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Re: Towards a cyberinfrastructure for the biological sciences: progress, visions and challenges

From: Carole Goble <carole.goble@manchester.ac.uk>
Date: Thu, 28 Aug 2008 15:07:42 +0100
Message-ID: <48B6B12E.8080703@manchester.ac.uk>
To: Kei Cheung <kei.cheung@yale.edu>
CC: Phillip Lord <phillip.lord@newcastle.ac.uk>, Peter Ansell <ansell.peter@gmail.com>, Marco Roos <M.Roos1@uva.nl>, public-semweb-lifesci <public-semweb-lifesci@w3.org>, mygrid@listserv.manchester.ac.uk, myexperiment-discuss@nongnu.org, Matthias Samwald <samwald@gmx.at>

Kei

yes - reproducibility is predicated on preservability -- that is one of 
Phil's points

Carole

>
> Hi Carole et al.,
>
> Does preservability relate to the 3 R's?
>
> -Kei
>
> Carole Goble wrote:
>> Phil
>>
>> er.... which bit of "I agree" with you don't you get? :-) :-)
>>
>> I agree with you! That is why we have a whole programme of work with 
>> BioCatalogue for workflow monitoring, workflow decay management, 
>> service monitoring, sharing data using packs in myExperiment and 
>> e-Labs etc.....
>>
>>
>> Carole
>>
>>>
>>> Carole
>>>
>>> I don't confuse the concepts, although I sometimes get the names 
>>> mixed up.
>>> In this case, uploading a workflow (taverna or otherwise) is not 
>>> going to
>>> guarantee either. I would not expect the workflow that you gave me 
>>> last year
>>> would necessarily either run now, nor give me the same results for 
>>> the same
>>> input.
>>> Of course, this is true in general for any computational artifact; 
>>> in the case
>>> of something like Java (with it's "forwardly compatibility") if it 
>>> doesn't,
>>> then this defined to be a bug. In the case of other languages. In 
>>> the case of
>>> workflows, I guess, we have to take the W3C line on 404 and say it's 
>>> a feature
>>> not a bug.
>>>
>>> Not that this means that I think that submissions of workflows is a 
>>> bad idea.
>>> I just think that they are going to be affected by the ravages of 
>>> time even
>>> more quickly than raw data is.
>>> Phil
>>>
>>>
>>>  
>>>>>>>> "Carole" == Carole Goble <carole.goble@manchester.ac.uk> writes:
>>>>>>>>             
>>>
>>>   Carole> Phil
>>>
>>>   Carole> yes - do not confuse Reproducibility with Repeatability or
>>>   Carole> Reusability
>>>
>>>   Carole> Carole
>>>
>>>   Carole> Carole Goble University of Manchester. UK
>>>   >>>>>>> "KC" == Kei Cheung <kei.cheung@yale.edu> writes:
>>>   >>>>>>>   >>   KC> Peter Ansell wrote:
>>>   >> >> Wiki's explicitly allow for a permanent link to a particular 
>>> version
>>>   >> >> of something. Hopefully an implementation of a wiki-like 
>>> workflow
>>>   >> >> editor online, will have similar characteristics so that you 
>>> can still
>>>   >> >> use a particular version to reproduce a past result if you 
>>> need to,
>>>   >> >> provided the web services still exist and haven't changed their
>>>   >> >> interface ;-) It would also be nice to be able to get corrected
>>>   >> >> versions via the wiki mechanism though and that would suit 
>>> the Web 2.0
>>>   >> >> way, as opposed to publications to which corrections are 
>>> hard to make.
>>>   >> >>   >>   >>   KC> If some journals are requiring raw data (e.g.,
>>>   >> microarray data) to be
>>>   KC> submitted to a public data repository, I wonder if workflows 
>>> that are
>>>   KC> used to analyze the data should also be submitted to a public 
>>> workflow
>>>   KC> repository.
>>>   >>   >>   >>   >> It's a nice idea but doesn't quite allow the 
>>> same level of repeatability.
>>>   >> Most taverna workflows need updating periodically, as the 
>>> services go
>>>   >> offline or change their interfaces. Even if they don't, they 
>>> return
>>>   >> different results as the implementation changes.
>>>   >>   >> Ultimately, you need to store more than the workflow to 
>>> allow any degree
>>>   >> of repeatability. Still, it would be a good step forward which 
>>> is no bad
>>>   >> thing.
>>>   >>   >> Phil
>>>   >>   >>   >>
>>>
>>>
>>>
>>>   
>>
>
>
>
Received on Thursday, 28 August 2008 14:08:17 GMT

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