Programmer FTEs for GBrowse & Chado?

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Programmer FTEs for GBrowse & Chado?

Tomer Altman
To whom it may concern,

I sent this first to [hidden email], but I haven't yet received a reply.
Hopefully it is okay to post this message to the project email lists.

I'm trying to assemble some empirical data on the sizes of various
bioinformatics software systems, and the associated software development
resources allocated to them.

Could you provide me with an estimate for how many programmers work on
GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?

Also, I analyzed the lines of code in the GBrowse tar ball, but I was
unable to find the source code download for Chado (any help would be
appreciated).

I've used a tool called cloc (cloc.sf.net) to analyze the source code of
GBrowse, but I was unable to find the source code download for Chado
(any help would be appreciated).

Please let me know if the lines-of-code per programming language in the
output looks correct to you. Also, if there are major libraries in the
source code that were not written by the GBrowse team that I should
exclude from this analysis, please let me know (same question for Chado
too, once I get access to the source code).

Thanks in advance,

~Tomer Altman

---
(this output is best-read in a fixed-width font, or in a text editor)

arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
GBrowse-2.26
      438 text files.
      420 unique files.
      179 files ignored.

http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
-------------------------------------------------------------------------------
Language          files     blank   comment      code    scale   3rd
gen. equiv
-------------------------------------------------------------------------------
Perl                188     14573      7632     50535 x   4.00 =      
202140.00
Javascript           33      2555      1251     14989 x   1.48 =      
22183.72
HTML                 11      1914       470      6968 x   1.90 =      
13239.20
XML                   1        28         0      1900 x   1.90 =        
3610.00
C                     2       183       223      1171 x   0.77 =        
901.67
CSS                  16        82        60      1099 x   1.00 =        
1099.00
YAML                  1         0         0       209 x   0.90 =        
188.10
Bourne Shell          3         9        11        92 x   3.81 =        
350.52
SQL                   1         8         0        55 x   2.29 =        
125.95
C/C++ Header          2        11         9        41 x   1.00
=          41.00
-------------------------------------------------------------------------------
SUM:                258     19363      9656     77059 x   3.16 =      
243879.16
-------------------------------------------------------------------------------

--
Tomer Altman
[hidden email]
(650)859-2692
http://www.ai.sri.com/people/taltman

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International

http://bioinformatics.ai.sri.com/


------------------------------------------------------------------------------
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smartphone on the nation's most reliable network.
And it wants your games.
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Re: Programmer FTEs for GBrowse & Chado?

Robert Buels
Hi Tomer,

I'm not really equipped to guess at FTE's for these projects, somebody
else will need to take a stab at that, but as for a Chado tarball, you
can get that here:

   http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/

And sure those number look believable to me for GBrowse.  You might be
the first one to measure it in this way.

Hope this helps!

Rob


On 04/07/2011 02:49 PM, Tomer Altman wrote:

> To whom it may concern,
>
> I sent this first to [hidden email], but I haven't yet received a reply.
> Hopefully it is okay to post this message to the project email lists.
>
> I'm trying to assemble some empirical data on the sizes of various
> bioinformatics software systems, and the associated software development
> resources allocated to them.
>
> Could you provide me with an estimate for how many programmers work on
> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>
> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
> unable to find the source code download for Chado (any help would be
> appreciated).
>
> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
> GBrowse, but I was unable to find the source code download for Chado
> (any help would be appreciated).
>
> Please let me know if the lines-of-code per programming language in the
> output looks correct to you. Also, if there are major libraries in the
> source code that were not written by the GBrowse team that I should
> exclude from this analysis, please let me know (same question for Chado
> too, once I get access to the source code).
>
> Thanks in advance,
>
> ~Tomer Altman
>
> ---
> (this output is best-read in a fixed-width font, or in a text editor)
>
> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
> GBrowse-2.26
>        438 text files.
>        420 unique files.
>        179 files ignored.
>
> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
> -------------------------------------------------------------------------------
> Language          files     blank   comment      code    scale   3rd
> gen. equiv
> -------------------------------------------------------------------------------
> Perl                188     14573      7632     50535 x   4.00 =
> 202140.00
> Javascript           33      2555      1251     14989 x   1.48 =
> 22183.72
> HTML                 11      1914       470      6968 x   1.90 =
> 13239.20
> XML                   1        28         0      1900 x   1.90 =
> 3610.00
> C                     2       183       223      1171 x   0.77 =
> 901.67
> CSS                  16        82        60      1099 x   1.00 =
> 1099.00
> YAML                  1         0         0       209 x   0.90 =
> 188.10
> Bourne Shell          3         9        11        92 x   3.81 =
> 350.52
> SQL                   1         8         0        55 x   2.29 =
> 125.95
> C/C++ Header          2        11         9        41 x   1.00
> =          41.00
> -------------------------------------------------------------------------------
> SUM:                258     19363      9656     77059 x   3.16 =
> 243879.16
> -------------------------------------------------------------------------------
>


------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
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Re: Programmer FTEs for GBrowse & Chado?

Daniel Quest
Hey Tomer

Chado is mostly lines of sql
Just an FYI

Also, it would be very helpful to know WHY you would like to do this assessment.  I.e. What are your business drivers?

IMHO the ontologies, community, widespread acceptance and syntax standards far exceed the value of the GMOD software stack.  

So if you calculate value based on loc then you are missing a big part of what gmod is about.  I believe many decisions inside of gmod are better than software independently created because a lot of thought goes into engineering decisions.  

At Oak Ridge we had the resources to deviate from what gmod did.  I can think of 3 cases where what we where doing was so different from running a model organism database that we had to make changes.  In every other case the community standard was superior to our alternative.  That says something about the quality of the approach and the support in gmod.  I for one will always be so thankful to everyone on this list for taking the time to help me out and get the gmod way into my thick head

- Daniel


Sent from my iPod

On Apr 7, 2011, at 7:13 PM, Robert Buels <[hidden email]> wrote:

> Hi Tomer,
>
> I'm not really equipped to guess at FTE's for these projects, somebody
> else will need to take a stab at that, but as for a Chado tarball, you
> can get that here:
>
>   http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/
>
> And sure those number look believable to me for GBrowse.  You might be
> the first one to measure it in this way.
>
> Hope this helps!
>
> Rob
>
>
> On 04/07/2011 02:49 PM, Tomer Altman wrote:
>> To whom it may concern,
>>
>> I sent this first to [hidden email], but I haven't yet received a reply.
>> Hopefully it is okay to post this message to the project email lists.
>>
>> I'm trying to assemble some empirical data on the sizes of various
>> bioinformatics software systems, and the associated software development
>> resources allocated to them.
>>
>> Could you provide me with an estimate for how many programmers work on
>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>
>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>> unable to find the source code download for Chado (any help would be
>> appreciated).
>>
>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>> GBrowse, but I was unable to find the source code download for Chado
>> (any help would be appreciated).
>>
>> Please let me know if the lines-of-code per programming language in the
>> output looks correct to you. Also, if there are major libraries in the
>> source code that were not written by the GBrowse team that I should
>> exclude from this analysis, please let me know (same question for Chado
>> too, once I get access to the source code).
>>
>> Thanks in advance,
>>
>> ~Tomer Altman
>>
>> ---
>> (this output is best-read in a fixed-width font, or in a text editor)
>>
>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>> GBrowse-2.26
>>       438 text files.
>>       420 unique files.
>>       179 files ignored.
>>
>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
>> -------------------------------------------------------------------------------
>> Language          files     blank   comment      code    scale   3rd
>> gen. equiv
>> -------------------------------------------------------------------------------
>> Perl                188     14573      7632     50535 x   4.00 =
>> 202140.00
>> Javascript           33      2555      1251     14989 x   1.48 =
>> 22183.72
>> HTML                 11      1914       470      6968 x   1.90 =
>> 13239.20
>> XML                   1        28         0      1900 x   1.90 =
>> 3610.00
>> C                     2       183       223      1171 x   0.77 =
>> 901.67
>> CSS                  16        82        60      1099 x   1.00 =
>> 1099.00
>> YAML                  1         0         0       209 x   0.90 =
>> 188.10
>> Bourne Shell          3         9        11        92 x   3.81 =
>> 350.52
>> SQL                   1         8         0        55 x   2.29 =
>> 125.95
>> C/C++ Header          2        11         9        41 x   1.00
>> =          41.00
>> -------------------------------------------------------------------------------
>> SUM:                258     19363      9656     77059 x   3.16 =
>> 243879.16
>> -------------------------------------------------------------------------------
>>
>
>
> ------------------------------------------------------------------------------
> Xperia(TM) PLAY
> It's a major breakthrough. An authentic gaming
> smartphone on the nation's most reliable network.
> And it wants your games.
> http://p.sf.net/sfu/verizon-sfdev
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema

------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
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Re: Programmer FTEs for GBrowse & Chado?

Olen Vance Sluder Jr
In reply to this post by Robert Buels
Tomer,
 
Bear in mind that the GMOD components are open source projects to which a number of people from many organizations have contributed varying amounts of effort over a long period of time, so I suspect it will be nearly impossible to come up with a truly empirical value for "FTEs".
 
Also, lines of code are a notoriously bad metric for software measurement without a carefully calibrated model supporting them (e.g., Boehm's COCOMO, etc.), which is especially true when dealing with code bases consisting of multiple programming languages. I say this from nearly a decade of experience with a technical services firm where my speciality was software assessment.
 
Good luck with your analysis.
 
Regards,
Olen

On Thu, Apr 7, 2011 at 6:13 PM, Robert Buels <[hidden email]> wrote:
Hi Tomer,

I'm not really equipped to guess at FTE's for these projects, somebody
else will need to take a stab at that, but as for a Chado tarball, you
can get that here:

  http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/

And sure those number look believable to me for GBrowse.  You might be
the first one to measure it in this way.

Hope this helps!

Rob


On 04/07/2011 02:49 PM, Tomer Altman wrote:
> To whom it may concern,
>
> I sent this first to [hidden email], but I haven't yet received a reply.
> Hopefully it is okay to post this message to the project email lists.
>
> I'm trying to assemble some empirical data on the sizes of various
> bioinformatics software systems, and the associated software development
> resources allocated to them.
>
> Could you provide me with an estimate for how many programmers work on
> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>
> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
> unable to find the source code download for Chado (any help would be
> appreciated).
>
> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
> GBrowse, but I was unable to find the source code download for Chado
> (any help would be appreciated).
>
> Please let me know if the lines-of-code per programming language in the
> output looks correct to you. Also, if there are major libraries in the
> source code that were not written by the GBrowse team that I should
> exclude from this analysis, please let me know (same question for Chado
> too, once I get access to the source code).
>
> Thanks in advance,
>
> ~Tomer Altman
>
> ---
> (this output is best-read in a fixed-width font, or in a text editor)
>
> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
> GBrowse-2.26
>        438 text files.
>        420 unique files.
>        179 files ignored.
>
> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
> -------------------------------------------------------------------------------
> Language          files     blank   comment      code    scale   3rd
> gen. equiv
> -------------------------------------------------------------------------------
> Perl                188     14573      7632     50535 x   4.00 =
> 202140.00
> Javascript           33      2555      1251     14989 x   1.48 =
> 22183.72
> HTML                 11      1914       470      6968 x   1.90 =
> 13239.20
> XML                   1        28         0      1900 x   1.90 =
> 3610.00
> C                     2       183       223      1171 x   0.77 =
> 901.67
> CSS                  16        82        60      1099 x   1.00 =
> 1099.00
> YAML                  1         0         0       209 x   0.90 =
> 188.10
> Bourne Shell          3         9        11        92 x   3.81 =
> 350.52
> SQL                   1         8         0        55 x   2.29 =
> 125.95
> C/C++ Header          2        11         9        41 x   1.00
> =          41.00
> -------------------------------------------------------------------------------
> SUM:                258     19363      9656     77059 x   3.16 =
> 243879.16
> -------------------------------------------------------------------------------
>


------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema


------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Re: Programmer FTEs for GBrowse & Chado?

