenses/by-sa/3.0/">the
> CC-BY-SA
> >     >     3.0 license</a>. Everybody is invited to copy, modify, extend,
> and
> >     >     share the code further. The code can be found in <a
> >     >     href="http://r-forge.r-project.org/scm/?group_id=505">the
> GenABEL
> >     >     project SCM at the RForge</a>.
> >     >
> >     >
> >     >
> >     >
> >     > _______________________________________________
> >     > genabel-devel mailing list
> >     > genabel-devel at lists.r-forge.r-project.org
> >     <mailto: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 <mailto: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
> >     <mailto:genabel-devel at lists.r-forge.r-project.org>
> >
> https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >
> >
> >
> >
> > --
> > -----------------------------------------------------
> > Yurii S. Aulchenko
> >
> > [ LinkedIn <http://nl.linkedin.com/in/yuriiaulchenko> ] [ Twitter
> > <http://twitter.com/YuriiAulchenko> ] [ Blog
> > <http://yurii-aulchenko.blogspot.nl/> ]
>
> --
> -----------------------------------------------------------------
> 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
> ------------------------------------------------------------------
>
>


-- 
-----------------------------------------------------
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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From fabregat at aices.rwth-aachen.de  Wed Jun 26 16:16:15 2013
From: fabregat at aices.rwth-aachen.de (Diego Fabregat Traver)
Date: Wed, 26 Jun 2013 16:16:15 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <51C2B324.1010706@karssen.org>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>
 <51C2B324.1010706@karssen.org>
Message-ID: <fb5504221a5b85.51cb13cf@aices.rwth-aachen.de>


Congrats to whoever designed these logos, they look very nice :)

With respect to my preferences, I fully agree with Lennart: "C with capital ABEL and statistical genomics below it" would be my choice.

Best,
Diego


On 20/06/13, "L.C. Karssen"  <lennart at karssen.org> wrote:

> Wow! Those look really nice!
> 
> I like options C and F the most. Actually a combination would be even
> better IMHO: use C with capital ABEL and statistical genomics below it.
> 
> 
> Looking forward to head the opinion of others,
> 
> Lennart.
> 
> On 20-06-13 09:34, Yurii Aulchenko wrote:
> > Please find attached few more logo variants
> > 
> > Yurii
> > 
> > On Mon, Apr 29, 2013 at 10:15 PM, Yurii Aulchenko
> > <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com(javascript:main.compose()>> wrote:
> > 
> >???? Agree.
> > 
> >???? We have discussed this a bit during EMGM-2013 with Lennart and
> >???? Nicola, and our suggestion (N, L, please correct me if I am wrong)
> >???? is to 
> > 
> >???? 1) Pick up Maarten's variant 
> > 
> >???? 2) Replace "project" with "Statistical Genomics" as suggested below
> > 
> >???? 3) Send this to a professional designer to make it 'nice' (I am
> >???? willing to pay it unless it is too expensive)
> > 
> >???? And of cause the logo can evolve later on if we get better ideas :)
> > 
> >???? Please let us know what you think. 
> > 
> >???? YA
> > 
> > 
> >???? On Sat, Apr 20, 2013 at 11:09 PM, L.C. Karssen <lennart at karssen.org
> >???? <mailto:lennart at karssen.org(javascript:main.compose()>> wrote:
> > 
> >???????? Short is better in marketing, so in that sense I agree with
> >???????? Maarten and
> >???????? Yurii. But it should cover what we do in/with the project.
> >???????? What about:
> > 
> >???????? GenABEL
> >???????? Statistical Genetics
> > 
> > 
> >???????? Methodology is too "open", our project is focused on statistical
> >???????? genetics (in all its aspects, from methodology development to
> >???????? implementation and user support, but the core is about analysing
> >???????? genetic
> >???????? data).
> > 
> > 
> >???????? Best,
> > 
> >???????? Lennart.
> > 
> >???????? On 20/04/13 18:22, Yurii Aulchenko wrote:
> >???????? > Dear All,
> >???????? >
> >???????? > I now tend to agree with Maarten. I have discussed the logos
> >???????? with a
> >???????? > couple of people who know more about design, and it seems that
> >???????? > introducing Greek letters, 0/1 etc may be bad idea - the logo
> >???????? must be
> >???????? > simple. So if we want to deliver extra message it should
> >???????? probably go
> >???????? > to "subheading". The subheading "project" does not carry much
> >???????? info, I
> >???????? > think. I personally like the "statistical toolkit", but I
> >???????? think it may
> >???????? > miss the point that the idea of the project is a bit broader
> >???????? than the
> >???????? > software.
> >???????? >
> >???????? > So, on the top of Maarten's suggestions, what about:
> >???????? >
> >???????? > - methodology project
> >???????? > - open methodology
> >???????? > - methodological toolbox
> >???????? > - methodology
> >???????? > - agile methodology
> >???????? >
> >???????? > YA
> >???????? > ----------------------
> >???????? > Yurii Aulchenko
> >???????? > (sent from mobile device)
> >???????? >
> >???????? > On 12 Apr 2013, at 09:18, Maarten Kooyman <kooyman at gmail.com
> >???????? <mailto:kooyman at gmail.com(javascript:main.compose()>> wrote:
> >???????? >
> >???????? >> I think a logo must deliver the message in one go. I think it
> >???????? misses is goal if you have to play "where is Waldo?" in a logo:
> >???????? the simpler the better. Adding some greek symbols somewhere
> >???????? increase the "where is Waldo?"-effect.
> >???????? >>
> >???????? >> Maybe it is a idea to replace "project" with "Statistical
> >???????? toolkit" or "statistics project"(or is this plainly rude?)
> >???????? >>
> >???????? >> Maarten
> >???????? >>
> >???????? >> On 04/11/2013 11:46 PM, Nicola Pirastu wrote:
> >???????? >>> I think that the greek letters are a good idea although in
> >???????? GenABEL would look very much the same, maybe in project?
> >???????? >>>
> >???????? >>> N.
> >???????? >>>
> >???????? >>> Inviato da iPhone
> >???????? >>>
> >???????? >>> Il giorno 11/apr/2013, alle ore 23:34, Yurii Aulchenko
> >???????? <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com(javascript:main.compose()>>
> >???????? ha scritto:
> >???????? >>>
> >???????? >>>> What about replacing some letters with Greek ones - this
> >???????? may give some
> >???????? >>>> math flavor?
> >???????? >>>>
> >???????? >>>> YA
> >???????? >>>>
> >???????? >>>> ----------------------
> >???????? >>>> Yurii Aulchenko
> >???????? >>>> (sent from mobile device)
> >???????? >>>>
> >???????? >>>> On 11 Apr 2013, at 22:14, "L.C. Karssen"
> >???????? <lennart at karssen.org <mailto:lennart at karssen.org(javascript:main.compose()>> wrote:
> >???????? >>>>
> >???????? >>>>> Not bad! I really like the way you mixed the G and the DNA.
> >???????? >>>>> Can't we make a combination with Nicola's creation so that
> >???????? we get some
> >???????? >>>>> math in as well? That would nicely integrate two major
> >???????? components of the
> >???????? >>>>> project (only programming would be missing).
> >???????? >>>>>
> >???????? >>>>>
> >???????? >>>>> Lennart
> >???????? >>>>>
> >???????? >>>>> On 11/04/13 21:39, Maarten Kooyman wrote:
> >???????? >>>>>> Dear All,
> >???????? >>>>>>
> >???????? >>>>>> I made also a small sketch of a logo. It is pretty raw,
> >???????? colours are
> >???????? >>>>>> wrong , etcetera, etcetera.
> >???????? >>>>>>
> >???????? >>>>>> To quote Nicola:
> >???????? >>>>>> " If you hate it or think it should go in another
> >???????? direction, I'm not
> >???????? >>>>>> touchy so please do tell me. "
> >???????? >>>>>>
> >???????? >>>>>>
> >???????? >>>>>> Cheers,
> >???????? >>>>>>
> >???????? >>>>>> Maarten
> >???????? >>>>>>
> >???????? >>>>>>
> >???????? >>>>>> On 04/06/2013 01:36 AM, Nicola Pirastu wrote:
> >???????? >>>>>>> Dear all,
> >???????? >>>>>>>
> >???????? >>>>>>>
> >???????? >>>>>>> I gave a shot at the logo, it's very simple. Let me know
> >???????? if you like
> >???????? >>>>>>> the general idea, if you'd like to add something or
> >???????? change it.
> >???????? >>>>>>>
> >???????? >>>>>>> As colors I've sticked to those of the website but they
> >???????? can be
> >???????? >>>>>>> changed. Also the pattern for the formulas have some
> >???????? white spaces, but
> >???????? >>>>>>> this is just a quick draft.
> >???????? >>>>>>>
> >???????? >>>>>>> If you hate it or think it should go in another
> >???????? direction, I'm not
> >???????? >>>>>>> touchy so please do tell me.
> >???????? >>>>>>>
