Posts Tagged ‘Technology/Internet’

Re-inventing the anatomy of a research article.

Saturday, December 29th, 2018
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The traditional structure of the research article has been honed and perfected for over 350 years by its custodians, the publishers of scientific journals. Nowadays, for some journals at least, it might be viewed as much as a profit centre as the perfected mechanism for scientific communication. Here I take a look at the components of such articles to try to envisage its future, with the focus on molecules and chemistry.

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Open Access journal publishing debates – the elephant in the room?

Sunday, November 4th, 2018
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For perhaps ten years now, the future of scientific publishing has been hotly debated. The traditional models are often thought to be badly broken, although convergence to a consensus of what a better model should be is not apparently close. But to my mind, much of this debate seems to miss one important point, how to publish data.

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A Theoretical Method for Distinguishing X‐H Bond Activation Mechanisms.

Wednesday, July 25th, 2018
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Consider the four reactions. The first two are taught in introductory organic chemistry as (a) a proton transfer, often abbreviated PT, from X to B (a base) and (b) a hydride transfer from X to A (an acid). The third example is taught as a hydrogen atom transfer or HAT from X to (in this example) O. Recently an article has appeared[1] citing an example of a fourth fundamental type (d), which is given the acronym cPCET which I will expand later. Here I explore this last type a bit further, in the context that X-H bond activations are currently a very active area of research.

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References

  1. J.E.M.N. Klein, and G. Knizia, "cPCET versus HAT: A Direct Theoretical Method for Distinguishing X-H Bond-Activation Mechanisms", Angewandte Chemie International Edition, vol. 57, pp. 11913-11917, 2018. http://dx.doi.org/10.1002/anie.201805511

FAIR Data in Amsterdam – FAIR data points.

Wednesday, July 18th, 2018
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FAIR is one of those acronyms that spreads rapidly, acquires a life of its own and can mean many things to different groups. A two-day event has just been held in Amsterdam to bring some of those groups from the chemical sciences together to better understand FAIR. Here I note a few items that caught my attention.

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Ten years on: Jmol and WordPress.

Wednesday, May 16th, 2018
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Ten years are a long time when it comes to (recent) technologies. The first post on this blog was on the topic of how to present chemistry with three intact dimensions. I had in mind molecular models, molecular isosurfaces and molecular vibrations (arguably a further dimension). Here I reflect on how ten years of progress in technology has required changes and the challenge of how any necessary changes might be kept “under the hood” of this blog.

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Examples please of FAIR (data); good and bad.

Sunday, May 6th, 2018
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The site fairsharing.org is a repository of information about FAIR (Findable, Accessible, Interoperable and Reusable) objects such as research data.

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How FAIR are the data associated with the 2017 Molecules-of-the-Year?

Wednesday, March 7th, 2018
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C&EN has again run a vote for the 2017 Molecules of the year. Here I take a look not just at these molecules, but at how FAIR (Findable, Accessible, Interoperable and Reusable) the data associated with these molecules actually is.

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PIDapalooza 2018. A conference like no other!

Tuesday, January 23rd, 2018
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Another occasional conference report (day 1). So why is one about “persistent identifiers” important, and particularly to the chemistry domain?

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FAIR data ⇌ Raw data.

Thursday, December 7th, 2017
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FAIR data is increasingly accepted as a description of what research data should aspire to; Findable, Accessible, Inter-operable and Re-usable, with Context added by rich metadata (and also that it should be Open). But there are two sides to data, one of which is the raw data emerging from say an instrument or software simulations and the other in which some kind of model is applied to produce semi- or even fully processed/interpreted data. Here I illustrate a new example of how both kinds of data can be made to co-exist.

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Two stories about Open Peer Review (OPR), the next stage in Open Access (OA).

Thursday, October 5th, 2017
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We have heard a lot about OA or Open Access (of journal articles) in the last five years, often in association with the APC (Article Processing Charge) model of funding such OA availability. Rather less discussed is how the model of the peer review of these articles might also evolve into an Open environment. Here I muse about two experiences I had recently.

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