W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > August 2008

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

From: Kei Cheung <kei.cheung@yale.edu>
Date: Thu, 28 Aug 2008 10:01:34 -0400
To: Carole Goble <carole.goble@manchester.ac.uk>
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>
Message-id: <48B6AFBE.5070309@yale.edu>

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 14:02:16 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:53 GMT