> >???????? >>>>>>> Best.
> >???????? >>>>>>>
> >???????? >>>>>>> Nicola
> >???????? >>>>>>
> >???????? >>>>>>> Dear all,
> >???????? >>>>>>>> I really like the proposal, I just to add a few ideas
> >???????? to the discussion.
> >???????? >>>>>>>> I think that there are some important concepts that
> >???????? could be used for
> >???????? >>>>>>>> a logo:
> >???????? >>>>>>>>
> >???????? >>>>>>>> 1) ABEL which is able in the end could be something
> >???????? like a hammer or a
> >???????? >>>>>>>> tool of some sort.
> >???????? >>>>>>>>
> >???????? >>>>>>>> 2) I think that the great thing about the *ABEL project
> >???????? is that it is not
> >???????? >>>>>>>> a single group but it is a network of people and we
> >???????? could rappresent that
> >???????? >>>>>>>> also.
> >???????? >>>>>>>>
> >???????? >>>>>>>> 3) the * in *ABEL could be made by two crossed
> >???????? Chromosomes or something
> >???????? >>>>>>>> else or maybe a DNA strand a tool and something else
> >???????? (Although I do
> >???????? >>>>>>>> realize that it could remind of the comunist party this
> >???????? way :) ).
> >???????? >>>>>>>>
> >???????? >>>>>>>> 4) I do like animals, but I it should be meanigful
> >???????? somehow (although
> >???????? >>>>>>>> Linux
> >???????? >>>>>>>> does have a penguin for some obscure reason).
> >???????? >>>>>>>>
> >???????? >>>>>>>> Best
> >???????? >>>>>>>>
> >???????? >>>>>>>> Nicola
> >???????? >>>>>>>>
> >???????? >>>>>>>>
> >???????? >>>>>>>>
> >???????? >>>>>>>>
> >???????? >>>>>>>>
> >???????? >>>>>>>>
> >???????? >>>>>>>>> Dear Maarten,
> >???????? >>>>>>>>>
> >???????? >>>>>>>>> I have also some irritation about the fact that there
> >???????? is no recognisable
> >???????? >>>>>>>>>> logo on the page. I looks like a complete default
> >???????? page to me: which
> >???????? >>>>>>>>>> gives
> >???????? >>>>>>>>>> me the impression that there is not any on it. Does
> >???????? someone has
> >???????? >>>>>>>>>> graphical
> >???????? >>>>>>>>>> skills to create a nice logo which we can use on the
> >???????? site, posters or
> >???????? >>>>>>>>>> presentations? Having a neat logo, is like wearing a
> >???????? suite: people
> >???????? >>>>>>>>>> think
> >???????? >>>>>>>>>> at
> >???????? >>>>>>>>>> first sight you are more trustworthy,intelligent etc
> >???????? ect. ;)
> >???????? >>>>>>>>> Completely agree and fully support the idea! I even
> >???????? tried to design
> >???????? >>>>>>>>> something myself, but it was SO bad :)
> >???????? >>>>>>>>>
> >???????? >>>>>>>>> Part of the problem is that obvious meaningful symbols
> >???????? (like
> >???????? >>>>>>>>> chromosomes,
> >???????? >>>>>>>>> sigmas and Gaussians) are boring and used for long
> >???????? time. Another part is
> >???????? >>>>>>>>> that we can not just pick say a cute kitty and stop -
> >???????? there should
> >???????? >>>>>>>>> be some
> >???????? >>>>>>>>> meaning to the symbol (or not?).
> >???????? >>>>>>>>>
> >???????? >>>>>>>>> Do we have examples of successful, recognizable logos
> >???????? we like?I like
> >???????? >>>>>>>>> FreeBSD, GNU's Gnu, also Firefox and Chrome are very
> >???????? distinguished.
> >???????? >>>>>>>>>
> >???????? >>>>>>>>> Yurii
> >???????? >>>>>>>>> _______________________________________________
> >???????? >>>>>>>>> genabel-devel mailing list
> >???????? >>>>>>>>> genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>>
> >???????? >>>>>>>>>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >>>>>>>>
> >???????? >>>>>>>> _______________________________________________
> >???????? >>>>>>>> genabel-devel mailing list
> >???????? >>>>>>>> genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>>>>>>> <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>>
> >???????? >>>>>>>>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >>>>>>>
> >???????? >>>>>>>
> >???????? >>>>>>> _______________________________________________
> >???????? >>>>>>> genabel-devel mailing list
> >???????? >>>>>>> genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>>>>>>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >>>>>>
> >???????? >>>>>>
> >???????? >>>>>> _______________________________________________
> >???????? >>>>>> genabel-devel mailing list
> >???????? >>>>>> genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>>>>>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >>>>> --
> >???????? >>>>>
> >???????? -----------------------------------------------------------------
> >???????? >>>>> L.C. Karssen
> >???????? >>>>> Utrecht
> >???????? >>>>> The Netherlands
> >???????? >>>>>
> >???????? >>>>> lennart at karssen.org <mailto:lennart at karssen.org(javascript:main.compose()>
> >???????? >>>>> 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
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>>>>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >>>> _______________________________________________
> >???????? >>>> genabel-devel mailing list
> >???????? >>>> genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>>>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >>> _______________________________________________
> >???????? >>> genabel-devel mailing list
> >???????? >>> genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >>
> >???????? >> _______________________________________________
> >???????? >> genabel-devel mailing list
> >???????? >> genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? > _______________________________________________
> >???????? > genabel-devel mailing list
> >???????? > genabel-devel at lists.r-forge.r-project.org
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? >
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> >???????? >
> > 
> >???????? --
> >???????? -----------------------------------------------------------------
> >???????? L.C. Karssen
> >???????? Utrecht
> >???????? The Netherlands
> > 
> >???????? lennart at karssen.org <mailto:lennart at karssen.org(javascript:main.compose()>
> >???????? 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
> >???????? <mailto:genabel-devel at lists.r-forge.r-project.org(javascript:main.compose()>
> >???????? https://lists.r-forge.r-project.org/cgi-bin/mailman/listinfo/genabel-devel
> > 
> > 
> > 
> > 
> >???? -- 
> >???? -----------------------------------------------------
> >???? 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/> ]
> > 
> > 
> > _______________________________________________
> > 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

