[GenABEL-dev] presentation at UseR!-2013

Yurii Aulchenko yurii.aulchenko at gmail.com
Wed Jul 10 20:42:45 CEST 2013 

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/> ]
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