Posts Tagged ‘Technology/Internet’

Research data: Gravitational waves as an example from the astrophysics community.

Friday, June 2nd, 2017
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In 2016, the world heard that gravitational waves had been detected and now a third instance is reported. Given that the data associated with these detections are perhaps amongst the most important instances in recent times, I thought I might take a peek at how it was managed.

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Curating a nine year old journal FAIR data table.

Monday, May 29th, 2017
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As the Internet and its Web-components age, so early pages start to decay as technology moves on. A few posts ago, I talked about the maintenance of a relatively simple page first hosted some 21 years ago. In my notes on the curation, I wrote the phrase “Less successful was the attempt to include buttons which could be used to annotate the structures with highlights. These buttons no longer work and will have to be entirely replaced in the future at some stage.” Well, that time has now come, for a rather more crucial page associated with a journal article published more recently in 2009.[1]

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References

  1. H.S. Rzepa, "Wormholes in chemical space connecting torus knot and torus link π-electron density topologies", Phys. Chem. Chem. Phys., vol. 11, pp. 1340-1345, 2009. http://dx.doi.org/10.1039/b810301a

Conference report: an example of collaborative open science (reaction IRCs).

Thursday, May 25th, 2017
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It is a sign of the times that one travels to a conference well-connected. By which I mean email is on a constant drip-feed, with venue organisers ensuring each delegate receives their WiFi password even before their room key. So whilst I was at a conference espousing the benefits of open science, a nice example of open collaboration was initiated as a result of a received email.

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The challenges in curating research data: one case study.

Friday, April 28th, 2017
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Research data (and its management) is rapidly emerging as a focal point for the development of research dissemination practices. An important aspect of ensuring that such data remains fit for purpose is identifying what curation activities need to be associated with it. Here I revisit one particular case study associated with the molecular structure of a product identified from a photolysis reaction[1] and the curation of the crystallographic data associated with this study.

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References

  1. Y. Legrand, A. van der Lee, and M. Barboiu, "Single-Crystal X-ray Structure of 1,3-Dimethylcyclobutadiene by Confinement in a Crystalline Matrix", Science, vol. 329, pp. 299-302, 2010. http://dx.doi.org/10.1126/science.1188002

Supporting information: chemical graveyard or invaluable resource for chemical structures.

Friday, March 31st, 2017
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Nowadays, data supporting most publications relating to the synthesis of organic compounds is more likely than not to be found in associated “supporting information” rather than the (often page limited) article itself. For example, this article[1] has an SI which is paginated at 907; almost a mini-database in its own right! Here I ponder whether such dissemination of data is FAIR (Findable, accessible, interoperable and re-usable).[2]

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References

  1. J.M. Lopchuk, K. Fjelbye, Y. Kawamata, L.R. Malins, C. Pan, R. Gianatassio, J. Wang, L. Prieto, J. Bradow, T.A. Brandt, M.R. Collins, J. Elleraas, J. Ewanicki, W. Farrell, O.O. Fadeyi, G.M. Gallego, J.J. Mousseau, R. Oliver, N.W. Sach, J.K. Smith, J.E. Spangler, H. Zhu, J. Zhu, and P.S. Baran, "Strain-Release Heteroatom Functionalization: Development, Scope, and Stereospecificity", Journal of the American Chemical Society, vol. 139, pp. 3209-3226, 2017. http://dx.doi.org/10.1021/jacs.6b13229
  2. M.D. Wilkinson, M. Dumontier, I.J. Aalbersberg, G. Appleton, M. Axton, A. Baak, N. Blomberg, J. Boiten, L.B. da Silva Santos, P.E. Bourne, J. Bouwman, A.J. Brookes, T. Clark, M. Crosas, I. Dillo, O. Dumon, S. Edmunds, C.T. Evelo, R. Finkers, A. Gonzalez-Beltran, A.J. Gray, P. Groth, C. Goble, J.S. Grethe, J. Heringa, P.A. ’t Hoen, R. Hooft, T. Kuhn, R. Kok, J. Kok, S.J. Lusher, M.E. Martone, A. Mons, A.L. Packer, B. Persson, P. Rocca-Serra, M. Roos, R. van Schaik, S. Sansone, E. Schultes, T. Sengstag, T. Slater, G. Strawn, M.A. Swertz, M. Thompson, J. van der Lei, E. van Mulligen, J. Velterop, A. Waagmeester, P. Wittenburg, K. Wolstencroft, J. Zhao, and B. Mons, "The FAIR Guiding Principles for scientific data management and stewardship", Scientific Data, vol. 3, pp. 160018, 2016. http://dx.doi.org/10.1038/sdata.2016.18

The provenance of scientific data – establishing an audit trail.

Thursday, March 30th, 2017
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In an era when alternative facts and fake news afflict us, the provenance of scientific data becomes ever more important. Especially if that data is available as open access and exploitable by others for both valid scientific reasons but potentially also by those with other motives. Here I consider the audit trail that might serve to establish data provenance in one typical situation in chemistry, the acquisition of NMR instrumental data. 

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A nice example of open data (in London).

Sunday, March 5th, 2017
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Living in London, travelling using public transport is often the best way to get around. Before setting out on a journey one checks the status of the network. Doing so today I came across this page: our open data from Transport for London. 

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Open science and the chemistry lab of the future.

Thursday, February 9th, 2017
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The title refers to an upcoming symposium on the topic on 22-24 May, 2017.  I quote here some of the issues tabled for discussion:

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Revisiting (and maintaining) a twenty year old web page. Mauveine: The First Industrial Organic Fine-Chemical.

Thursday, February 2nd, 2017
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Almost exactly 20 years ago, I started what can be regarded as the precursor to this blog. As part of a celebration of this anniversary,[1] I revisited the page to see whether any of it had withstood the test of time. Here I recount what I discovered.

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References

  1. P.W. May, S.A. Cotton, K. Harrison, and H.S. Rzepa, "The ‘Molecule of the Month’ Website—An Extraordinary Chemistry Educational Resource Online for over 20 Years", Molecules, vol. 22, pp. 549, 2017. http://dx.doi.org/10.3390/molecules22040549