Dear Tim, While I agree that the papers describing XDS are excellent (and acknowledge precisely this every time I talk about DIALS!) I am certain that the actual implementation of XDS deviates significantly from the mathematical descriptions in the paper for the simple reason that writing data processing programs is hard and XDS is good.
I think the spirit behind the original question is that the opportunity exists to inspect every calculation which took you from your measured data to whatever the science result is - in the general case I would imagine the number of people who _do_ inspect is vanishingly small, but there are no fundamental limitations to this. Having things be open is however independent of them being good :-) - I would not conflate these ideas I also recognise the distinction between free and open source highlighted in the thread - with xia2 and DIALS we have been fortunate to get funding from Diamond Light Source, CCP4, Lawrence Berkeley National Lab, the EU, NIH and Wellcome Trust (with enthusiastic letters of support from many who are on this list) which puts us in the position of being able to make the product free to all end users as well as making the source code available for inspection - someone needs to pay the bills, ultimately, so I want to thank the various funding agencies for this, as well as end users for citations and letters of support. Best wishes Graeme On 7 May 2020, at 21:32, Tim Gruene <[email protected]<mailto:[email protected]>> wrote: Dear Pietro, to add a bit to Ethan's warning, you might even consider XDS open source: although the very source is not freely downloadable, it is so well documented that one could rewrite the program just from its documentation. At least, this is how the program SAINT started, as far as I now. Best regards, Tim On Thu, 7 May 2020 17:18:38 +0000 "Roversi, Pietro (Dr.)" <[email protected]<mailto:[email protected]>> 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? 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 <[email protected]> Sent: 07 May 2020 18:08 To: Roversi, Pietro (Dr.) <[email protected]> Cc: [email protected] <[email protected]> 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 ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CCP4BB&A=1 -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. 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