David Emmert
In reply to this post by Tomer Altman
Hi Tomer,

>> Could you provide me with an estimate for how many programmers work on
>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?

Regarding Chado, if you're asking how many FTE work -with- chado, I would say
we have 4 FTE working on chado at FlyBase.  If you're asking how many FTE are actively
developing the chado schema itself, I would say we average <.25 FTE doing active schema
development.

>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>> unable to find the source code download for Chado (any help would be
>> appreciated).

In the GMOD SVN look in trunk/chado/

I'd love to hear your results when you finish compiling data.

-Dave


>From [hidden email]  Thu Apr  7 18:08:49 2011
>> To: [hidden email], [hidden email]
>> Subject: [Gmod-schema] Programmer FTEs for GBrowse & Chado?
>>
>> To whom it may concern,
>>
>> I sent this first to [hidden email], but I haven't yet received a reply.
>> Hopefully it is okay to post this message to the project email lists.
>>
>> I'm trying to assemble some empirical data on the sizes of various
>> bioinformatics software systems, and the associated software development
>> resources allocated to them.
>>
>> Could you provide me with an estimate for how many programmers work on
>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>
>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>> unable to find the source code download for Chado (any help would be
>> appreciated).
>>
>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>> GBrowse, but I was unable to find the source code download for Chado
>> (any help would be appreciated).
>>
>> Please let me know if the lines-of-code per programming language in the
>> output looks correct to you. Also, if there are major libraries in the
>> source code that were not written by the GBrowse team that I should
>> exclude from this analysis, please let me know (same question for Chado
>> too, once I get access to the source code).
>>
>> Thanks in advance,
>>
>> ~Tomer Altman
>>
>> ---
>> (this output is best-read in a fixed-width font, or in a text editor)
>>
>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>> GBrowse-2.26
>>       438 text files.
>>       420 unique files.
>>       179 files ignored.
>>
>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
>> -------------------------------------------------------------------------------
>> Language          files     blank   comment      code    scale   3rd
>> gen. equiv
>> -------------------------------------------------------------------------------
>> Perl                188     14573      7632     50535 x   4.00 =      
>> 202140.00
>> Javascript           33      2555      1251     14989 x   1.48 =      
>> 22183.72
>> HTML                 11      1914       470      6968 x   1.90 =      
>> 13239.20
>> XML                   1        28         0      1900 x   1.90 =        
>> 3610.00
>> C                     2       183       223      1171 x   0.77 =        
>> 901.67
>> CSS                  16        82        60      1099 x   1.00 =        
>> 1099.00
>> YAML                  1         0         0       209 x   0.90 =        
>> 188.10
>> Bourne Shell          3         9        11        92 x   3.81 =        
>> 350.52
>> SQL                   1         8         0        55 x   2.29 =        
>> 125.95
>> C/C++ Header          2        11         9        41 x   1.00
>> =          41.00
>> -------------------------------------------------------------------------------
>> SUM:                258     19363      9656     77059 x   3.16 =      
>> 243879.16
>> -------------------------------------------------------------------------------
>>
>> --
>> Tomer Altman
>> [hidden email]
>> (650)859-2692
>> http://www.ai.sri.com/people/taltman
>>
>> Bioinformatics Research Group
>> Artificial Intelligence Center
>> SRI, International
>>
>> http://bioinformatics.ai.sri.com/
>>
>>
>> ------------------------------------------------------------------------------
>> Xperia(TM) PLAY
>> It's a major breakthrough. An authentic gaming
>> smartphone on the nation's most reliable network.
>> And it wants your games.
>> http://p.sf.net/sfu/verizon-sfdev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>>

------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Re: Programmer FTEs for GBrowse & Chado?

Tomer Altman
  On 4/8/11 6:04 AM, David Emmert wrote:
> Hi Tomer,
>
>>> Could you provide me with an estimate for how many programmers work on
>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
> Regarding Chado, if you're asking how many FTE work -with- chado, I would say
> we have 4 FTE working on chado at FlyBase.  If you're asking how many FTE are actively
> developing the chado schema itself, I would say we average<.25 FTE doing active schema
> development.
Thank you David, that's exactly what I was looking for.

Are there any third-party "libraries" in the Chado SQL code? I just want
to be sure that I'm measuring the code correctly.

Thanks,

~Tomer

>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>> unable to find the source code download for Chado (any help would be
>>> appreciated).
> In the GMOD SVN look in trunk/chado/
>
> I'd love to hear your results when you finish compiling data.
>
> -Dave
>
>
> > From [hidden email]  Thu Apr  7 18:08:49 2011
>>> To: [hidden email], [hidden email]
>>> Subject: [Gmod-schema] Programmer FTEs for GBrowse&  Chado?
>>>
>>> To whom it may concern,
>>>
>>> I sent this first to [hidden email], but I haven't yet received a reply.
>>> Hopefully it is okay to post this message to the project email lists.
>>>
>>> I'm trying to assemble some empirical data on the sizes of various
>>> bioinformatics software systems, and the associated software development
>>> resources allocated to them.
>>>
>>> Could you provide me with an estimate for how many programmers work on
>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>>
>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>> unable to find the source code download for Chado (any help would be
>>> appreciated).
>>>
>>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>>> GBrowse, but I was unable to find the source code download for Chado
>>> (any help would be appreciated).
>>>
>>> Please let me know if the lines-of-code per programming language in the
>>> output looks correct to you. Also, if there are major libraries in the
>>> source code that were not written by the GBrowse team that I should
>>> exclude from this analysis, please let me know (same question for Chado
>>> too, once I get access to the source code).
>>>
>>> Thanks in advance,
>>>
>>> ~Tomer Altman
>>>
>>> ---
>>> (this output is best-read in a fixed-width font, or in a text editor)
>>>
>>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>>> GBrowse-2.26
>>>        438 text files.
>>>        420 unique files.
>>>        179 files ignored.
>>>
>>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
>>> -------------------------------------------------------------------------------
>>> Language          files     blank   comment      code    scale   3rd
>>> gen. equiv
>>> -------------------------------------------------------------------------------
>>> Perl                188     14573      7632     50535 x   4.00 =
>>> 202140.00
>>> Javascript           33      2555      1251     14989 x   1.48 =
>>> 22183.72
>>> HTML                 11      1914       470      6968 x   1.90 =
>>> 13239.20
>>> XML                   1        28         0      1900 x   1.90 =
>>> 3610.00
>>> C                     2       183       223      1171 x   0.77 =
>>> 901.67
>>> CSS                  16        82        60      1099 x   1.00 =
>>> 1099.00
>>> YAML                  1         0         0       209 x   0.90 =
>>> 188.10
>>> Bourne Shell          3         9        11        92 x   3.81 =
>>> 350.52
>>> SQL                   1         8         0        55 x   2.29 =
>>> 125.95
>>> C/C++ Header          2        11         9        41 x   1.00
>>> =          41.00
>>> -------------------------------------------------------------------------------
>>> SUM:                258     19363      9656     77059 x   3.16 =
>>> 243879.16
>>> -------------------------------------------------------------------------------
>>>
>>> --
>>> Tomer Altman
>>> [hidden email]
>>> (650)859-2692
>>> http://www.ai.sri.com/people/taltman
>>>
>>> Bioinformatics Research Group
>>> Artificial Intelligence Center
>>> SRI, International
>>>
>>> http://bioinformatics.ai.sri.com/
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Xperia(TM) PLAY
>>> It's a major breakthrough. An authentic gaming
>>> smartphone on the nation's most reliable network.
>>> And it wants your games.
>>> http://p.sf.net/sfu/verizon-sfdev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>>


--
Tomer Altman
[hidden email]
(650)859-2692
http://www.ai.sri.com/people/taltman

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International

http://bioinformatics.ai.sri.com/



------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
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Re: Programmer FTEs for GBrowse & Chado?

Tomer Altman
In reply to this post by Olen Vance Sluder Jr
Hi Olen,

While I acknowledge that it will be difficult to get perfect precision with this query, I'm comparing projects to one another, so hopefully I'll be comparing numbers of equal precision. I understand that it's more difficult to estimate the amount of hours put in collectively to a "bazaar-like" open-source project as compared to one that is centrally-lead and where allotted time comes directly from organizational budgets. But I'm hoping that the project leaders can provide an estimate of the average amount of FTEs (or hours, if that is a more convenient measure) that are put in to these GMOD projects in a given year.

Thanks,

~Tomer

On 4/7/11 9:13 PM, Olen Vance Sluder Jr wrote:
Tomer,
 
Bear in mind that the GMOD components are open source projects to which a number of people from many organizations have contributed varying amounts of effort over a long period of time, so I suspect it will be nearly impossible to come up with a truly empirical value for "FTEs".
 
Also, lines of code are a notoriously bad metric for software measurement without a carefully calibrated model supporting them (e.g., Boehm's COCOMO, etc.), which is especially true when dealing with code bases consisting of multiple programming languages. I say this from nearly a decade of experience with a technical services firm where my speciality was software assessment.
 
Good luck with your analysis.
 
Regards,
Olen

On Thu, Apr 7, 2011 at 6:13 PM, Robert Buels <[hidden email]> wrote:
Hi Tomer,

I'm not really equipped to guess at FTE's for these projects, somebody
else will need to take a stab at that, but as for a Chado tarball, you
can get that here:

  http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/

And sure those number look believable to me for GBrowse.  You might be
the first one to measure it in this way.

Hope this helps!

