Discussion List Archives

[Date Prev][Date Next][Thread Prev][Thread Next][Date Index][Thread Index]

Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward

Thanks everyone – I’ll have a play around (particularly when I am not at home on a ‘rural’ network!).

My example is a small molecule single crystal diffraction experiment on a commercial diffractometer (although it is far from being a small structure!!). We have the bulk of the paper written so I just need to ‘top and tail’ it, sort out ESI and put it into a template and I will then upload raw data to get a citable DOI (all this depends on how well I cope with the start of the academic year!). Zenodo certainly looks like a good option, but I cant see a way of bulk downloading files? Graeme’s suggestion, blended with Andy’s, would seem to be the approach that should be “recommended” ie take the images from each run and wrap in HDF5 container (although I will have to put some more effort in to make the latter happen!).

All the best,
Simon.

Simon Coles FRSC, SFHEA.
Professor of Structural Chemistry.
Director, UK National Crystallography Service.
Chemistry, Faculty of Natural and Environmental Sciences,
University of Southampton.
Southampton, SO17 1BJ. UK.
+44(0)2380596721
Staff Page: http://www.soton.ac.uk/chemistry/about/staff/sjc5.page
NCS: http://www.ncs.ac.uk | Southampton Diffraction Centre: http://www.soton.ac.uk/sdc
ResearcherID: http://www.researcherid.com/rid/A-1795-2009 | ORCID: http://orcid.org/0000-0001-8414-9272


From: Kamil Dziubek <rumianek@amu.edu.pl>
Date: Tuesday, 27 September 2016 at 15:56
To: "mail=s. uk" <S.J.Coles@soton.ac.uk>
Cc: "john.helliwell@manchester.ac.uk" <john.helliwell@manchester.ac.uk>, "dddwg@iucr.org" <dddwg@iucr.org>
Subject: Re: [dddwg] To contribute to Open Science using Zenodo I found quite straightforward


Hello Simon,

Good to hear from you! Is your example a small molecule crystallography experiment carried out using a commercial diffractometer? Since all the other examples so far have concerned biocrystallography, I would be delighted to see it, especially the way of addressing different experiment strategies (series of omega and phi scans, etc.) In what format are you going to store the images?

Best regards and wishes,

Kamil

On 2016-09-27 23:27, Coles S.J. wrote:
John,

This is very good to hear!

I personally have an example where I wish to make the images available for a data collection associated with a remarkable structure we are going to submit to an IUCr journal quite soon. The primary reason I want to make the raw data available is so that others can take them and 'have a go themselves' to see if they can come up with a different / better model.

All fine – but I note you uploaded individual images? Or did Zenodo unpack a zipfile? I don't want to go through the effort of uploading 300 individual files – and I'm absolutely sure nobody wants to go through the effort of downloading 300 individual files to reprocess and reuse the dataset! Is there a reason for this - why not bundle them together in a package of some sort (Zip too big)? Or am I missing something?

Thanks!
Simon.

Simon Coles FRSC, SFHEA.
Professor of Structural Chemistry.
Director, UK National Crystallography Service.
Chemistry, Faculty of Natural and Environmental Sciences,
University of Southampton.
Southampton, SO17 1BJ. UK.
+44(0)2380596721
Staff Page: http://www.soton.ac.uk/chemistry/about/staff/sjc5.page
NCS: http://www.ncs.ac.uk | Southampton Diffraction Centre: http://www.soton.ac.uk/sdc
ResearcherID: http://www.researcherid.com/rid/A-1795-2009 | ORCID: http://orcid.org/0000-0001-8414-9272


From: dddwg <dddwg-bounces@iucr.org<mailto:dddwg-bounces@iucr.org>> on behalf of "john.helliwell@manchester.ac.uk<mailto:john.helliwell@manchester.ac.uk>" <john.helliwell@manchester.ac.uk<mailto:john.helliwell@manchester.ac.uk>>
Date: Tuesday, 27 September 2016 at 14:48
To: "dddwg@iucr.org<mailto:dddwg@iucr.org>" <dddwg@iucr.org<mailto:dddwg@iucr.org>>
Subject: [dddwg] To contribute to Open Science using Zenodo I found quite straightforward

Dear Colleagues,
I imagine that it will be of general interest that to contribute to "OpenScience" harnessing Zenodo is quite straightforward ie:- preprint and raw data uploaded and assigned dois on Sept 24th 2016 and then for good measure announced on my twitter account @HelliwellJohn on Sept 25th 2016:-

#OpenScience Our atomic resolution cisplatin lysozyme study; the dois are here:- http://doi.org/10.5281/zenodo.155068 http://doi.org/10.5281/zenodo.154704

The PDB code (5LXW) is cited in the preprint at the first Zenodo doi above. My instruction to PDB to release the entry 5LXW I made on Sept 25th 2016.

Greetings,
John

Emeritus Prof of Chemistry John R Helliwell DSc_Physics
Perspectives in Crystallography<https://outlook.manchester.ac.uk/owa/redir.aspx?SURL=JLjRW0_uSO2uCWXoeK-_YEiBuCJ_wkHJ5QxVDbIIAj0l57JRLfrSCGgAdAB0AHAAcwA6AC8ALwB3AHcAdwAuAGMAcgBjAHAAcgBlAHMAcwAuAGMAbwBtAC8AUABlAHIAcwBwAGUAYwB0AGkAdgBlAHMALQBpAG4ALQBDAHIAeQBzAHQAYQBsAGwAbwBnAHIAYQBwAGgAeQAvAEgAZQBsAGwAaQB3AGUAbABsAC8AOQA3ADgAMQA0ADkAOAA3ADMAMgAxADAAOQA.&URL=https%3a%2f%2fwww.crcpress.com%2fPerspectives-in-Crystallography%2fHelliwell%2f9781498732109>

Skills for a Scientific Life<https://www.crcpress.com/Skills-for-a-Scientific-Life/Helliwell/p/book/9781498768757>
_______________________________________________
dddwg mailing list
dddwg@iucr.org<mailto:dddwg@iucr.org>
http://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg



_______________________________________________dddwg mailing listdddwg@iucr.orghttp://mailman.iucr.org/cgi-bin/mailman/listinfo/dddwg

Reply to: [list | sender only]
International Union of Crystallography

Scientific Union Member of the International Science Council (admitted 1947). Member of CODATA, the ISC Committee on Data. Partner with UNESCO, the United Nations Educational, Scientific and Cultural Organization in the International Year of Crystallography 2014.

International Science Council Scientific Freedom Policy

The IUCr observes the basic policy of non-discrimination and affirms the right and freedom of scientists to associate in international scientific activity without regard to such factors as ethnic origin, religion, citizenship, language, political stance, gender, sex or age, in accordance with the Statutes of the International Council for Science.

Useful links