Dear Tim,
This is tricky: I both completely agree with you and at the same time agree with Takanori.
Let me be more clear! [hindsight: turns out I fail to do so]
I completely respect the rights of Wolfgang Kabsch, Kay Diederichs and MPI to keep XDS closed source, and I also understand the requirement to "retire" support for old platforms as sooner or later they cease to be useful and are sometimes hard to support. At the same time there is also an essential principle of science that the results of an experiment may be reproduced - if software stops working (i.e. binaries "die") and the algorithms change then the results cannot be reproduced from the raw data => the science cannot strictly be verified. Clearly if the application is still available then from a practical perspective the results can be reproduced, but this is not guaranteed.
DIALS was written in part to fulfil this brief i.e. to be open source such that every line can in principle be studied, not that I recommend you do that unless you have a very long flight planned. It does however give the user the opportunity if something anomalous is discovered to go and find out exactly where that result came from, which has to be a good thing.
The tricky part of all of this is when software becomes a part of the infrastructure, and people are expected to rely on it's being there - then you step away from the "courtesy of the developer" into a land where the developer and those supporting the software have a responsibility to the user community: by and large I am certain that the developers of XDS feel this responsibility and respond to user problems accordingly, at least this is my experience. My interpretation of Takanori's request was that the perfectly satisfactory binaries which were available a few days ago and would still work have been withdrawn, with no suggestion of how to proceed. This goes against that implied responsibility, and would not broadly be a problem for open source or unlimited lifetime binaries. An additional relevant comment is "how much did you pay" - if nothing, well...
I suspect that this thread will generate much debate - I was having a discussion only last week about the merits of open source data processing software, though at the time XDS was not included in the discussion (which leaves rather a short list..!)
Best wishes Graeme
-----Original Message-----
From: CCP4 bulletin board [mailto:[log in to unmask]] On Behalf Of Tim Gruene
Sent: 20 October 2015 14:16
To: ccp4bb
Subject: Re: [ccp4bb] new version of (academic user) XDS package
Dear Takanori Nakane,
as far as I know, there is only one XDS developer, namely Wolfgang Kabsch.
As Linus Torvalds phrased it: if you are not happy with a software (license),
then you may write your own, although you don't even need to do so: dials and
mosflm are open source, and maybe others, so you can choose a different
program. If you take into account who develops (crystallographic) software and
under what conditions (e.g. in their spare time), providing of the software
should not be considered a service, but a courtesy of the developer.
Best regards,
Tim
On Tuesday, October 20, 2015 09:35:14 PM Takanori Nakane wrote:
> Dear XDS developers,
>
> I object to the decision to stop the distribution of
> 32 bit binary. I know many people who still use 32-bit Linux.
> I don't mean that the new version should be built for 32-bit.
> I know a huge burden associated with the maintenance of building and
> testing environment. Still, I believe that the last 32-bit build
> (version June 17, 2015) be available without time limit. For example,
> although CCP4 dropped support of 32-bit Mac OS, we can still
> download older versions or build 32-bit binary from source codes.
> Both options are unavailable for XDS.
>
> Honestly speaking, the way XDS is distributed is frustrating, where
> only the latest binary with time limit is available. How can we
> guarantee reproducibility of our research, if the exact version of a
> scientific program used for the research is no longer available [1]?
> Even worse, since XDS is a closed-source, black-box program, we do not
> know what actually changed in each update. For example, what does
> "simplification in the method for calculating the initial value of the
> mosaicity" [2] mean? How does it differ from the previous, published
> method? If the authors insist on keeping XDS source code confidential,
> they should at least provide detailed explanations of the algorithms
> in natural language, although it never substitutes source codes [3].
> It is understandable that some authors want to charge non-academic users
> to secure funding. But it does not justify secrecy of internals and
> unavailability of earlier versions.
>
> [1] See discussion on ccp4bb last May
> [log in to unmask]" target="_blank">https:[log in to unmask]
> [2] XDS Release notes
> http://xds.mpimf-heidelberg.mpg.de/html_doc/Release_Notes.html
> [3] Ince, Darrel C., Leslie Hatton, and John Graham-Cumming.
> "The case for open computer programs." Nature 482.7386 (2012): 485-488.
> http://www.nature.com/nature/journal/v482/n7386/full/nature10836.html
>
> Best regards,
>
> Takanori Nakane
>
> (This is my personal opinion, and is not necessarily that of
> my employer or projects I am/was involved with.)
>
> On 2015/10/19 23:07, Kay Diederichs wrote:
> > Dear XDS users,
> >
> > a new package has been released for academic users; the download link is
> > at http://xds.mpimf-heidelberg.mpg.de/ .
> >
> > There is no longer a 32bit version for Linux, and there is only a single
> > package for OSX 10.6 and up. Those of you who still use 32bit Linux or
> > OSX 10.5 thus should consider upgrading their operating system; the
> > current (academic user) XDS package expires in less than 6 months so
> > there is still some time left!
> >
> > As always, if there are bugs/crashes/problems then pls tell Wolfgang
> > Kabsch or me about them; we can only fix bugs if we can reproduce them
> > so pls be prepared to share (confidentially) the minimal amount of data
> > with us that allows to reproduce the problem.
> >
> > best wishes,
> >
> > Kay
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Dr. Tim Gruene
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