From nicola.pirastu at burlo.trieste.it  Thu Jun 27 11:10:55 2013
From: nicola.pirastu at burlo.trieste.it (Nicola Pirastu)
Date: Thu, 27 Jun 2013 11:10:55 +0200
Subject: [GenABEL-dev] joining the GenABEL project - what is the
	procedure?
In-Reply-To: <CAHX9t6+3Bk6tyLbtmBtZX55LWtuzmSY8gj4NFhEzM99U795_QQ@mail.gmail.com>
References: <CAHX9t6+LDcyCnSNmhywWY5Wz9y+zrZO93CF+0jS5D6SefQsM9w@mail.gmail.com>
 <51916427.8020307@karssen.org>
 <CB4CF543-7387-4B98-B412-7ED794CEB37B@burlo.trieste.it>
 <CAHX9t6+kfOPUCosuAaOhQsJLWdtef-cTmCH509fRrnj-fuNf7A@mail.gmail.com>
 <E6BAADB6-B7B5-4DBF-BB6C-BED1013740AD@burlo.trieste.it>
 <CAHX9t6Lmb-L9RXDspAD+8L+dQWC4OgwgG-GeHQBX3A9oMqaJ0Q@mail.gmail.com>
 <CAHX9t6+3Bk6tyLbtmBtZX55LWtuzmSY8gj4NFhEzM99U795_QQ@mail.gmail.com>
Message-ID: <75533175-C431-46A8-8B57-AC12B67C968E@burlo.trieste.it>

