Dear Ethan, 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.
This surprised me greatly. I wondered if perhaps you were referring to the ccp4i2 GUI for xia2, for which I must admit responsibility. However, I can't find "Copyright (C) 2013 David Waterman" anywhere within the current release of CCP4, so I am perplexed. I would like to make it clear that xia2 is not distributed under the terms of the CCP4 licence. It has a permissive free software licence, namely BSD-3, which must surely conform to any reasonable definition of Open Source. See here https://github.com/xia2/xia2/blob/master/LICENSE While xia2 has certain modes that run non-open software, Graeme's point is that the default mode runs DIALS, which is BSD-3 as well. -- David On Thu, 7 May 2020 at 18:56, Ethan A Merritt <merr...@uw.edu> wrote: > 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 > > > > > > > > > > > > > ######################################################################## > > > > > > To unsubscribe from the CCP4BB list, click the following link: > > > > https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.jiscmail.ac.uk%2Fcgi-bin%2Fwebadmin%3FSUBED1%3DCCP4BB%26A%3D1&data=02%7C01%7Cpr159%40leicester.ac.uk%7Cf8cc2fb23bb84707d7a708d7f2a96338%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C0%7C637244681673138009&sdata=nfhtEWy2FS96MYwaHsT4qoQi%2BMbPetQdTwfAf3FDjGg%3D&reserved=0 > > > > > > > > > -- > > 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 > > ######################################################################## > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1