Rob


On 04/07/2011 02:49 PM, Tomer Altman wrote:
> To whom it may concern,
>
> I sent this first to [hidden email], but I haven't yet received a reply.
> Hopefully it is okay to post this message to the project email lists.
>
> I'm trying to assemble some empirical data on the sizes of various
> bioinformatics software systems, and the associated software development
> resources allocated to them.
>
> Could you provide me with an estimate for how many programmers work on
> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>
> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
> unable to find the source code download for Chado (any help would be
> appreciated).
>
> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
> GBrowse, but I was unable to find the source code download for Chado
> (any help would be appreciated).
>
> Please let me know if the lines-of-code per programming language in the
> output looks correct to you. Also, if there are major libraries in the
> source code that were not written by the GBrowse team that I should
> exclude from this analysis, please let me know (same question for Chado
> too, once I get access to the source code).
>
> Thanks in advance,
>
> ~Tomer Altman
>
> ---
> (this output is best-read in a fixed-width font, or in a text editor)
>
> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
> GBrowse-2.26
>        438 text files.
>        420 unique files.
>        179 files ignored.
>
> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
> -------------------------------------------------------------------------------
> Language          files     blank   comment      code    scale   3rd
> gen. equiv
> -------------------------------------------------------------------------------
> Perl                188     14573      7632     50535 x   4.00 =
> 202140.00
> Javascript           33      2555      1251     14989 x   1.48 =
> 22183.72
> HTML                 11      1914       470      6968 x   1.90 =
> 13239.20
> XML                   1        28         0      1900 x   1.90 =
> 3610.00
> C                     2       183       223      1171 x   0.77 =
> 901.67
> CSS                  16        82        60      1099 x   1.00 =
> 1099.00
> YAML                  1         0         0       209 x   0.90 =
> 188.10
> Bourne Shell          3         9        11        92 x   3.81 =
> 350.52
> SQL                   1         8         0        55 x   2.29 =
> 125.95
> C/C++ Header          2        11         9        41 x   1.00
> =          41.00
> -------------------------------------------------------------------------------
> SUM:                258     19363      9656     77059 x   3.16 =
> 243879.16
> -------------------------------------------------------------------------------
>


------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



-- 
Tomer Altman
[hidden email]
(650)859-2692
http://www.ai.sri.com/people/taltman

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International

http://bioinformatics.ai.sri.com/


------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
_______________________________________________
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Re: Programmer FTEs for GBrowse & Chado?

Tomer Altman
In reply to this post by Robert Buels
  Thank you for pointing me in the right direction for the source code.

Best regards,

~Tomer


On 4/7/11 4:13 PM, Robert Buels wrote:

> Hi Tomer,
>
> I'm not really equipped to guess at FTE's for these projects, somebody
> else will need to take a stab at that, but as for a Chado tarball, you
> can get that here:
>
>   http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/
>
> And sure those number look believable to me for GBrowse.  You might be
> the first one to measure it in this way.
>
> Hope this helps!
>
> Rob
>
>
> On 04/07/2011 02:49 PM, Tomer Altman wrote:
>> To whom it may concern,
>>
>> I sent this first to [hidden email], but I haven't yet received a reply.
>> Hopefully it is okay to post this message to the project email lists.
>>
>> I'm trying to assemble some empirical data on the sizes of various
>> bioinformatics software systems, and the associated software development
>> resources allocated to them.
>>
>> Could you provide me with an estimate for how many programmers work on
>> GBrowse and Chado (separately), as measured in Full-Time Equivalents
>> (FTEs)?
>>
>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>> unable to find the source code download for Chado (any help would be
>> appreciated).
>>
>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>> GBrowse, but I was unable to find the source code download for Chado
>> (any help would be appreciated).
>>
>> Please let me know if the lines-of-code per programming language in the
>> output looks correct to you. Also, if there are major libraries in the
>> source code that were not written by the GBrowse team that I should
>> exclude from this analysis, please let me know (same question for Chado
>> too, once I get access to the source code).
>>
>> Thanks in advance,
>>
>> ~Tomer Altman
>>
>> ---
>> (this output is best-read in a fixed-width font, or in a text editor)
>>
>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>> GBrowse-2.26
>>        438 text files.
>>        420 unique files.
>>        179 files ignored.
>>
>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8
>> lines/s)
>> -------------------------------------------------------------------------------
>>
>> Language          files     blank   comment      code    scale   3rd
>> gen. equiv
>> -------------------------------------------------------------------------------
>>
>> Perl                188     14573      7632     50535 x   4.00 =
>> 202140.00
>> Javascript           33      2555      1251     14989 x   1.48 =
>> 22183.72
>> HTML                 11      1914       470      6968 x   1.90 =
>> 13239.20
>> XML                   1        28         0      1900 x   1.90 =
>> 3610.00
>> C                     2       183       223      1171 x   0.77 =
>> 901.67
>> CSS                  16        82        60      1099 x   1.00 =
>> 1099.00
>> YAML                  1         0         0       209 x   0.90 =
>> 188.10
>> Bourne Shell          3         9        11        92 x   3.81 =
>> 350.52
>> SQL                   1         8         0        55 x   2.29 =
>> 125.95
>> C/C++ Header          2        11         9        41 x   1.00
>> =          41.00
>> -------------------------------------------------------------------------------
>>
>> SUM:                258     19363      9656     77059 x   3.16 =
>> 243879.16
>> -------------------------------------------------------------------------------
>>
>>


--
Tomer Altman
[hidden email]
(650)859-2692
http://www.ai.sri.com/people/taltman

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International

http://bioinformatics.ai.sri.com/



------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
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Re: Programmer FTEs for GBrowse & Chado?

Tomer Altman
In reply to this post by Daniel Quest
  Hi Daniel,

In terms of my "drivers", I'm doing research into the correlation
between the size of bioinformatic software projects and the number of
FTEs that are needed to maintain & extend the software.

I'm happy that the gmod-schema folks have been helpful with my research.
I'm hoping that I can get in touch with some of the gmod-gbrowse folks
as well.

P.S.- I am one of the maintainers of the BioWarehouse open-source
bioinformatic database warehousing project (www.biowarehouse.org).


On 4/7/11 5:10 PM, Daniel Quest wrote:

> Hey Tomer
>
> Chado is mostly lines of sql
> Just an FYI
>
> Also, it would be very helpful to know WHY you would like to do this assessment.  I.e. What are your business drivers?
>
> IMHO the ontologies, community, widespread acceptance and syntax standards far exceed the value of the GMOD software stack.
>
> So if you calculate value based on loc then you are missing a big part of what gmod is about.  I believe many decisions inside of gmod are better than software independently created because a lot of thought goes into engineering decisions.
>
> At Oak Ridge we had the resources to deviate from what gmod did.  I can think of 3 cases where what we where doing was so different from running a model organism database that we had to make changes.  In every other case the community standard was superior to our alternative.  That says something about the quality of the approach and the support in gmod.  I for one will always be so thankful to everyone on this list for taking the time to help me out and get the gmod way into my thick head
>
> - Daniel
>
>
> Sent from my iPod
>
> On Apr 7, 2011, at 7:13 PM, Robert Buels<[hidden email]>  wrote:
>
>> Hi Tomer,
>>
>> I'm not really equipped to guess at FTE's for these projects, somebody
>> else will need to take a stab at that, but as for a Chado tarball, you
>> can get that here:
>>
>>    http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/
>>
>> And sure those number look believable to me for GBrowse.  You might be
>> the first one to measure it in this way.
>>
>> Hope this helps!
>>
>> Rob
>>
>>
>> On 04/07/2011 02:49 PM, Tomer Altman wrote:
>>> To whom it may concern,
>>>
>>> I sent this first to [hidden email], but I haven't yet received a reply.
>>> Hopefully it is okay to post this message to the project email lists.
>>>
>>> I'm trying to assemble some empirical data on the sizes of various
>>> bioinformatics software systems, and the associated software development
>>> resources allocated to them.
>>>
>>> Could you provide me with an estimate for how many programmers work on
>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>>
>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>> unable to find the source code download for Chado (any help would be
>>> appreciated).
>>>
>>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>>> GBrowse, but I was unable to find the source code download for Chado
>>> (any help would be appreciated).
>>>
>>> Please let me know if the lines-of-code per programming language in the
>>> output looks correct to you. Also, if there are major libraries in the
>>> source code that were not written by the GBrowse team that I should
>>> exclude from this analysis, please let me know (same question for Chado
>>> too, once I get access to the source code).
>>>
>>> Thanks in advance,
>>>
>>> ~Tomer Altman
>>>
>>> ---
>>> (this output is best-read in a fixed-width font, or in a text editor)
>>>
>>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>>> GBrowse-2.26
>>>        438 text files.
>>>        420 unique files.
>>>        179 files ignored.
>>>
>>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
>>> -------------------------------------------------------------------------------
>>> Language          files     blank   comment      code    scale   3rd
>>> gen. equiv
>>> -------------------------------------------------------------------------------
>>> Perl                188     14573      7632     50535 x   4.00 =
>>> 202140.00
>>> Javascript           33      2555      1251     14989 x   1.48 =
>>> 22183.72
>>> HTML                 11      1914       470      6968 x   1.90 =
>>> 13239.20
>>> XML                   1        28         0      1900 x   1.90 =
>>> 3610.00
>>> C                     2       183       223      1171 x   0.77 =
>>> 901.67
>>> CSS                  16        82        60      1099 x   1.00 =
>>> 1099.00
>>> YAML                  1         0         0       209 x   0.90 =
>>> 188.10
>>> Bourne Shell          3         9        11        92 x   3.81 =
>>> 350.52
>>> SQL                   1         8         0        55 x   2.29 =
>>> 125.95
>>> C/C++ Header          2        11         9        41 x   1.00
>>> =          41.00
>>> -------------------------------------------------------------------------------
>>> SUM:                258     19363      9656     77059 x   3.16 =
>>> 243879.16
>>> -------------------------------------------------------------------------------
>>>
>>
>> ------------------------------------------------------------------------------
>> Xperia(TM) PLAY
>> It's a major breakthrough. An authentic gaming
>> smartphone on the nation's most reliable network.
>> And it wants your games.
>> http://p.sf.net/sfu/verizon-sfdev
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema


--
Tomer Altman
[hidden email]
(650)859-2692
http://www.ai.sri.com/people/taltman

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International

http://bioinformatics.ai.sri.com/



------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
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Re: Programmer FTEs for GBrowse & Chado?

David Emmert
In reply to this post by Tomer Altman
Hi Tomer,

>> Are there any third-party "libraries" in the Chado SQL code? I just want
>> to be sure that I'm measuring the code correctly.

I'm not sure what you mean.  Its an open project, so in a sense the whole thing
is "third-party".  

AFAIK, there aren't (and there certainly shouldn't be) any modules of chado which
were imported whole-cloth from other software packages.

