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

From: Phillip Lord <phillip.lord@newcastle.ac.uk>
Date: Thu, 28 Aug 2008 14:36:49 +0100
To: Carole Goble <carole.goble@manchester.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>
Message-ID: <EMEW-k7REand7287e7e8904ac9f3fd7ad538e514d90-87bpzdtg5q.fsf@dinley.ncl.ac.uk>



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
  >> 
  >> 
  >> 




-- 
Phillip Lord,                           Phone: +44 (0) 191 222 7827
Lecturer in Bioinformatics,             Email: phillip.lord@newcastle.ac.uk
School of Computing Science,            http://homepages.cs.ncl.ac.uk/phillip.lord
Claremont Tower Room 909,               skype: russet_apples
Newcastle University,                   msn: msn@russet.org.uk
NE1 7RU
Received on Thursday, 28 August 2008 13:37:52 GMT

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