On Thursday, 7 May 2020 10:18:38 PDT Roversi, Pietro (Dr.) wrote:
> Thank you Ethan for taking the the time to answer and explain.
> Yes I am sure I have asked a vague and imprecise question.
>
> Practically, I am going to point to xia2 for data processing:
> https://www.ccp4.ac.uk/newsletters/newsletter48/articles/Xia2/manual.html
>
> and hope it is "Open Source enough" - without too much scrutiny on
> dependencies?
I may misundertand the full scope of xia2, but I believe it is a scripted
pipeline
that invokes other programs. Those other programs individually may have
their own very different licensing or distribution or use restrictions.
The user guide you linked to says
if you use xia2 in published work please include the references
for the programs it has used, which are printed at the end of the
output.
The copy of xia2 that I have on my machine says at the top of the source
# Copyright (C) 2013 David Waterman
#
# This code is distributed under the terms and conditions of the
# CCP4 Program Suite Licence Agreement as a CCP4 Application.
So I guess the first question is whether the CCP4 License Agreement
meets your definition of Open Source.
The next question would be what programs did xia2 choose to run?
Some of these may meet your criteria for Open Source, others not.
For example, does xia2 invoke shelx? Does shelx meet your criteria?
Ethan
>
> So, what about a refinement suite of programs that is "just as Open Source"
> as xia2 is for data processing?
>
> Unless this second message of mine is making my re-drafted question worse
> than the original one 🙂.
>
> with best wishes,
>
> Pietro
>
>
> Pietro Roversi
>
> Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/
>
> LISCB Wellcome Trust ISSF Fellow
>
> <https://bit.ly/2I4Wm5Z>https://le.ac.uk/liscb/research-groups/pietro-roversi
>
>
> Leicester Institute of Structural and Chemical Biology
> Department of Molecular and Cell Biology, University of Leicester
> Henry Wellcome Building
> Lancaster Road, Leicester, LE1 7HB
> England, United Kingdom
>
> Skype: roversipietro
> Mobile phone +44 (0) 7927952047
> Tel. +44 (0)116 2297237
>
>
>
> ________________________________
> From: Ethan A Merritt <merr...@uw.edu>
> Sent: 07 May 2020 18:08
> To: Roversi, Pietro (Dr.) <pr...@leicester.ac.uk>
> Cc: CCP4BB@jiscmail.ac.uk <CCP4BB@jiscmail.ac.uk>
> Subject: Re: [ccp4bb] What refinement programs are fully Open Source?
>
> On Thursday, 7 May 2020 09:34:13 PDT Roversi, Pietro (Dr.) wrote:
> > Dear all,
> >
> > we are in the editorial stages of a manuscript that I submitted to Wellcome
> > Open Research for publication.
> >
> > The journal/editor ask us to list fully Open Source alternatives to the
> > pieces of software we used, for example for data processing and refinement.
> >
> > What refinement programs are fully Open Source?
>
> There are recurring battles and philosophical fractures over what exactly
> "open source" means, either in practice or aspirationally.
> You would do well to provide a definition before asking people for
> suggestions that meet your criteria.
>
> At one point the Open Source Foundation (OSF) claimed to have the authority
> to declare something was or was not "open source" and kept lists of
> approved code, but their definition was in conflict with guidelines from
> other places including funding agencies [*]. Also the OSF itself seems to
> have largely disappeared from view, so maybe that's a bad place to start.
>
> There are at least two fracture lines in this battle.
> The one created by people who feel a need to distinguish between
> "free/libre code" and "open code", and the one created by people
> whose main concern is "documentation and claims are not enough;
> I need to see the code actually used for the calculations reported in
> this work".
> Then there's the concern mostly of interest to corporate legal
> departments "can we use this in our commercial products".
>
> Ethan (coding veteran with scars from this battle)
>
>
> [*] it was also in conflict with the ordinary English language meaning
> of "open" and "source", which didn't help any.
>
>
> >
> > Thanks!
> >
> > Pietro
> >
> >
> > Pietro Roversi
> >
> > Lecturer (Teaching and Research) https://le.ac.uk/natural-sciences/
> >
> > LISCB Wellcome Trust ISSF Fellow
> >
> > <https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fbit.ly%2F2I4Wm5Z&data=02%7C01%7Cpr159%40leicester.ac.uk%7Cf8cc2fb23bb84707d7a708d7f2a96338%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637244681673138009&sdata=q7trhrormT%2FziGp11z5wJyroZ1uylcu9KvJVPLSIljg%3D&reserved=0>https://le.ac.uk/liscb/research-groups/pietro-roversi
> >
> >
> > Leicester Institute of Structural and Chemical Biology
> > Department of Molecular and Cell Biology, University of Leicester
> > Henry Wellcome Building
> > Lancaster Road, Leicester, LE1 7HB
> > England, United Kingdom
> >
> > Skype: roversipietro
> > Mobile phone +44 (0) 7927952047
> > Tel. +44 (0)116 2297237
> >
> >
> >
> > ########################################################################
> >
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>
>
> --
> Ethan A Merritt
> Biomolecular Structure Center, K-428 Health Sciences Bldg
> MS 357742, University of Washington, Seattle 98195-7742
>
>
>
--
Ethan A Merritt
Biomolecular Structure Center, K-428 Health Sciences Bldg
MS 357742, University of Washington, Seattle 98195-7742
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