Best,

-Dave


>From [hidden email]  Tue Apr 12 01:17:52 2011
>> To: David Emmert <[hidden email]>
>> CC: [hidden email], [hidden email],
>>         [hidden email]
>> Subject: Re: [Gmod-schema] Programmer FTEs for GBrowse & Chado?
>>
>>   On 4/8/11 6:04 AM, David Emmert wrote:
>> > Hi Tomer,
>> >
>> >>> Could you provide me with an estimate for how many programmers work on
>> >>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>> > Regarding Chado, if you're asking how many FTE work -with- chado, I would say
>> > we have 4 FTE working on chado at FlyBase.  If you're asking how many FTE are actively
>> > developing the chado schema itself, I would say we average<.25 FTE doing active schema
>> > development.
>> Thank you David, that's exactly what I was looking for.
>>
>> Are there any third-party "libraries" in the Chado SQL code? I just want
>> to be sure that I'm measuring the code correctly.
>>
>> Thanks,
>>
>> ~Tomer
>> >>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>> >>> unable to find the source code download for Chado (any help would be
>> >>> appreciated).
>> > In the GMOD SVN look in trunk/chado/
>> >
>> > I'd love to hear your results when you finish compiling data.
>> >
>> > -Dave
>> >
>> >
>> > > From [hidden email]  Thu Apr  7 18:08:49 2011
>> >>> To: [hidden email], [hidden email]
>> >>> Subject: [Gmod-schema] Programmer FTEs for GBrowse&  Chado?
>> >>>
>> >>> To whom it may concern,
>> >>>
>> >>> I sent this first to [hidden email], but I haven't yet received a reply.
>> >>> Hopefully it is okay to post this message to the project email lists.
>> >>>
>> >>> I'm trying to assemble some empirical data on the sizes of various
>> >>> bioinformatics software systems, and the associated software development
>> >>> resources allocated to them.
>> >>>
>> >>> Could you provide me with an estimate for how many programmers work on
>> >>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>> >>>
>> >>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>> >>> unable to find the source code download for Chado (any help would be
>> >>> appreciated).
>> >>>
>> >>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>> >>> GBrowse, but I was unable to find the source code download for Chado
>> >>> (any help would be appreciated).
>> >>>
>> >>> Please let me know if the lines-of-code per programming language in the
>> >>> output looks correct to you. Also, if there are major libraries in the
>> >>> source code that were not written by the GBrowse team that I should
>> >>> exclude from this analysis, please let me know (same question for Chado
>> >>> too, once I get access to the source code).
>> >>>
>> >>> Thanks in advance,
>> >>>
>> >>> ~Tomer Altman
>> >>>
>> >>> ---
>> >>> (this output is best-read in a fixed-width font, or in a text editor)
>> >>>
>> >>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>> >>> GBrowse-2.26
>> >>>        438 text files.
>> >>>        420 unique files.
>> >>>        179 files ignored.
>> >>>
>> >>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
>> >>> -------------------------------------------------------------------------------
>> >>> Language          files     blank   comment      code    scale   3rd
>> >>> gen. equiv
>> >>> -------------------------------------------------------------------------------
>> >>> Perl                188     14573      7632     50535 x   4.00 =
>> >>> 202140.00
>> >>> Javascript           33      2555      1251     14989 x   1.48 =
>> >>> 22183.72
>> >>> HTML                 11      1914       470      6968 x   1.90 =
>> >>> 13239.20
>> >>> XML                   1        28         0      1900 x   1.90 =
>> >>> 3610.00
>> >>> C                     2       183       223      1171 x   0.77 =
>> >>> 901.67
>> >>> CSS                  16        82        60      1099 x   1.00 =
>> >>> 1099.00
>> >>> YAML                  1         0         0       209 x   0.90 =
>> >>> 188.10
>> >>> Bourne Shell          3         9        11        92 x   3.81 =
>> >>> 350.52
>> >>> SQL                   1         8         0        55 x   2.29 =
>> >>> 125.95
>> >>> C/C++ Header          2        11         9        41 x   1.00
>> >>> =          41.00
>> >>> -------------------------------------------------------------------------------
>> >>> SUM:                258     19363      9656     77059 x   3.16 =
>> >>> 243879.16
>> >>> -------------------------------------------------------------------------------
>> >>>
>> >>> --
>> >>> Tomer Altman
>> >>> [hidden email]
>> >>> (650)859-2692
>> >>> http://www.ai.sri.com/people/taltman
>> >>>
>> >>> Bioinformatics Research Group
>> >>> Artificial Intelligence Center
>> >>> SRI, International
>> >>>
>> >>> http://bioinformatics.ai.sri.com/
>> >>>
>> >>>
>> >>> ------------------------------------------------------------------------------
>> >>> Xperia(TM) PLAY
>> >>> It's a major breakthrough. An authentic gaming
>> >>> smartphone on the nation's most reliable network.
>> >>> And it wants your games.
>> >>> http://p.sf.net/sfu/verizon-sfdev
>> >>> _______________________________________________
>> >>> Gmod-schema mailing list
>> >>> [hidden email]
>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>> >>>
>> >>>
>>
>>
>> --
>> Tomer Altman
>> [hidden email]
>> (650)859-2692
>> http://www.ai.sri.com/people/taltman
>>
>> Bioinformatics Research Group
>> Artificial Intelligence Center
>> SRI, International
>>
>> http://bioinformatics.ai.sri.com/
>>
>>
>>

------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
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Re: Programmer FTEs for GBrowse & Chado?

Scott Cain
Hi Dave and Tomer,

There are "third party" perl modules and Java classes though.  For example:

* Bio::DB::Das::Chado:
http://search.cpan.org/~scain/Bio-DB-Das-Chado-0.31/lib/Bio/DB/Das/Chado.pm
* Bio::Chado::Schema:
http://search.cpan.org/~rbuels/Bio-Chado-Schema-0.08100/lib/Bio/Chado/Schema.pm
* Modware: http://gmod-ware.sourceforge.net/

There are also open source Java classes but they are significantly
harder to find.

Scott


On Tue, Apr 12, 2011 at 8:58 AM, David Emmert <[hidden email]> wrote:

> Hi Tomer,
>
>>> Are there any third-party "libraries" in the Chado SQL code? I just want
>>> to be sure that I'm measuring the code correctly.
>
> I'm not sure what you mean.  Its an open project, so in a sense the whole thing
> is "third-party".
>
> AFAIK, there aren't (and there certainly shouldn't be) any modules of chado which
> were imported whole-cloth from other software packages.
>
> Best,
>
> -Dave
>
>
> >From [hidden email]  Tue Apr 12 01:17:52 2011
>>> To: David Emmert <[hidden email]>
>>> CC: [hidden email], [hidden email],
>>>         [hidden email]
>>> Subject: Re: [Gmod-schema] Programmer FTEs for GBrowse & Chado?
>>>
>>>   On 4/8/11 6:04 AM, David Emmert wrote:
>>> > Hi Tomer,
>>> >
>>> >>> Could you provide me with an estimate for how many programmers work on
>>> >>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>> > Regarding Chado, if you're asking how many FTE work -with- chado, I would say
>>> > we have 4 FTE working on chado at FlyBase.  If you're asking how many FTE are actively
>>> > developing the chado schema itself, I would say we average<.25 FTE doing active schema
>>> > development.
>>> Thank you David, that's exactly what I was looking for.
>>>
>>> Are there any third-party "libraries" in the Chado SQL code? I just want
>>> to be sure that I'm measuring the code correctly.
>>>
>>> Thanks,
>>>
>>> ~Tomer
>>> >>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>> >>> unable to find the source code download for Chado (any help would be
>>> >>> appreciated).
>>> > In the GMOD SVN look in trunk/chado/
>>> >
>>> > I'd love to hear your results when you finish compiling data.
>>> >
>>> > -Dave
>>> >
>>> >
>>> > > From [hidden email]  Thu Apr  7 18:08:49 2011
>>> >>> To: [hidden email], [hidden email]
>>> >>> Subject: [Gmod-schema] Programmer FTEs for GBrowse&  Chado?
>>> >>>
>>> >>> To whom it may concern,
>>> >>>
>>> >>> I sent this first to [hidden email], but I haven't yet received a reply.
>>> >>> Hopefully it is okay to post this message to the project email lists.
>>> >>>
>>> >>> I'm trying to assemble some empirical data on the sizes of various
>>> >>> bioinformatics software systems, and the associated software development
>>> >>> resources allocated to them.
>>> >>>
>>> >>> Could you provide me with an estimate for how many programmers work on
>>> >>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>> >>>
>>> >>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>> >>> unable to find the source code download for Chado (any help would be
>>> >>> appreciated).
>>> >>>
>>> >>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>>> >>> GBrowse, but I was unable to find the source code download for Chado
>>> >>> (any help would be appreciated).
>>> >>>
>>> >>> Please let me know if the lines-of-code per programming language in the
>>> >>> output looks correct to you. Also, if there are major libraries in the
>>> >>> source code that were not written by the GBrowse team that I should
>>> >>> exclude from this analysis, please let me know (same question for Chado
>>> >>> too, once I get access to the source code).
>>> >>>
>>> >>> Thanks in advance,
>>> >>>
>>> >>> ~Tomer Altman
>>> >>>
>>> >>> ---
>>> >>> (this output is best-read in a fixed-width font, or in a text editor)
>>> >>>
>>> >>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>>> >>> GBrowse-2.26
>>> >>>        438 text files.
>>> >>>        420 unique files.
>>> >>>        179 files ignored.
>>> >>>
>>> >>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
>>> >>> -------------------------------------------------------------------------------
>>> >>> Language          files     blank   comment      code    scale   3rd
>>> >>> gen. equiv
>>> >>> -------------------------------------------------------------------------------
>>> >>> Perl                188     14573      7632     50535 x   4.00 =
>>> >>> 202140.00
>>> >>> Javascript           33      2555      1251     14989 x   1.48 =
>>> >>> 22183.72
>>> >>> HTML                 11      1914       470      6968 x   1.90 =
>>> >>> 13239.20
>>> >>> XML                   1        28         0      1900 x   1.90 =
>>> >>> 3610.00
>>> >>> C                     2       183       223      1171 x   0.77 =
>>> >>> 901.67
>>> >>> CSS                  16        82        60      1099 x   1.00 =
>>> >>> 1099.00
>>> >>> YAML                  1         0         0       209 x   0.90 =
>>> >>> 188.10
>>> >>> Bourne Shell          3         9        11        92 x   3.81 =
>>> >>> 350.52
>>> >>> SQL                   1         8         0        55 x   2.29 =
>>> >>> 125.95
>>> >>> C/C++ Header          2        11         9        41 x   1.00
>>> >>> =          41.00
>>> >>> -------------------------------------------------------------------------------
>>> >>> SUM:                258     19363      9656     77059 x   3.16 =
>>> >>> 243879.16
>>> >>> -------------------------------------------------------------------------------
>>> >>>
>>> >>> --
>>> >>> Tomer Altman
>>> >>> [hidden email]
>>> >>> (650)859-2692
>>> >>> http://www.ai.sri.com/people/taltman
>>> >>>
>>> >>> Bioinformatics Research Group
>>> >>> Artificial Intelligence Center
>>> >>> SRI, International
>>> >>>
>>> >>> http://bioinformatics.ai.sri.com/
>>> >>>
>>> >>>
>>> >>> ------------------------------------------------------------------------------
>>> >>> Xperia(TM) PLAY
>>> >>> It's a major breakthrough. An authentic gaming
>>> >>> smartphone on the nation's most reliable network.
>>> >>> And it wants your games.
>>> >>> http://p.sf.net/sfu/verizon-sfdev
>>> >>> _______________________________________________
>>> >>> Gmod-schema mailing list
>>> >>> [hidden email]
>>> >>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>> >>>
>>> >>>
>>>
>>>
>>> --
>>> Tomer Altman
>>> [hidden email]
>>> (650)859-2692
>>> http://www.ai.sri.com/people/taltman
>>>
>>> Bioinformatics Research Group
>>> Artificial Intelligence Center
>>> SRI, International
>>>
>>> http://bioinformatics.ai.sri.com/
>>>
>>>
>>>
>
> ------------------------------------------------------------------------------
> Forrester Wave Report - Recovery time is now measured in hours and minutes
> not days. Key insights are discussed in the 2010 Forrester Wave Report as
> part of an in-depth evaluation of disaster recovery service providers.
> Forrester found the best-in-class provider in terms of services and vision.
> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
> _______________________________________________
> Gmod-schema mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
_______________________________________________
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Re: Programmer FTEs for GBrowse & Chado?