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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<mailto: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<http://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<mailto: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<mailto:lennart at karssen.org>
> http://blog.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<mailto: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 nel messaggio o nei suoi allegati. Se non siete i destinatari indicati nel 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> ] [ 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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From yurii.aulchenko at gmail.com  Thu Jun 27 13:16:31 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 27 Jun 2013 13:16:31 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <fb5504221a5b85.51cb13cf@aices.rwth-aachen.de>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
 <51671169.5090608@gmail.com> <51671992.9070100@karssen.org>
 <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>
 <5167B525.6030608@gmail.com> <7783033322271622686@unknownmsgid>
 <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>
 <51C2B324.1010706@karssen.org>
 <fb5504221a5b85.51cb13cf@aices.rwth-aachen.de>
Message-ID: <CAHX9t6KVUf2v7oZB7qMc+NbT-rwrW1UfgqR7wN76XHQ6E42qWA@mail.gmail.com>

Dear Nicola, Diego, Lennart,

Thanks for your feedback! I will ask Grant Borodin, who kindly designed
these logos, if he could change C according to your comment (capital "ABEL"
and "statistical genomics" as in F).

Yurii

On Wed, Jun 26, 2013 at 4:16 PM, Diego Fabregat Traver <
fabregat at aices.rwth-aachen.de> wrote:

>
> Congrats to whoever designed these logos, they look very nice :)
>
> With respect to my preferences, I fully agree with Lennart: "C with
> capital ABEL and statistical genomics below it" would be my choice.
>
> Best,
> Diego
>
>
> On 20/06/13, "L.C. Karssen"  <lennart at karssen.org> wrote:
>
> > Wow! Those look really nice!
> >
> > I like options C and F the most. Actually a combination would be even
> > better IMHO: use C with capital ABEL and statistical genomics below it.
> >
> >
> > Looking forward to head the opinion of others,
> >
> > Lennart.
> >
> > On 20-06-13 09:34, Yurii Aulchenko wrote:
> > > Please find attached few more logo variants
> > >
> > > Yurii
>
>
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From yurii.aulchenko at gmail.com  Thu Jun 27 14:58:44 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Thu, 27 Jun 2013 14:58:44 +0200
Subject: [GenABEL-dev] announcements
Message-ID: <CAHX9t6LbpNFKt5NhgbirX-O7oQhaLR5DHS+4yhypcA-jSB5VXA@mail.gmail.com>

Dear All,

I'd like to publish the following news on genabel.org in coming days. Your
comments are welcome!

YA


A manuscript on a new region-based association analysis method and GRAMMAR+
transformation

The team led by Prof. Axenovich has published the manuscript on <a href="
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0065395">"Region-Based
Association Analysis of Human Quantitative Traits in Related
Individuals"</a>. Additionally to providing a region-based analysis method,
the manuscript also features description of the GRAMMAR+ transformation,
which allows treating transformed trait values as if they were measured in
a population-based study of unrelated individuals. We foresee this
transformation will be very useful, e.g. it allows application of multiple
methods developed in the population-based context to the analysis of data
with genetic (sub)structure.

