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July 2008

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From:
Christophe Leterrier <[log in to unmask]>
Reply To:
Confocal Microscopy List <[log in to unmask]>
Date:
Wed, 2 Jul 2008 12:34:14 +0200
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Search the CONFOCAL archive at
http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal

I agree with Guy that finding lots of web space can be difficult.
However, things are moving slowly, and initatives such as Google Open
Source Science Data Hosting are trying to adress this problem :
http://blog.wired.com/wiredscience/2008/01/google-to-provi.html
This whole "open source" science is a very interesting topic that
generates a lot of initiatives now. Of course one has to be careful
about the open source licenses used for data, but we're lucky that
software people already thought a lot about this issues. Why not
imagine that a public-founded organism does the same kind of thing for
public-founded research than Google is doing, i.e. hosting the data at
a much larger scale than what is possible at the personal/university
level ?

Christophe

On Wed, Jul 2, 2008 at 10:47, Guy Cox <[log in to unmask]> wrote:
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> The scale is several orders of magnitude larger than the storage of
> theses (which, by the way, this university does on paper - and that's
> probably still the most secure archive.)  And I think few, if any,
> Universities
> grant Web access to theses even if they do store them digitally.
>
>                                                                  Guy
>
> Optical Imaging Techniques in Cell Biology
> by Guy Cox    CRC Press / Taylor & Francis
>    http://www.guycox.com/optical.htm
> ______________________________________________
> Associate Professor Guy Cox, MA, DPhil(Oxon)
> Electron Microscope Unit, Madsen Building F09,
> University of Sydney, NSW 2006
> ______________________________________________
> Phone +61 2 9351 3176     Fax +61 2 9351 7682
> Mobile 0413 281 861
> ______________________________________________
>
>
> -----Original Message-----
> From: Confocal Microscopy List [mailto:[log in to unmask]] On
> Behalf Of Larry Tague
> Sent: Wednesday, 2 July 2008 2:52 PM
> To: [log in to unmask]
> Subject: Re: An alarming amount of (statistical) image manipulation
>
> Search the CONFOCAL archive at
> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>
> Guy,
>
> You bet there would be archival problems, but no worse
> (for the most part) than what we currently have with
> electronic thesis and dissertations.  Many universities
> are now storing 400+ very large documents/yr with images,
> etc., and some of these institutions also publish
> supporting data, i.e., CalTech.  However, with that said,
> your statement, "And since most Universities have rules
> requiring authors to keep data for X years anyway, I can't
> see the point" means that the data is already stored...
> make it part of the data stream for publications research.
> Yes, it will take organization, etc., but why loose or
> close data, unless for national security, that at least in
> public institutions, and in some private institutions, the
> public has already paid for with their hard earned taxes.
>
> If the original data is already stored, and today that
> means in many or most cases stored in digital format
> (digital images are the only kind I collect these days),
> and the authors do not want to allow others access, you
> begin to wonder why. I would suggest with public data,
> storage and public access should be a requirement before
> receiving public funds for research.  Already with some
> NIH grant programs (not bench research) there is an
> external evaluation requirement that must be included in
> the budget request... no if ands or buts. For bench
> research, maybe accessible data storage should now be a
> budget item in the proposal process..
>
> Yes, this diatribe strays somewhat from the original image
> manipulation question, but if there is no data to check or
> continue using, how could you possibly know if an improper
> image analysis had been applied.  Even if rules for image
> analysis exist, there is no good way to be sure mistakes
> were not made... especially when there are questions post
> publication and no raw data to check. Cheers!
>
> Larry
>