Olen Vance Sluder Jr
In reply to this post by Tomer Altman
Tomer,
Since your interest is ongoing maintenance, you may try looking at the the "dev" lists associated with each component <http://gmod.org/wiki/GMOD_Mailing_Lists>, which may yield specifics about the volume of change for a given time, etc.
 
I'll take some additional comments regarding the CLOC tool off-list so as not to use up the group's bandwidth.
 
Regards,
Olen

 
On Mon, Apr 11, 2011 at 8:18 PM, Tomer Altman <[hidden email]> wrote:
Hi Olen,

While I acknowledge that it will be difficult to get perfect precision with this query, I'm comparing projects to one another, so hopefully I'll be comparing numbers of equal precision. I understand that it's more difficult to estimate the amount of hours put in collectively to a "bazaar-like" open-source project as compared to one that is centrally-lead and where allotted time comes directly from organizational budgets. But I'm hoping that the project leaders can provide an estimate of the average amount of FTEs (or hours, if that is a more convenient measure) that are put in to these GMOD projects in a given year.

Thanks,

~Tomer


On 4/7/11 9:13 PM, Olen Vance Sluder Jr wrote:
Tomer,
 
Bear in mind that the GMOD components are open source projects to which a number of people from many organizations have contributed varying amounts of effort over a long period of time, so I suspect it will be nearly impossible to come up with a truly empirical value for "FTEs".
 
Also, lines of code are a notoriously bad metric for software measurement without a carefully calibrated model supporting them (e.g., Boehm's COCOMO, etc.), which is especially true when dealing with code bases consisting of multiple programming languages. I say this from nearly a decade of experience with a technical services firm where my speciality was software assessment.
 
Good luck with your analysis.
 
Regards,
Olen

On Thu, Apr 7, 2011 at 6:13 PM, Robert Buels <[hidden email]> wrote:
Hi Tomer,

I'm not really equipped to guess at FTE's for these projects, somebody
else will need to take a stab at that, but as for a Chado tarball, you
can get that here:

  http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/

And sure those number look believable to me for GBrowse.  You might be
the first one to measure it in this way.

Hope this helps!

Rob


On 04/07/2011 02:49 PM, Tomer Altman wrote:
> To whom it may concern,
>
> I sent this first to [hidden email], but I haven't yet received a reply.
> Hopefully it is okay to post this message to the project email lists.
>
> I'm trying to assemble some empirical data on the sizes of various
> bioinformatics software systems, and the associated software development
> resources allocated to them.
>
> Could you provide me with an estimate for how many programmers work on
> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>
> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
> unable to find the source code download for Chado (any help would be
> appreciated).
>
> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
> GBrowse, but I was unable to find the source code download for Chado
> (any help would be appreciated).
>
> Please let me know if the lines-of-code per programming language in the
> output looks correct to you. Also, if there are major libraries in the
> source code that were not written by the GBrowse team that I should
> exclude from this analysis, please let me know (same question for Chado
> too, once I get access to the source code).
>
> Thanks in advance,
>
> ~Tomer Altman
>
> ---
> (this output is best-read in a fixed-width font, or in a text editor)
>
> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
> GBrowse-2.26
>        438 text files.
>        420 unique files.
>        179 files ignored.
>
> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
> -------------------------------------------------------------------------------
> Language          files     blank   comment      code    scale   3rd
> gen. equiv
> -------------------------------------------------------------------------------
> Perl                188     14573      7632     50535 x   4.00 =
> 202140.00
> Javascript           33      2555      1251     14989 x   1.48 =
> 22183.72
> HTML                 11      1914       470      6968 x   1.90 =
> 13239.20
> XML                   1        28         0      1900 x   1.90 =
> 3610.00
> C                     2       183       223      1171 x   0.77 =
> 901.67
> CSS                  16        82        60      1099 x   1.00 =
> 1099.00
> YAML                  1         0         0       209 x   0.90 =
> 188.10
> Bourne Shell          3         9        11        92 x   3.81 =
> 350.52
> SQL                   1         8         0        55 x   2.29 =
> 125.95
> C/C++ Header          2        11         9        41 x   1.00
> =          41.00
> -------------------------------------------------------------------------------
> SUM:                258     19363      9656     77059 x   3.16 =
> 243879.16
> -------------------------------------------------------------------------------
>


------------------------------------------------------------------------------
Xperia(TM) PLAY
It's a major breakthrough. An authentic gaming
smartphone on the nation's most reliable network.
And it wants your games.
http://p.sf.net/sfu/verizon-sfdev
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema



-- 
Tomer Altman
[hidden email]
<a href="tel:%28650%29859-2692" target="_blank" value="+16508592692">(650)859-2692
http://www.ai.sri.com/people/taltman

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International

http://bioinformatics.ai.sri.com/



------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
_______________________________________________
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Re: Programmer FTEs for GBrowse & Chado?

Tomer Altman
In reply to this post by Scott Cain
  Hi Scott,

Thanks for pointing these modules/classes out. These are distributed
separately from the Chado sources that were pointed out to me earlier in
this thread, correct?

Thanks,

~Tomer

On 4/12/11 6:26 AM, Scott Cain wrote:

> Hi Dave and Tomer,
>
> There are "third party" perl modules and Java classes though.  For example:
>
> * Bio::DB::Das::Chado:
> http://search.cpan.org/~scain/Bio-DB-Das-Chado-0.31/lib/Bio/DB/Das/Chado.pm
> * Bio::Chado::Schema:
> http://search.cpan.org/~rbuels/Bio-Chado-Schema-0.08100/lib/Bio/Chado/Schema.pm
> * Modware: http://gmod-ware.sourceforge.net/
>
> There are also open source Java classes but they are significantly
> harder to find.
>
> Scott
>
>
> On Tue, Apr 12, 2011 at 8:58 AM, David Emmert<[hidden email]>  wrote:
>> Hi Tomer,
>>
>>>> Are there any third-party "libraries" in the Chado SQL code? I just want
>>>> to be sure that I'm measuring the code correctly.
>> I'm not sure what you mean.  Its an open project, so in a sense the whole thing
>> is "third-party".
>>
>> AFAIK, there aren't (and there certainly shouldn't be) any modules of chado which
>> were imported whole-cloth from other software packages.
>>
>> Best,
>>
>> -Dave
>>
>>
>> > From [hidden email]  Tue Apr 12 01:17:52 2011
>>>> To: David Emmert<[hidden email]>
>>>> CC: [hidden email], [hidden email],
>>>>          [hidden email]
>>>> Subject: Re: [Gmod-schema] Programmer FTEs for GBrowse&  Chado?
>>>>
>>>>    On 4/8/11 6:04 AM, David Emmert wrote:
>>>>> Hi Tomer,
>>>>>
>>>>>>> Could you provide me with an estimate for how many programmers work on
>>>>>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>>>> Regarding Chado, if you're asking how many FTE work -with- chado, I would say
>>>>> we have 4 FTE working on chado at FlyBase.  If you're asking how many FTE are actively
>>>>> developing the chado schema itself, I would say we average<.25 FTE doing active schema
>>>>> development.
>>>> Thank you David, that's exactly what I was looking for.
>>>>
>>>> Are there any third-party "libraries" in the Chado SQL code? I just want
>>>> to be sure that I'm measuring the code correctly.
>>>>
>>>> Thanks,
>>>>
>>>> ~Tomer
>>>>>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>>>>>> unable to find the source code download for Chado (any help would be
>>>>>>> appreciated).
>>>>> In the GMOD SVN look in trunk/chado/
>>>>>
>>>>> I'd love to hear your results when you finish compiling data.
>>>>>
>>>>> -Dave
>>>>>
>>>>>
>>>>>>  From [hidden email]  Thu Apr  7 18:08:49 2011
>>>>>>> To: [hidden email], [hidden email]
>>>>>>> Subject: [Gmod-schema] Programmer FTEs for GBrowse&    Chado?
>>>>>>>
>>>>>>> To whom it may concern,
>>>>>>>
>>>>>>> I sent this first to [hidden email], but I haven't yet received a reply.
>>>>>>> Hopefully it is okay to post this message to the project email lists.
>>>>>>>
>>>>>>> I'm trying to assemble some empirical data on the sizes of various
>>>>>>> bioinformatics software systems, and the associated software development
>>>>>>> resources allocated to them.
>>>>>>>
>>>>>>> Could you provide me with an estimate for how many programmers work on
>>>>>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?
>>>>>>>
>>>>>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>>>>>> unable to find the source code download for Chado (any help would be
>>>>>>> appreciated).
>>>>>>>
>>>>>>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>>>>>>> GBrowse, but I was unable to find the source code download for Chado
>>>>>>> (any help would be appreciated).
>>>>>>>
>>>>>>> Please let me know if the lines-of-code per programming language in the
>>>>>>> output looks correct to you. Also, if there are major libraries in the
>>>>>>> source code that were not written by the GBrowse team that I should
>>>>>>> exclude from this analysis, please let me know (same question for Chado
>>>>>>> too, once I get access to the source code).
>>>>>>>
>>>>>>> Thanks in advance,
>>>>>>>
>>>>>>> ~Tomer Altman
>>>>>>>
>>>>>>> ---
>>>>>>> (this output is best-read in a fixed-width font, or in a text editor)
>>>>>>>
>>>>>>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>>>>>>> GBrowse-2.26
>>>>>>>         438 text files.
>>>>>>>         420 unique files.
>>>>>>>         179 files ignored.
>>>>>>>
>>>>>>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
>>>>>>> -------------------------------------------------------------------------------
>>>>>>> Language          files     blank   comment      code    scale   3rd
>>>>>>> gen. equiv
>>>>>>> -------------------------------------------------------------------------------
>>>>>>> Perl                188     14573      7632     50535 x   4.00 =
>>>>>>> 202140.00
>>>>>>> Javascript           33      2555      1251     14989 x   1.48 =
>>>>>>> 22183.72
>>>>>>> HTML                 11      1914       470      6968 x   1.90 =
>>>>>>> 13239.20
>>>>>>> XML                   1        28         0      1900 x   1.90 =
>>>>>>> 3610.00
>>>>>>> C                     2       183       223      1171 x   0.77 =
>>>>>>> 901.67
>>>>>>> CSS                  16        82        60      1099 x   1.00 =
>>>>>>> 1099.00
>>>>>>> YAML                  1         0         0       209 x   0.90 =
>>>>>>> 188.10
>>>>>>> Bourne Shell          3         9        11        92 x   3.81 =
>>>>>>> 350.52
>>>>>>> SQL                   1         8         0        55 x   2.29 =
>>>>>>> 125.95
>>>>>>> C/C++ Header          2        11         9        41 x   1.00
>>>>>>> =          41.00
>>>>>>> -------------------------------------------------------------------------------
>>>>>>> SUM:                258     19363      9656     77059 x   3.16 =
>>>>>>> 243879.16
>>>>>>> -------------------------------------------------------------------------------
>>>>>>>
>>>>>>> --
>>>>>>> Tomer Altman
>>>>>>> [hidden email]
>>>>>>> (650)859-2692
>>>>>>> http://www.ai.sri.com/people/taltman
>>>>>>>
>>>>>>> Bioinformatics Research Group
>>>>>>> Artificial Intelligence Center
>>>>>>> SRI, International
>>>>>>>
>>>>>>> http://bioinformatics.ai.sri.com/
>>>>>>>
>>>>>>>
>>>>>>> ------------------------------------------------------------------------------
>>>>>>> Xperia(TM) PLAY
>>>>>>> It's a major breakthrough. An authentic gaming
>>>>>>> smartphone on the nation's most reliable network.
>>>>>>> And it wants your games.
>>>>>>> http://p.sf.net/sfu/verizon-sfdev
>>>>>>> _______________________________________________
>>>>>>> Gmod-schema mailing list
>>>>>>> [hidden email]
>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>
>>>>>>>
>>>>
>>>> --
>>>> Tomer Altman
>>>> [hidden email]
>>>> (650)859-2692
>>>> http://www.ai.sri.com/people/taltman
>>>>
>>>> Bioinformatics Research Group
>>>> Artificial Intelligence Center
>>>> SRI, International
>>>>
>>>> http://bioinformatics.ai.sri.com/
>>>>
>>>>
>>>>
>> ------------------------------------------------------------------------------
>> Forrester Wave Report - Recovery time is now measured in hours and minutes
>> not days. Key insights are discussed in the 2010 Forrester Wave Report as
>> part of an in-depth evaluation of disaster recovery service providers.
>> Forrester found the best-in-class provider in terms of services and vision.
>> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
>> _______________________________________________
>> Gmod-schema mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>
>
>


