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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 14:56:17 +0100
Message-ID: <48B6AE81.5000208@manchester.ac.uk>
To: Phillip Lord <phillip.lord@newcastle.ac.uk>
CC: Kei Cheung <kei.cheung@yale.edu>, 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>

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 13:56:52 GMT

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