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Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward
- To: dddwg@iucr.org
- Subject: Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward
- From: Brian McMahon <bm@iucr.org>
- Date: Thu, 29 Sep 2016 17:48:25 +0100
- In-Reply-To: <28726D6B-2507-44B8-85B5-72FDCDEC44F9@soton.ac.uk>
- References: <5FDAAB132A30B7469258444FB7BD4C9101C3142543@MBXP07.ds.man.ac.uk><9DEEE21A-CAE5-431C-8540-F8579B8D4B31@soton.ac.uk><246e95c69906e16c4b17e64a77199341@amu.edu.pl><28726D6B-2507-44B8-85B5-72FDCDEC44F9@soton.ac.uk>
Following on from this part of the discussion, I'm interestedin the possibility of engaging DataCite or some otheragency to develop a protocol that would allow retrieval of specificsubsets of a large dataset/data collection to which a single DOI hadbeen assigned. I won't describe it here (the level of technical detailis not appropriate for this list), but I've posted a discussion onthe DDDWG forum at http://forums.iucr.org/viewtopic.php?f=21&t=382to which people are invited to contribute. ThanksBrian On 27/09/2016 16:42, Coles S.J. wrote:> 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 list> 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
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- References:
- [dddwg] To contribute to Open Science using Zenodo I found quitestraightforward (John Helliwell)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (Coles S.J.)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (Kamil Dziubek)
- Re: [dddwg] To contribute to Open Science using Zenodo I foundquite straightforward (Coles S.J.)
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