--
Tomer Altman
[hidden email]
(650)859-2692
http://www.ai.sri.com/people/taltman

Bioinformatics Research Group
Artificial Intelligence Center
SRI, International

http://bioinformatics.ai.sri.com/



------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
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Open this post in threaded view
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Re: Programmer FTEs for GBrowse & Chado?

Scott Cain
Hi Tomer,

Yes, Bio::DB::Das::Chado and Bio::Chado::Schema can be obtained from
cpan, and I don't think modware has be officially released yet.

Scott


On Wed, Apr 13, 2011 at 11:00 AM, Tomer Altman <[hidden email]> wrote:

>  Hi Scott,
>
> Thanks for pointing these modules/classes out. These are distributed
> separately from the Chado sources that were pointed out to me earlier in
> this thread, correct?
>
> Thanks,
>
> ~Tomer
>
> On 4/12/11 6:26 AM, Scott Cain wrote:
>>
>> Hi Dave and Tomer,
>>
>> There are "third party" perl modules and Java classes though.  For
>> example:
>>
>> * Bio::DB::Das::Chado:
>>
>> http://search.cpan.org/~scain/Bio-DB-Das-Chado-0.31/lib/Bio/DB/Das/Chado.pm
>> * Bio::Chado::Schema:
>>
>> http://search.cpan.org/~rbuels/Bio-Chado-Schema-0.08100/lib/Bio/Chado/Schema.pm
>> * Modware: http://gmod-ware.sourceforge.net/
>>
>> There are also open source Java classes but they are significantly
>> harder to find.
>>
>> Scott
>>
>>
>> On Tue, Apr 12, 2011 at 8:58 AM, David Emmert<[hidden email]>
>>  wrote:
>>>
>>> Hi Tomer,
>>>
>>>>> Are there any third-party "libraries" in the Chado SQL code? I just
>>>>> want
>>>>> to be sure that I'm measuring the code correctly.
>>>
>>> I'm not sure what you mean.  Its an open project, so in a sense the whole
>>> thing
>>> is "third-party".
>>>
>>> AFAIK, there aren't (and there certainly shouldn't be) any modules of
>>> chado which
>>> were imported whole-cloth from other software packages.
>>>
>>> Best,
>>>
>>> -Dave
>>>
>>>
>>> > From [hidden email]  Tue Apr 12 01:17:52 2011
>>>>>
>>>>> To: David Emmert<[hidden email]>
>>>>> CC: [hidden email],
>>>>> [hidden email],
>>>>>         [hidden email]
>>>>> Subject: Re: [Gmod-schema] Programmer FTEs for GBrowse&  Chado?
>>>>>
>>>>>   On 4/8/11 6:04 AM, David Emmert wrote:
>>>>>>
>>>>>> Hi Tomer,
>>>>>>
>>>>>>>> Could you provide me with an estimate for how many programmers work
>>>>>>>> on
>>>>>>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents
>>>>>>>> (FTEs)?
>>>>>>
>>>>>> Regarding Chado, if you're asking how many FTE work -with- chado, I
>>>>>> would say
>>>>>> we have 4 FTE working on chado at FlyBase.  If you're asking how many
>>>>>> FTE are actively
>>>>>> developing the chado schema itself, I would say we average<.25 FTE
>>>>>> doing active schema
>>>>>> development.
>>>>>
>>>>> Thank you David, that's exactly what I was looking for.
>>>>>
>>>>> Are there any third-party "libraries" in the Chado SQL code? I just
>>>>> want
>>>>> to be sure that I'm measuring the code correctly.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> ~Tomer
>>>>>>>>
>>>>>>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I
>>>>>>>> was
>>>>>>>> unable to find the source code download for Chado (any help would be
>>>>>>>> appreciated).
>>>>>>
>>>>>> In the GMOD SVN look in trunk/chado/
>>>>>>
>>>>>> I'd love to hear your results when you finish compiling data.
>>>>>>
>>>>>> -Dave
>>>>>>
>>>>>>
>>>>>>>  From [hidden email]  Thu Apr  7 18:08:49
>>>>>>> 2011
>>>>>>>>
>>>>>>>> To: [hidden email],
>>>>>>>> [hidden email]
>>>>>>>> Subject: [Gmod-schema] Programmer FTEs for GBrowse&    Chado?
>>>>>>>>
>>>>>>>> To whom it may concern,
>>>>>>>>
>>>>>>>> I sent this first to [hidden email], but I haven't yet received a
>>>>>>>> reply.
>>>>>>>> Hopefully it is okay to post this message to the project email
>>>>>>>> lists.
>>>>>>>>
>>>>>>>> I'm trying to assemble some empirical data on the sizes of various
>>>>>>>> bioinformatics software systems, and the associated software
>>>>>>>> development
>>>>>>>> resources allocated to them.
>>>>>>>>
>>>>>>>> Could you provide me with an estimate for how many programmers work
>>>>>>>> on
>>>>>>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents
>>>>>>>> (FTEs)?
>>>>>>>>
>>>>>>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I
>>>>>>>> was
>>>>>>>> unable to find the source code download for Chado (any help would be
>>>>>>>> appreciated).
>>>>>>>>
>>>>>>>> I've used a tool called cloc (cloc.sf.net) to analyze the source
>>>>>>>> code of
>>>>>>>> GBrowse, but I was unable to find the source code download for Chado
>>>>>>>> (any help would be appreciated).
>>>>>>>>
>>>>>>>> Please let me know if the lines-of-code per programming language in
>>>>>>>> the
>>>>>>>> output looks correct to you. Also, if there are major libraries in
>>>>>>>> the
>>>>>>>> source code that were not written by the GBrowse team that I should
>>>>>>>> exclude from this analysis, please let me know (same question for
>>>>>>>> Chado
>>>>>>>> too, once I get access to the source code).
>>>>>>>>
>>>>>>>> Thanks in advance,
>>>>>>>>
>>>>>>>> ~Tomer Altman
>>>>>>>>
>>>>>>>> ---
>>>>>>>> (this output is best-read in a fixed-width font, or in a text
>>>>>>>> editor)
>>>>>>>>
>>>>>>>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl
>>>>>>>> --3
>>>>>>>> GBrowse-2.26
>>>>>>>>        438 text files.
>>>>>>>>        420 unique files.
>>>>>>>>        179 files ignored.
>>>>>>>>
>>>>>>>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8
>>>>>>>> lines/s)
>>>>>>>>
>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>> Language          files     blank   comment      code    scale   3rd
>>>>>>>> gen. equiv
>>>>>>>>
>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>> Perl                188     14573      7632     50535 x   4.00 =
>>>>>>>> 202140.00
>>>>>>>> Javascript           33      2555      1251     14989 x   1.48 =
>>>>>>>> 22183.72
>>>>>>>> HTML                 11      1914       470      6968 x   1.90 =
>>>>>>>> 13239.20
>>>>>>>> XML                   1        28         0      1900 x   1.90 =
>>>>>>>> 3610.00
>>>>>>>> C                     2       183       223      1171 x   0.77 =
>>>>>>>> 901.67
>>>>>>>> CSS                  16        82        60      1099 x   1.00 =
>>>>>>>> 1099.00
>>>>>>>> YAML                  1         0         0       209 x   0.90 =
>>>>>>>> 188.10
>>>>>>>> Bourne Shell          3         9        11        92 x   3.81 =
>>>>>>>> 350.52
>>>>>>>> SQL                   1         8         0        55 x   2.29 =
>>>>>>>> 125.95
>>>>>>>> C/C++ Header          2        11         9        41 x   1.00
>>>>>>>> =          41.00
>>>>>>>>
>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>> SUM:                258     19363      9656     77059 x   3.16 =
>>>>>>>> 243879.16
>>>>>>>>
>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>>
>>>>>>>> --
>>>>>>>> Tomer Altman
>>>>>>>> [hidden email]
>>>>>>>> (650)859-2692
>>>>>>>> http://www.ai.sri.com/people/taltman
>>>>>>>>
>>>>>>>> Bioinformatics Research Group
>>>>>>>> Artificial Intelligence Center
>>>>>>>> SRI, International
>>>>>>>>
>>>>>>>> http://bioinformatics.ai.sri.com/
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>> Xperia(TM) PLAY
>>>>>>>> It's a major breakthrough. An authentic gaming
>>>>>>>> smartphone on the nation's most reliable network.
>>>>>>>> And it wants your games.
>>>>>>>> http://p.sf.net/sfu/verizon-sfdev
>>>>>>>> _______________________________________________
>>>>>>>> Gmod-schema mailing list
>>>>>>>> [hidden email]
>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>
>>>>>>>>
>>>>>
>>>>> --
>>>>> Tomer Altman
>>>>> [hidden email]
>>>>> (650)859-2692
>>>>> http://www.ai.sri.com/people/taltman
>>>>>
>>>>> Bioinformatics Research Group
>>>>> Artificial Intelligence Center
>>>>> SRI, International
>>>>>
>>>>> http://bioinformatics.ai.sri.com/
>>>>>
>>>>>
>>>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Forrester Wave Report - Recovery time is now measured in hours and
>>> minutes
>>> not days. Key insights are discussed in the 2010 Forrester Wave Report as
>>> part of an in-depth evaluation of disaster recovery service providers.
>>> Forrester found the best-in-class provider in terms of services and
>>> vision.
>>> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>
>>
>>
>
>
> --
> Tomer Altman
> [hidden email]
> (650)859-2692
> http://www.ai.sri.com/people/taltman
>
> Bioinformatics Research Group
> Artificial Intelligence Center
> SRI, International
>
> http://bioinformatics.ai.sri.com/
>
>
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: Programmer FTEs for GBrowse & Chado?

