[GenABEL-dev] presentation at UseR!-2013
Yurii Aulchenko
yurii.aulchenko at gmail.com
Sun Jul 14 19:43:49 CEST 2013
Dear All,
I have composed a short report from UseR! conference, see
http://www.genabel.org/news20130714
for the links.
best wishes, and thanks again for your help,
Yurii
On Wed, Jul 10, 2013 at 8:42 PM, Yurii Aulchenko
<yurii.aulchenko at gmail.com>wrote:
> Dear All,
>
> The last variant of presentation - the one I presented at UseR!-2013 this
> morning - is available at previous link. The presentation went fine (though
> I was slightly over time and therefore was wrapping up a bit too quickly).
> Several people contacted me after the talk.
>
> Later, we should probably move that presentation to our web-site. (what
> section? showcase?..)
>
> Lennart, Maarten, many thanks for your input!
>
> YA
>
>
> On Sun, Jul 7, 2013 at 3:40 AM, Yurii Aulchenko <yurii.aulchenko at gmail.com
> > wrote:
>
>> Thank you very much, Lennart! - not sure I will manage to use this data
>> for current presentation - it is getting rather big now, and I am getting
>> tired... I probably can use these numbers to make a figure "how the
>> community sets off", but not sure, did not have time to present these
>> numbers graphically yet.
>>
>> You can find the current draft of presentation at my public Dropbox,
>> https://dl.dropboxusercontent.com/u/13260693/GenABEL-1.odp
>>
>> Comments/suggestions/improvements are welcome!
>>
>> Note that I have 15-17 minutes for the presentation, so slide count is
>> already too high. Can probably cut short on the "history". Also wonder if
>> this presentation will be interesting for the R people - it is kind of very
>> general one at the moment.
>>
>> YA
>>
>>
>> On Sat, Jul 6, 2013 at 6:10 PM, L.C. Karssen <lennart at karssen.org> wrote:
>>
>>> Hi Yurii,
>>>
>>> Please find attached the output of the MySQL statement. I added another
>>> column in which the week numbers are separated from the year by a dash,
>>> that makes it easier to read in e.g. R:
>>>
>>> posts <- read.table("tmp/posts_per_week_converted.out", header=TRUE,
>>> sep=" ", row.names=NULL)
>>>
>>> colnames(posts) <- c("date", "num_posts")
>>>
>>> # Convert year-week to year-month-day
>>> posts$weekdate <- as.Date(paste(posts$date, 1), format="%Y-%U %u")
>>>
>>> head(posts)
>>> date num_posts weekdate
>>> 1 2011-01 1 2011-01-03
>>> 2 2011-04 15 2011-01-24
>>> 3 2011-05 7 2011-01-31
>>> 4 2011-06 24 2011-02-07
>>> 5 2011-07 10 2011-02-14
>>> 6 2011-08 7 2011-02-21
>>>
>>>
>>> This should help making a bar plot of "weekdate" vs. "num_posts".
>>>
>>>
>>> By the way, the SQL script is in the ~/scripts/ directory on the SSH
>>> server of our hoster. You can execute it like this:
>>> mysql -u USERNAME --password=PASSWORD -h HOSTNAME <
>>> get_weekly_posts.sql > posts_per_week.out
>>>
>>> The user name, password and host name can be found in the backup scripts
>>> in that same directory.
>>>
>>>
>>> Best,
>>>
>>> Lennart.
>>>
>>>
>>> On 05-07-13 14:04, Yurii Aulchenko wrote:
>>> >
>>> >
>>> > On Fri, Jul 5, 2013 at 12:30 PM, L.C. Karssen <lennart at karssen.org
>>> > <mailto:lennart at karssen.org>> wrote:
>>> >
>>> > Hi Yurii,
>>> >
>>> > On 07/05/2013 11:04 AM, Yurii Aulchenko wrote:
>>> > > Dear All,
>>> > >
>>> > > I am now drafting my presentation for UseR!-2013 (
>>> > > http://www.edii.uclm.es/~useR-2013/). My presentation about "The
>>> > GenABEL
>>> > > suite for genome-wide association analyses" is scheduled for Wed
>>> > July 10
>>> > > morning. I will send it to the list for the discussion as soon as
>>> > I have a
>>> > > draft (most likely by Saturday eve).
>>> > >
>>> > > I thought it may be a good idea to present the evolution of the
>>> > GenABEL in
>>> > > number, so the idea is to get the numbers by years/quartes of
>>> the year
>>> > > (say, #posts in 2009=x1, 2010=x2...) and present them
>>> graphically.
>>> > For some
>>> > > of growth metrics I can get the dynamics by years easily, but for
>>> > some I
>>> > > have no idea and hope you could help me (may be also by
>>> providing the
>>> > > numbers directly).
>>> > >
>>> > > Here a small list of metrics I thought of:
>>> > >
>>> > > #packages: very easy to count :)
>>> > > #posts on GenABEL-devel: possible to count
>>> > > #posts on forum: no idea how to do that for defined time periods
>>> >
>>> > I guess you need to run a query on the database to get those. Our
>>> hoster
>>> > has a phpmyadmin interface yuo can use for that (or you could
>>> probably
>>> > use the SSH account and run the MySQL client from the command
>>> line).
>>> > Probably a query along this line:
>>> >
>>> > SELECT yearweek(date(from_unixtime(post_time))) AS week, COUNT(*)
>>> AS
>>> > num_posts FROM phpbb_posts GROUP BY
>>> > yearweek(date(from_unixtime(post_time)))
>>> >
>>> >
>>> > arrgh... probably I can figure this out if I had enough time, but gonna
>>> > to invest into presentation now. If you/someone could give a hand,
>>> would
>>> > be great :)
>>> >
>>> >
>>> >
>>> >
>>> > > #number of lines of code in our SVN repo: no idea
>>> >
>>> > Probably SLOCcount will help: http://www.dwheeler.com/sloccount/
>>> >
>>> >
>>> > This is a nice one! Two problems: it does not count/recognize R; did
>>> not
>>> > see how to use it to see the dynamics (what was there in repo 2 years
>>> > ago?..)
>>> >
>>> > But I like that even without the R code counts (which is 148,000
>>> lines),
>>> > for ~65,000 lines of mostly C/C++ I get the message indicating that
>>> > GenABEL is worth few millions of dollars:
>>> >
>>> > Development Effort Estimate, Person-Years (Person-Months) = 15.44
>>> (185.24)
>>> > (Basic COCOMO model, Person-Months = 2.4 * (KSLOC**1.05))
>>> > Schedule Estimate, Years (Months) = 1.05
>>> (12.61)
>>> > (Basic COCOMO model, Months = 2.5 * (person-months**0.38))
>>> > Total Estimated Cost to Develop = $ 2,085,323
>>> > (average salary = $56,286/year, overhead = 2.40).
>>> >
>>> > So I think I should use these figures in my presentation :)
>>> >
>>> > > #citations (GenA, ProbA...): easy to count thanks to Google
>>> Scholar
>>> > > #mentions on the Web: ???
>>> > >
>>> > > Any other nice and easily computed metrics?
>>> > >
>>> > > I will appreciate your help and suggestions, and sorry for late
>>> > notice.
>>> > >
>>> >
>>> >
>>> > Good luck,
>>> >
>>> > Lennart.
>>> >
>>> > > best,
>>> > > 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
>>> > >
>>> >
>>> >
>>> > --
>>> > -----------------------------------------------------------------
>>> > 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/> ]
>>
>
>
>
> --
> -----------------------------------------------------
> 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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