The GRAMMAR+ transformation is an improvement of the <a href="
http://www.genetics.org/content/177/1/577">original GRAMMAR-residuals</a>
(aka "environmental residuals"), which are known to lead to conservative
analysis. This is not the case with the new GRAMMAR+ transform.

GRAMMAR+ transformation is available in the GenABEL package as one of the
objects (...$grresidualY) returned by the 'polygenic' command.



Update of the open "GenABEL tutorial"

Open <a href="http://www.genabel.org/tutorials">GenABEL tutorial</a> -- as
announced in <a href="http://www.genabel.org/news20130625">previous
story</a> -- has reached total length of 261 pages after a recent update.
The update mostly concerns the chapter "GWA analysis in presence of
stratification: theory".

The text of this chapter is in large part based on a chapter "Effects of
Population Structure in Genome-wide Association Studies" of a the book <a
href="
http://store.elsevier.com/Analysis-of-Complex-Disease-Association-Studies/isbn-9780123751423/">"Analysis
of Complex Disease Association Studies: A Practical Guide"</a> published by
Elsvier in 2011.

We thank Elsvier for the permission to reproduce the text and figures in
our tutorial.
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From yurii.aulchenko at gmail.com  Fri Jun 28 22:52:07 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Fri, 28 Jun 2013 22:52:07 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6KVUf2v7oZB7qMc+NbT-rwrW1UfgqR7wN76XHQ6E42qWA@mail.gmail.com>
References: <515446DC.6040602@karssen.org> <515B075B.4080502@karssen.org>
 <84251364983103@web2f.yandex.ru>
 <CAHX9t6+UFEuEqiJvkwKyjCu8GQVY_3RYFoGgGLfVPK69YapxOQ@mail.gmail.com>
 <515C1080.9010606@karssen.org>
 <9176724B-D86D-4644-A711-67BA51EB33D3@burlo.trieste.it>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com>
 <51671169.5090608@gmail.com> <51671992.9070100@karssen.org>
 <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com>
 <5167B525.6030608@gmail.com> <7783033322271622686@unknownmsgid>
 <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>
 <51C2B324.1010706@karssen.org>
 <fb5504221a5b85.51cb13cf@aices.rwth-aachen.de>
 <CAHX9t6KVUf2v7oZB7qMc+NbT-rwrW1UfgqR7wN76XHQ6E42qWA@mail.gmail.com>
Message-ID: <CAHX9t6LBj-SJkZ0YBwsEBkq11Re+wh9RzUtFYw5L9qjvqs+Aug@mail.gmail.com>

How do you like this one?

YA

On Thu, Jun 27, 2013 at 1:16 PM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:

> Dear Nicola, Diego, Lennart,
>
> Thanks for your feedback! I will ask Grant Borodin, who kindly designed
> these logos, if he could change C according to your comment (capital "ABEL"
> and "statistical genomics" as in F).
>
> Yurii
>
>
> On Wed, Jun 26, 2013 at 4:16 PM, Diego Fabregat Traver <
> fabregat at aices.rwth-aachen.de> wrote:
>
>>
>> Congrats to whoever designed these logos, they look very nice :)
>>
>> With respect to my preferences, I fully agree with Lennart: "C with
>> capital ABEL and statistical genomics below it" would be my choice.
>>
>> Best,
>> Diego
>>
>>
>> On 20/06/13, "L.C. Karssen"  <lennart at karssen.org> wrote:
>>
>> > Wow! Those look really nice!
>> >
>> > I like options C and F the most. Actually a combination would be even
>> > better IMHO: use C with capital ABEL and statistical genomics below it.
>> >
>> >
>> > Looking forward to head the opinion of others,
>> >
>> > Lennart.
>> >
>> > On 20-06-13 09:34, Yurii Aulchenko wrote:
>> > > Please find attached few more logo variants
>> > >
>> > > Yurii
>>
>>
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From lennart at karssen.org  Fri Jun 28 23:31:46 2013
From: lennart at karssen.org (L.C. Karssen)
Date: Fri, 28 Jun 2013 23:31:46 +0200
Subject: [GenABEL-dev] layout of GenABEL main page
In-Reply-To: <CAHX9t6LBj-SJkZ0YBwsEBkq11Re+wh9RzUtFYw5L9qjvqs+Aug@mail.gmail.com>
References: <515446DC.6040602@karssen.org>
 <CAHX9t6KKAUMqRt5mkf=PDJQMEutjytJ_O6OqK2jQvyOpwZ_HNA@mail.gmail.com>
 <267251364989776@web10f.yandex.ru> <515DE59F.60809@gmail.com>
 <CAHX9t6JbC6yMWNOvnBoYC=kkYmk93vivMnXLU=zfUWTHwWSfMw@mail.gmail.com>
 <1d37042ddf3f9fbd34262ae10502ff50.squirrel@webmail-rupar.regione.fvg.it>
 <EAF4AFDE-C730-4169-865E-AD757A38AE74@gmail.com> <51671169.5090608@gmail.com>
 <51671992.9070100@karssen.org> <6274237547129198468@unknownmsgid>
 <9DC1FE20-D285-4185-B890-F50EAF503E4D@gmail.com> <5167B525.6030608@gmail.com>
 <7783033322271622686@unknownmsgid> <517303F7.9020806@karssen.org>
 <CAHX9t6LwbHTukWoVP6vnt6ZeiwSV69RcUVXL+v6R4=_m8SiUKg@mail.gmail.com>
 <CAHX9t6JC4=sqqW3YRQXDXa5QgF-=qxG5dtGqxApmY0KiFRBL1Q@mail.gmail.com>
 <51C2B324.1010706@karssen.org> <fb5504221a5b85.51cb13cf@aices.rwth-aachen.de>
 <CAHX9t6KVUf2v7oZB7qMc+NbT-rwrW1UfgqR7wN76XHQ6E42qWA@mail.gmail.com>
 <CAHX9t6LBj-SJkZ0YBwsEBkq11Re+wh9RzUtFYw5L9qjvqs+Aug@mail.gmail.com>
Message-ID: <51CE00C2.1040806@karssen.org>

That looks really nice! Nice job, Grant!

I'm all for it. I do agree with Nicola that we should change the base
colours of the website and forum to the same green as in the logo
(although I haven't looked into how much work that is).


Best,

Lennart.

On 28-06-13 22:52, Yurii Aulchenko wrote:
> How do you like this one?
> 
> YA
> 
> On Thu, Jun 27, 2013 at 1:16 PM, Yurii Aulchenko
> <yurii.aulchenko at gmail.com <mailto:yurii.aulchenko at gmail.com>> wrote:
> 
>     Dear Nicola, Diego, Lennart, 
> 
>     Thanks for your feedback! I will ask Grant Borodin, who kindly
>     designed these logos, if he could change C according to your comment
>     (capital "ABEL" and "statistical genomics" as in F).
> 
>     Yurii
> 
> 
>     On Wed, Jun 26, 2013 at 4:16 PM, Diego Fabregat Traver
>     <fabregat at aices.rwth-aachen.de
>     <mailto:fabregat at aices.rwth-aachen.de>> wrote:
> 
> 
>         Congrats to whoever designed these logos, they look very nice :)
> 
>         With respect to my preferences, I fully agree with Lennart: "C
>         with capital ABEL and statistical genomics below it" would be my
>         choice.
> 
>         Best,
>         Diego
> 
> 
>         On 20/06/13, "L.C. Karssen"  <lennart at karssen.org
>         <mailto:lennart at karssen.org>> wrote:
> 
>         > Wow! Those look really nice!
>         >
>         > I like options C and F the most. Actually a combination would
>         be even
>         > better IMHO: use C with capital ABEL and statistical genomics
>         below it.
>         >
>         >
>         > Looking forward to head the opinion of others,
>         >
>         > Lennart.
>         >
>         > On 20-06-13 09:34, Yurii Aulchenko wrote:
>         > > Please find attached few more logo variants
>         > >
>         > > Yurii
> 
> 
> 
> 
> _______________________________________________
> 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
------------------------------------------------------------------