Scott Cain
Oops.  Modware can be obtained here:

  http://sourceforge.net/projects/gmod-ware/

Scott


On Wed, Apr 13, 2011 at 12:41 PM, Scott Cain <[hidden email]> wrote:

> Hi Tomer,
>
> Yes, Bio::DB::Das::Chado and Bio::Chado::Schema can be obtained from
> cpan, and I don't think modware has be officially released yet.
>
> Scott
>
>
> On Wed, Apr 13, 2011 at 11:00 AM, Tomer Altman <[hidden email]> wrote:
>>  Hi Scott,
>>
>> Thanks for pointing these modules/classes out. These are distributed
>> separately from the Chado sources that were pointed out to me earlier in
>> this thread, correct?
>>
>> Thanks,
>>
>> ~Tomer
>>
>> On 4/12/11 6:26 AM, Scott Cain wrote:
>>>
>>> Hi Dave and Tomer,
>>>
>>> There are "third party" perl modules and Java classes though.  For
>>> example:
>>>
>>> * Bio::DB::Das::Chado:
>>>
>>> http://search.cpan.org/~scain/Bio-DB-Das-Chado-0.31/lib/Bio/DB/Das/Chado.pm
>>> * Bio::Chado::Schema:
>>>
>>> http://search.cpan.org/~rbuels/Bio-Chado-Schema-0.08100/lib/Bio/Chado/Schema.pm
>>> * Modware: http://gmod-ware.sourceforge.net/
>>>
>>> There are also open source Java classes but they are significantly
>>> harder to find.
>>>
>>> Scott
>>>
>>>
>>> On Tue, Apr 12, 2011 at 8:58 AM, David Emmert<[hidden email]>
>>>  wrote:
>>>>
>>>> Hi Tomer,
>>>>
>>>>>> Are there any third-party "libraries" in the Chado SQL code? I just
>>>>>> want
>>>>>> to be sure that I'm measuring the code correctly.
>>>>
>>>> I'm not sure what you mean.  Its an open project, so in a sense the whole
>>>> thing
>>>> is "third-party".
>>>>
>>>> AFAIK, there aren't (and there certainly shouldn't be) any modules of
>>>> chado which
>>>> were imported whole-cloth from other software packages.
>>>>
>>>> Best,
>>>>
>>>> -Dave
>>>>
>>>>
>>>> > From [hidden email]  Tue Apr 12 01:17:52 2011
>>>>>>
>>>>>> To: David Emmert<[hidden email]>
>>>>>> CC: [hidden email],
>>>>>> [hidden email],
>>>>>>         [hidden email]
>>>>>> Subject: Re: [Gmod-schema] Programmer FTEs for GBrowse&  Chado?
>>>>>>
>>>>>>   On 4/8/11 6:04 AM, David Emmert wrote:
>>>>>>>
>>>>>>> Hi Tomer,
>>>>>>>
>>>>>>>>> Could you provide me with an estimate for how many programmers work
>>>>>>>>> on
>>>>>>>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents
>>>>>>>>> (FTEs)?
>>>>>>>
>>>>>>> Regarding Chado, if you're asking how many FTE work -with- chado, I
>>>>>>> would say
>>>>>>> we have 4 FTE working on chado at FlyBase.  If you're asking how many
>>>>>>> FTE are actively
>>>>>>> developing the chado schema itself, I would say we average<.25 FTE
>>>>>>> doing active schema
>>>>>>> development.
>>>>>>
>>>>>> Thank you David, that's exactly what I was looking for.
>>>>>>
>>>>>> Are there any third-party "libraries" in the Chado SQL code? I just
>>>>>> want
>>>>>> to be sure that I'm measuring the code correctly.
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>> ~Tomer
>>>>>>>>>
>>>>>>>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I
>>>>>>>>> was
>>>>>>>>> unable to find the source code download for Chado (any help would be
>>>>>>>>> appreciated).
>>>>>>>
>>>>>>> In the GMOD SVN look in trunk/chado/
>>>>>>>
>>>>>>> I'd love to hear your results when you finish compiling data.
>>>>>>>
>>>>>>> -Dave
>>>>>>>
>>>>>>>
>>>>>>>>  From [hidden email]  Thu Apr  7 18:08:49
>>>>>>>> 2011
>>>>>>>>>
>>>>>>>>> To: [hidden email],
>>>>>>>>> [hidden email]
>>>>>>>>> Subject: [Gmod-schema] Programmer FTEs for GBrowse&    Chado?
>>>>>>>>>
>>>>>>>>> To whom it may concern,
>>>>>>>>>
>>>>>>>>> I sent this first to [hidden email], but I haven't yet received a
>>>>>>>>> reply.
>>>>>>>>> Hopefully it is okay to post this message to the project email
>>>>>>>>> lists.
>>>>>>>>>
>>>>>>>>> I'm trying to assemble some empirical data on the sizes of various
>>>>>>>>> bioinformatics software systems, and the associated software
>>>>>>>>> development
>>>>>>>>> resources allocated to them.
>>>>>>>>>
>>>>>>>>> Could you provide me with an estimate for how many programmers work
>>>>>>>>> on
>>>>>>>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents
>>>>>>>>> (FTEs)?
>>>>>>>>>
>>>>>>>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I
>>>>>>>>> was
>>>>>>>>> unable to find the source code download for Chado (any help would be
>>>>>>>>> appreciated).
>>>>>>>>>
>>>>>>>>> I've used a tool called cloc (cloc.sf.net) to analyze the source
>>>>>>>>> code of
>>>>>>>>> GBrowse, but I was unable to find the source code download for Chado
>>>>>>>>> (any help would be appreciated).
>>>>>>>>>
>>>>>>>>> Please let me know if the lines-of-code per programming language in
>>>>>>>>> the
>>>>>>>>> output looks correct to you. Also, if there are major libraries in
>>>>>>>>> the
>>>>>>>>> source code that were not written by the GBrowse team that I should
>>>>>>>>> exclude from this analysis, please let me know (same question for
>>>>>>>>> Chado
>>>>>>>>> too, once I get access to the source code).
>>>>>>>>>
>>>>>>>>> Thanks in advance,
>>>>>>>>>
>>>>>>>>> ~Tomer Altman
>>>>>>>>>
>>>>>>>>> ---
>>>>>>>>> (this output is best-read in a fixed-width font, or in a text
>>>>>>>>> editor)
>>>>>>>>>
>>>>>>>>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl
>>>>>>>>> --3
>>>>>>>>> GBrowse-2.26
>>>>>>>>>        438 text files.
>>>>>>>>>        420 unique files.
>>>>>>>>>        179 files ignored.
>>>>>>>>>
>>>>>>>>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8
>>>>>>>>> lines/s)
>>>>>>>>>
>>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>>> Language          files     blank   comment      code    scale   3rd
>>>>>>>>> gen. equiv
>>>>>>>>>
>>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>>> Perl                188     14573      7632     50535 x   4.00 =
>>>>>>>>> 202140.00
>>>>>>>>> Javascript           33      2555      1251     14989 x   1.48 =
>>>>>>>>> 22183.72
>>>>>>>>> HTML                 11      1914       470      6968 x   1.90 =
>>>>>>>>> 13239.20
>>>>>>>>> XML                   1        28         0      1900 x   1.90 =
>>>>>>>>> 3610.00
>>>>>>>>> C                     2       183       223      1171 x   0.77 =
>>>>>>>>> 901.67
>>>>>>>>> CSS                  16        82        60      1099 x   1.00 =
>>>>>>>>> 1099.00
>>>>>>>>> YAML                  1         0         0       209 x   0.90 =
>>>>>>>>> 188.10
>>>>>>>>> Bourne Shell          3         9        11        92 x   3.81 =
>>>>>>>>> 350.52
>>>>>>>>> SQL                   1         8         0        55 x   2.29 =
>>>>>>>>> 125.95
>>>>>>>>> C/C++ Header          2        11         9        41 x   1.00
>>>>>>>>> =          41.00
>>>>>>>>>
>>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>>> SUM:                258     19363      9656     77059 x   3.16 =
>>>>>>>>> 243879.16
>>>>>>>>>
>>>>>>>>> -------------------------------------------------------------------------------
>>>>>>>>>
>>>>>>>>> --
>>>>>>>>> Tomer Altman
>>>>>>>>> [hidden email]
>>>>>>>>> (650)859-2692
>>>>>>>>> http://www.ai.sri.com/people/taltman
>>>>>>>>>
>>>>>>>>> Bioinformatics Research Group
>>>>>>>>> Artificial Intelligence Center
>>>>>>>>> SRI, International
>>>>>>>>>
>>>>>>>>> http://bioinformatics.ai.sri.com/
>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>> ------------------------------------------------------------------------------
>>>>>>>>> Xperia(TM) PLAY
>>>>>>>>> It's a major breakthrough. An authentic gaming
>>>>>>>>> smartphone on the nation's most reliable network.
>>>>>>>>> And it wants your games.
>>>>>>>>> http://p.sf.net/sfu/verizon-sfdev
>>>>>>>>> _______________________________________________
>>>>>>>>> Gmod-schema mailing list
>>>>>>>>> [hidden email]
>>>>>>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>>>>>>
>>>>>>>>>
>>>>>>
>>>>>> --
>>>>>> Tomer Altman
>>>>>> [hidden email]
>>>>>> (650)859-2692
>>>>>> http://www.ai.sri.com/people/taltman
>>>>>>
>>>>>> Bioinformatics Research Group
>>>>>> Artificial Intelligence Center
>>>>>> SRI, International
>>>>>>
>>>>>> http://bioinformatics.ai.sri.com/
>>>>>>
>>>>>>
>>>>>>
>>>>
>>>> ------------------------------------------------------------------------------
>>>> Forrester Wave Report - Recovery time is now measured in hours and
>>>> minutes
>>>> not days. Key insights are discussed in the 2010 Forrester Wave Report as
>>>> part of an in-depth evaluation of disaster recovery service providers.
>>>> Forrester found the best-in-class provider in terms of services and
>>>> vision.
>>>> Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
>>>> _______________________________________________
>>>> Gmod-schema mailing list
>>>> [hidden email]
>>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>>>>
>>>
>>>
>>
>>
>> --
>> Tomer Altman
>> [hidden email]
>> (650)859-2692
>> http://www.ai.sri.com/people/taltman
>>
>> Bioinformatics Research Group
>> Artificial Intelligence Center
>> SRI, International
>>
>> http://bioinformatics.ai.sri.com/
>>
>>
>>
>
>
>
> --
> ------------------------------------------------------------------------
> Scott Cain, Ph. D.                                   scott at scottcain dot net
> GMOD Coordinator (http://gmod.org/)                     216-392-3087
> Ontario Institute for Cancer Research
>