> On Wed, 2 Jul 2008 12:14:13 +1000
>  Guy Cox <[log in to unmask]> wrote:
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>> Well, I don't know what web space all you good folk have
>>available to you but there's no way I have access to
>>anywhere enough to post the several gigabytes of images
>>which lie behind a typical confocal / multiphoton /
>>second harmonic paper.  My University web site allows me
>>something like 10Mb which wouldn't hold a single Z-stack
>>or spectral series.  And it will go as soon as I leave
>>the University - so much for being archival.  My private
>>(paid for) site has a lot more but still nowhere near
>>enough, and it's only there as long as I pay the bills.
>>
>> It's all very well to say you can but a terabyte drive
>>for however many dollars, but that's just the start.
>> There's the power to run it (and replace it every few
>>years), there's the backup facility without which it's
>>not remotely archival, and most of all there's the
>>bandwidth needed to access it.  On the scale people are
>>talking about that's a huge operation.  A moderately
>>popular paid site I administer, for example, has 4
>>GB/month allowed - and comes close to it every month.
>> That's not involving any confocal images!  When I put
>>the Pawley/Cox Zeiss Diffraction Kit simulation on my
>>personal site, and announced it to this list, it reached
>>the site quota within 48 hours, and shut the whole thing
>>down.
>>
>> About the only way you could have a sensible archive
>>would be to get authors to mail a few DVDs to some sort
>>of repository.  Then anyone would wanted to check the
>>data could pay a search fee and get copies of the disks.
>> The search fee would not be cheap, though.  And since
>>most Universities have rules requiring authors to keep
>>data for X years anyway, I can't see the point.  In any
>>case, anyone who is being selective with the data they
>>publish is likely to be selective in what they archive,
>>too.
>>
>>
>>       Guy
>>
>>
>> Optical Imaging Techniques in Cell Biology
>> by Guy Cox    CRC Press / Taylor & Francis
>>    http://www.guycox.com/optical.htm
>> ______________________________________________
>> Associate Professor Guy Cox, MA, DPhil(Oxon)
>> Electron Microscope Unit, Madsen Building F09,
>> University of Sydney, NSW 2006
>> ______________________________________________
>> Phone +61 2 9351 3176     Fax +61 2 9351 7682
>> Mobile 0413 281 861
>> ______________________________________________
>>     http://www.guycox.net
>> -----Original Message-----
>>From: Confocal Microscopy List
>>[mailto:[log in to unmask]] On Behalf Of
>>Christophe Leterrier
>> Sent: Wednesday, 2 July 2008 3:16 AM
>> To: [log in to unmask]
>> Subject: Re: An alarming amount of (statistical) image
>>manipulation
>>
>> Search the CONFOCAL archive at
>> http://listserv.acsu.buffalo.edu/cgi-bin/wa?S1=confocal
>>
>>> That's fine.  But that's not how most journals work
>>>right now, as far
>>> as I know, and we are talking about how it works now.
>>> If, five or ten
>>> years from now, paper journals are no longer the
>>>standard, then the
>>> limitations won't exist.  As long as they do, however,
>>>they do.
>>>
>>> billo
>>>
>>
>> This is true, however it is not uncommon to see 40-60
>>pages supplementary data in Science or Nature papers
>>nowadays. Furthermore, as Larry pointed out, nothing
>>keeps you today from hosting your 140 pages pdf by
>>yourself (your university, your lab...) and link to it in
>>your article, as a web link only takes half a line in a
>>paper !
>>
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>
> Larry Tague
> Co-Investigator BBHSL*
> Co-Director of MECCA**
> Research Associate                       Dept. of
> Physiology
> Phone Bus.: 901-448-7152                 U.T. Memphis
> Phone FAX:  901-448-7126                 894 Union Ave.
> e-mail:[log in to unmask]          Memphis, TN
>        [log in to unmask]                  38163
>        [log in to unmask]
>
> *BBHSL (Building Bridges to Health Science Literacy). An
> NIH Science Education Partnership Award (SEPA)2005-2010
> URL: http://bbhsl.mecca.org
> **MECCA (Memphis Educational Computer Connectivity
> Alliance)
> URL: http://www.mecca.org/
>
> No virus found in this incoming message.
> Checked by AVG.
> Version: 7.5.526 / Virus Database: 270.4.3/1529 - Release Date:
> 1/07/2008 7:23 PM
>
>

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