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From yurii.aulchenko at gmail.com  Sat Jun 29 22:13:25 2013
From: yurii.aulchenko at gmail.com (Yurii Aulchenko)
Date: Sat, 29 Jun 2013 22:13:25 +0200
Subject: [GenABEL-dev] extracting results from OmicABEL runs - something is
	wrong
Message-ID: <CAHX9t6LCQ=5YW2T0jAwdBW8M=40Zht8aT=LvM61hayAmoiXvTQ@mail.gmail.com>

Dear Sodbo, Diego,

It looks like either 'reshuffle' or CLACK-GWAS do something wrong - and I
actually think this is reshuffle (see my tests below). Basically, I run
analysis on 'big' genotype set (gtDataChr1) and a thinned one, where I take
every 100th marker only (gtDataChr1small). When I extract results with
reshuffle, I see a marker with chi2>25 in small, but not in the original
big data set!

You can find the test-files in my public dropbox folder (I am going to send
the link to you separately; if anyone else is interested in testing, let me
know); the commands I used for testing are provided below.

best, and let mw know,
YA

Running analysis:

CLAK-GWAS -cov covData -phi gKinId -pheno phDataChr1 -snp gtDataChr1small
-out BAllSmall -var eigen -nths 4
reshuffle BAllSmall --chi=25
[identifies one SNP-trait pair, rs3738547-GI_7657133.S, with chi2>25]
CLAK-GWAS -cov covData -phi gKinId -pheno phDataChr1 -snp gtDataChr1 -out
BAll -var eigen -nths 4
reshuffle BAll --chi=25
[no SNP-trait pairs identified at chi2>25]

To make sure that actually the data are right, I ran the following tests in
R making sure that the SNP is present in both big and thinned data set

> library(DatABEL)
DatABEL v.0.9-4 (March 12, 2013) loaded

> g <- databel("gtDataChr1")
> gs <- databel("gtDataChr1small")
> p <- databel("phDataChr1")
> snp <- as(g[,"rs3738547"],"vector")
> snps <- as(gs[,"rs3738547"],"vector")
> ph <- as(p[,"GI_7657133.S"],"vector")
> summary(lm(ph~snp))

Call:
lm(formula = ph ~ snp)

Residuals:
     Min       1Q   Median       3Q      Max
-0.33692 -0.04485  0.00333  0.05632  0.13978

Coefficients:
             Estimate Std. Error t value Pr(>|t|)
(Intercept)  0.009116   0.005337   1.708   0.0892 .
snp         -0.091529   0.015967  -5.732 3.53e-08 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.07357 on 204 degrees of freedom
Multiple R-squared:  0.1387, Adjusted R-squared:  0.1345
F-statistic: 32.86 on 1 and 204 DF,  p-value: 3.527e-08

> summary(lm(ph~snps))

Call:
lm(formula = ph ~ snps)

Residuals:
     Min       1Q   Median       3Q      Max
-0.33692 -0.04485  0.00333  0.05632  0.13978

Coefficients:
             Estimate Std. Error t value Pr(>|t|)
(Intercept)  0.009116   0.005337   1.708   0.0892 .
snps        -0.091529   0.015967  -5.732 3.53e-08 ***
---
Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1

Residual standard error: 0.07357 on 204 degrees of freedom
Multiple R-squared:  0.1387, Adjusted R-squared:  0.1345
F-statistic: 32.86 on 1 and 204 DF,  p-value: 3.527e-08



And this is why I blame this on reshuffle:

yuryaulchenko$ perl extractCell.pl BAll 1029 115001
 0.00911574810743332 -0.0915286764502525 0.00573702435940504
0.0171629786491394 -2.74352405540412e-05
YAMacBookPro:analysisOfHapMapeQTL yuryaulchenko$ perl extractCell.pl
BAllSmall 1029 1151
 0.00911574810743332 -0.0915286764502525 0.00573702435940504
0.0171629786491394 -2.74352405540412e-05
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