--
------------------------------------------------------------------------
Scott Cain, Ph. D.                                   scott at scottcain dot net
GMOD Coordinator (http://gmod.org/)                     216-392-3087
Ontario Institute for Cancer Research

------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
_______________________________________________
Gmod-schema mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/gmod-schema
Reply | Threaded
Open this post in threaded view
|

Re: [Gmod-gbrowse] Programmer FTEs for GBrowse & Chado?

Lincoln Stein
In reply to this post by Tomer Altman
Very roughly, because it fluctuates, GBrowse has 2 FTEs working on it at any time: usually 0.25-0.5 of my time, and 1-2 full time students or RAs.

Lincoln

On Thu, Apr 7, 2011 at 5:49 PM, Tomer Altman <[hidden email]> wrote:
To whom it may concern,

I sent this first to [hidden email], but I haven't yet received a reply.
Hopefully it is okay to post this message to the project email lists.

I'm trying to assemble some empirical data on the sizes of various
bioinformatics software systems, and the associated software development
resources allocated to them.

Could you provide me with an estimate for how many programmers work on
GBrowse and Chado (separately), as measured in Full-Time Equivalents (FTEs)?

Also, I analyzed the lines of code in the GBrowse tar ball, but I was
unable to find the source code download for Chado (any help would be
appreciated).

I've used a tool called cloc (cloc.sf.net) to analyze the source code of
GBrowse, but I was unable to find the source code download for Chado
(any help would be appreciated).

Please let me know if the lines-of-code per programming language in the
output looks correct to you. Also, if there are major libraries in the
source code that were not written by the GBrowse team that I should
exclude from this analysis, please let me know (same question for Chado
too, once I get access to the source code).

Thanks in advance,

~Tomer Altman

---
(this output is best-read in a fixed-width font, or in a text editor)

arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
GBrowse-2.26
     438 text files.
     420 unique files.
     179 files ignored.

http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8 lines/s)
-------------------------------------------------------------------------------
Language          files     blank   comment      code    scale   3rd
gen. equiv
-------------------------------------------------------------------------------
Perl                188     14573      7632     50535 x   4.00 =
202140.00
Javascript           33      2555      1251     14989 x   1.48 =
22183.72
HTML                 11      1914       470      6968 x   1.90 =
13239.20
XML                   1        28         0      1900 x   1.90 =
3610.00
C                     2       183       223      1171 x   0.77 =
901.67
CSS                  16        82        60      1099 x   1.00 =
1099.00
YAML                  1         0         0       209 x   0.90 =
188.10
Bourne Shell          3         9        11        92 x   3.81 =
350.52
SQL                   1         8         0        55 x   2.29 =
125.95
C/C++ Header          2        11         9        41 x   1.00
=          41.00
-------------------------------------------------------------------------------
SUM:                258     19363      9656     77059 x   3.16 =
243879.16
-------------------------------------------------------------------------------

--
Tomer Altman
[hidden email]
<a href="tel:%28650%29859-2692" value="+16508592692">(650)859-2692
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Re: Programmer FTEs for GBrowse & Chado?

Daniel Quest
In reply to this post by Tomer Altman
Awesome!  I think that would be pretty interesting.  I wonder if you
could compare it to Linux and other open source projects.

-Daniel

On Mon, Apr 11, 2011 at 9:24 PM, Tomer Altman <[hidden email]> wrote:

>  Hi Daniel,
>
> In terms of my "drivers", I'm doing research into the correlation between
> the size of bioinformatic software projects and the number of FTEs that are
> needed to maintain & extend the software.
>
> I'm happy that the gmod-schema folks have been helpful with my research. I'm
> hoping that I can get in touch with some of the gmod-gbrowse folks as well.
>
> P.S.- I am one of the maintainers of the BioWarehouse open-source
> bioinformatic database warehousing project (www.biowarehouse.org).
>
>
> On 4/7/11 5:10 PM, Daniel Quest wrote:
>>
>> Hey Tomer
>>
>> Chado is mostly lines of sql
>> Just an FYI
>>
>> Also, it would be very helpful to know WHY you would like to do this
>> assessment.  I.e. What are your business drivers?
>>
>> IMHO the ontologies, community, widespread acceptance and syntax standards
>> far exceed the value of the GMOD software stack.
>>
>> So if you calculate value based on loc then you are missing a big part of
>> what gmod is about.  I believe many decisions inside of gmod are better than
>> software independently created because a lot of thought goes into
>> engineering decisions.
>>
>> At Oak Ridge we had the resources to deviate from what gmod did.  I can
>> think of 3 cases where what we where doing was so different from running a
>> model organism database that we had to make changes.  In every other case
>> the community standard was superior to our alternative.  That says something
>> about the quality of the approach and the support in gmod.  I for one will
>> always be so thankful to everyone on this list for taking the time to help
>> me out and get the gmod way into my thick head
>>
>> - Daniel
>>
>>
>> Sent from my iPod
>>
>> On Apr 7, 2011, at 7:13 PM, Robert Buels<[hidden email]>  wrote:
>>
>>> Hi Tomer,
>>>
>>> I'm not really equipped to guess at FTE's for these projects, somebody
>>> else will need to take a stab at that, but as for a Chado tarball, you
>>> can get that here:
>>>
>>>   http://sourceforge.net/projects/gmod/files/gmod/chado-1.11/
>>>
>>> And sure those number look believable to me for GBrowse.  You might be
>>> the first one to measure it in this way.
>>>
>>> Hope this helps!
>>>
>>> Rob
>>>
>>>
>>> On 04/07/2011 02:49 PM, Tomer Altman wrote:
>>>>
>>>> To whom it may concern,
>>>>
>>>> I sent this first to [hidden email], but I haven't yet received a reply.
>>>> Hopefully it is okay to post this message to the project email lists.
>>>>
>>>> I'm trying to assemble some empirical data on the sizes of various
>>>> bioinformatics software systems, and the associated software development
>>>> resources allocated to them.
>>>>
>>>> Could you provide me with an estimate for how many programmers work on
>>>> GBrowse and Chado (separately), as measured in Full-Time Equivalents
>>>> (FTEs)?
>>>>
>>>> Also, I analyzed the lines of code in the GBrowse tar ball, but I was
>>>> unable to find the source code download for Chado (any help would be
>>>> appreciated).
>>>>
>>>> I've used a tool called cloc (cloc.sf.net) to analyze the source code of
>>>> GBrowse, but I was unable to find the source code download for Chado
>>>> (any help would be appreciated).
>>>>
>>>> Please let me know if the lines-of-code per programming language in the
>>>> output looks correct to you. Also, if there are major libraries in the
>>>> source code that were not written by the GBrowse team that I should
>>>> exclude from this analysis, please let me know (same question for Chado
>>>> too, once I get access to the source code).
>>>>
>>>> Thanks in advance,
>>>>
>>>> ~Tomer Altman
>>>>
>>>> ---
>>>> (this output is best-read in a fixed-width font, or in a text editor)
>>>>
>>>> arrowroot:/home/hapuna1/bio/software/gbrowse 65: ~/bin/cloc-1.53.pl --3
>>>> GBrowse-2.26
>>>>       438 text files.
>>>>       420 unique files.
>>>>       179 files ignored.
>>>>
>>>> http://cloc.sourceforge.net v 1.53  T=12.0 s (21.5 files/s, 8839.8
>>>> lines/s)
>>>>
>>>> -------------------------------------------------------------------------------
>>>> Language          files     blank   comment      code    scale   3rd
>>>> gen. equiv
>>>>
>>>> -------------------------------------------------------------------------------
>>>> Perl                188     14573      7632     50535 x   4.00 =
>>>> 202140.00
>>>> Javascript           33      2555      1251     14989 x   1.48 =
>>>> 22183.72
>>>> HTML                 11      1914       470      6968 x   1.90 =
>>>> 13239.20
>>>> XML                   1        28         0      1900 x   1.90 =
>>>> 3610.00
>>>> C                     2       183       223      1171 x   0.77 =
>>>> 901.67
>>>> CSS                  16        82        60      1099 x   1.00 =
>>>> 1099.00
>>>> YAML                  1         0         0       209 x   0.90 =
>>>> 188.10
>>>> Bourne Shell          3         9        11        92 x   3.81 =
>>>> 350.52
>>>> SQL                   1         8         0        55 x   2.29 =
>>>> 125.95
>>>> C/C++ Header          2        11         9        41 x   1.00
>>>> =          41.00
>>>>
>>>> -------------------------------------------------------------------------------
>>>> SUM:                258     19363      9656     77059 x   3.16 =
>>>> 243879.16
>>>>
>>>> -------------------------------------------------------------------------------
>>>>
>>>
>>>
>>> ------------------------------------------------------------------------------
>>> Xperia(TM) PLAY
>>> It's a major breakthrough. An authentic gaming
>>> smartphone on the nation's most reliable network.
>>> And it wants your games.
>>> http://p.sf.net/sfu/verizon-sfdev
>>> _______________________________________________
>>> Gmod-schema mailing list
>>> [hidden email]
>>> https://lists.sourceforge.net/lists/listinfo/gmod-schema
>
>
> --
> Tomer Altman
> [hidden email]
> (650)859-2692
> http://www.ai.sri.com/people/taltman
>
> Bioinformatics Research Group
> Artificial Intelligence Center
> SRI, International
>
> http://bioinformatics.ai.sri.com/
>
>
>

------------------------------------------------------------------------------
Forrester Wave Report - Recovery time is now measured in hours and minutes
not days. Key insights are discussed in the 2010 Forrester Wave Report as
part of an in-depth evaluation of disaster recovery service providers.
Forrester found the best-in-class provider in terms of services and vision.
Read this report now!  http://p.sf.net/sfu/ibm-webcastpromo
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